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Murphy M, Wang J, Jiang C, Wang LA, Kozhemiako N, Wang Y, Pan JQ, Purcell SM. A Potential Source of Bias in Group-Level EEG Microstate Analysis. Brain Topogr 2024; 37:232-242. [PMID: 37548801 DOI: 10.1007/s10548-023-00992-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/15/2023] [Indexed: 08/08/2023]
Abstract
Microstate analysis is a promising technique for analyzing high-density electroencephalographic data, but there are multiple questions about methodological best practices. Between and within individuals, microstates can differ both in terms of characteristic topographies and temporal dynamics, which leads to analytic challenges as the measurement of microstate dynamics is dependent on assumptions about their topographies. Here we focus on the analysis of group differences, using simulations seeded on real data from healthy control subjects to compare approaches that derive separate sets of maps within subgroups versus a single set of maps applied uniformly to the entire dataset. In the absence of true group differences in either microstate maps or temporal metrics, we found that using separate subgroup maps resulted in substantially inflated type I error rates. On the other hand, when groups truly differed in their microstate maps, analyses based on a single set of maps confounded topographic effects with differences in other derived metrics. We propose an approach to alleviate both classes of bias, based on a paired analysis of all subgroup maps. We illustrate the qualitative and quantitative impact of these issues in real data by comparing waking versus non-rapid eye movement sleep microstates. Overall, our results suggest that even subtle chance differences in microstate topography can have profound effects on derived microstate metrics and that future studies using microstate analysis should take steps to mitigate this large source of error.
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Affiliation(s)
- Michael Murphy
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Boston, USA
| | - Jun Wang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Chenguang Jiang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Lei A Wang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Nataliia Kozhemiako
- Department of Psychiatry, Brigham & Women's Hospital, Harvard Medical School, Boston, USA
| | - Yining Wang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Shaun M Purcell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, USA.
- Department of Psychiatry, Brigham & Women's Hospital, Harvard Medical School, Boston, USA.
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2
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Goodman MO, Faquih T, Paz V, Nagarajan P, Lane JM, Spitzer B, Maher M, Chung J, Cade BE, Purcell SM, Zhu X, Noordam R, Phillips AJK, Kyle SD, Spiegelhalder K, Weedon MN, Lawlor DA, Rotter JI, Taylor KD, Isasi CR, Sofer T, Dashti HS, Rutter MK, Redline S, Saxena R, Wang H. Genome-wide association analysis of composite sleep health scores in 413,904 individuals. medRxiv 2024:2024.02.02.24302211. [PMID: 38352337 PMCID: PMC10863010 DOI: 10.1101/2024.02.02.24302211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Recent genome-wide association studies (GWASs) of several individual sleep traits have identified hundreds of genetic loci, suggesting diverse mechanisms. Moreover, sleep traits are moderately correlated, and together may provide a more complete picture of sleep health, while also illuminating distinct domains. Here we construct novel sleep health scores (SHSs) incorporating five core self-report measures: sleep duration, insomnia symptoms, chronotype, snoring, and daytime sleepiness, using additive (SHS-ADD) and five principal components-based (SHS-PCs) approaches. GWASs of these six SHSs identify 28 significant novel loci adjusting for multiple testing on six traits (p<8.3e-9), along with 341 previously reported loci (p<5e-08). The heritability of the first three SHS-PCs equals or exceeds that of SHS-ADD (SNP-h2=0.094), while revealing sleep-domain-specific genetic discoveries. Significant loci enrich in multiple brain tissues and in metabolic and neuronal pathways. Post GWAS analyses uncover novel genetic mechanisms underlying sleep health and reveal connections to behavioral, psychological, and cardiometabolic traits.
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Affiliation(s)
- Matthew O Goodman
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Tariq Faquih
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Valentina Paz
- Instituto de Psicología Clínica, Facultad de Psicología, Universidad de la República, Montevideo, Uruguay
- MRC Unit for Lifelong Health & Ageing, Institute of Cardiovascular Science, University College London, London, United Kingdom
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Pavithra Nagarajan
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jacqueline M Lane
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Brian Spitzer
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matthew Maher
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joon Chung
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, MA, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew J. K. Phillips
- School of Psychological Sciences, Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | - Simon D. Kyle
- Sir Jules Thorn Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Kai Spiegelhalder
- Department of Psychiatry and Psychotherapy, Medical Centre - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael N Weedon
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Deborah A. Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hassan S Dashti
- Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Martin K Rutter
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Diabetes, Endocrinology and Metabolism Centre, Manchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester, UK
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Richa Saxena
- Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Neurology and Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
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Chung J, Goodman MO, Huang T, Castro-Diehl C, Chen JT, Sofer T, Bertisch SM, Purcell SM, Redline S. Objectively regular sleep patterns and mortality in a prospective cohort: The Multi-Ethnic Study of Atherosclerosis. J Sleep Res 2024; 33:e14048. [PMID: 37752591 DOI: 10.1111/jsr.14048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Irregular sleep and non-optimal sleep duration separately have been shown to be associated with increased disease and mortality risk. We used data from the prospective cohort Multi-Ethnic Study of Atherosclerosis sleep study (2010-2013) to investigate: do aging adults whose sleep is objectively high in regularity in timing and duration, and of sufficient duration tend to have increased survival compared with those whose sleep is lower in regularity and duration, in a diverse US sample? At baseline, sleep was measured by 7-day wrist actigraphy, concurrent with at-home polysomnography and questionnaires. Objective metrics of sleep regularity and duration from actigraphy were used for statistical clustering using sparse k-means clustering. Two sleep patterns were identified: "regular-optimal" (average duration: 7.0 ± 1.0 hr obtained regularly) and "irregular-insufficient" (duration: 5.8 ± 1.4 hr obtained with twice the irregularity). Using proportional hazard models with multivariate adjustment, we estimated all-cause mortality hazard ratios. Among 1759 participants followed for a median of 7.0 years (Q1-Q3, 6.4-7.4 years), 176 deaths were recorded. The "regular-optimal" group had a 39% lower mortality hazard than did the "irregular-insufficient" sleep group (hazard ratio [95% confidence interval]: 0.61 [0.45, 0.83]) after adjusting for socio-demographics, lifestyle, medical comorbidities and sleep disorders. In conclusion, a "regular-optimal" sleep pattern was significantly associated with a lower hazard of all-cause mortality. The regular-optimal phenotype maps behaviourally to regular bed and wake times, suggesting sleep benefits of adherence to recommended healthy sleep practices, with further potential benefits for longevity.
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Affiliation(s)
- Joon Chung
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew O Goodman
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tianyi Huang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Cecilia Castro-Diehl
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jarvis T Chen
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne M Bertisch
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Kozhemiako N, Jiang C, Sun Y, Guo Z, Chapman S, Gai G, Wang Z, Zhou L, Li S, Law RG, Wang LA, Mylonas D, Shen L, Murphy M, Qin S, Zhu W, Zhou Z, Stickgold R, Huang H, Tan S, Manoach DS, Wang J, Hall MH, Pan JQ, Purcell SM. A spectrum of altered non-rapid eye movement sleep in schizophrenia. bioRxiv 2023:2023.12.28.573548. [PMID: 38234726 PMCID: PMC10793442 DOI: 10.1101/2023.12.28.573548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Multiple facets of sleep neurophysiology, including electroencephalography (EEG) metrics such as non-rapid eye movement (NREM) spindles and slow oscillations (SO), are altered in individuals with schizophrenia (SCZ). However, beyond group-level analyses which treat all patients as a unitary set, the extent to which NREM deficits vary among patients is unclear, as are their relationships to other sources of heterogeneity including clinical factors, illness duration and ageing, cognitive profiles and medication regimens. Using newly collected high density sleep EEG data on 103 individuals with SCZ and 68 controls, we first sought to replicate our previously reported (Kozhemiako et. al, 2022) group-level mean differences between patients and controls (original N=130). Then in the combined sample (N=301 including 175 patients), we characterized patient-to-patient variability in NREM neurophysiology. Results We replicated all group-level mean differences and confirmed the high accuracy of our predictive model (Area Under the ROC Curve, AUC = 0.93 for diagnosis). Compared to controls, patients showed significantly increased between-individual variability across many (26%) sleep metrics, with patterns only partially recapitulating those for group-level mean differences. Although multiple clinical and cognitive factors were associated with NREM metrics including spindle density, collectively they did not account for much of the general increase in patient-to-patient variability. Medication regimen was a greater (albeit still partial) contributor to variability, although original group mean differences persisted after controlling for medications. Some sleep metrics including fast spindle density showed exaggerated age-related effects in SCZ, and patients exhibited older predicted biological ages based on an independent model of ageing and the sleep EEG. Conclusion We demonstrated robust and replicable alterations in sleep neurophysiology in individuals with SCZ and highlighted distinct patterns of effects contrasting between-group means versus within-group variances. We further documented and controlled for a major effect of medication use, and pointed to greater age-related change in NREM sleep in patients. That increased NREM heterogeneity was not explained by standard clinical or cognitive patient assessments suggests the sleep EEG provides novel, nonredundant information to support the goals of personalized medicine. Collectively, our results point to a spectrum of NREM sleep deficits among SCZ patients that can be measured objectively and at scale, and that may offer a unique window on the etiological and genetic diversity that underlies SCZ risk, treatment response and prognosis.
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Affiliation(s)
- Nataliia Kozhemiako
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School; Boston, USA
| | - Chenguang Jiang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University; Wuxi, China
| | - Yifan Sun
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University; Wuxi, China
| | - Zhenglin Guo
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Boston, USA
| | - Sinéad Chapman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Boston, USA
| | - Guanchen Gai
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University; Wuxi, China
| | - Zhe Wang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University; Wuxi, China
| | - Lin Zhou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Boston, USA
| | - Shen Li
- Department of Psychiatry, McLean Hospital, Harvard Medical School; Boston, USA
| | - Robert G. Law
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School; Boston, USA
| | - Lei A. Wang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Boston, USA
| | - Dimitrios Mylonas
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School; Boston, USA
| | - Lu Shen
- Bio-X Institutes, Shanghai Jiao Tong University; Shanghai China
| | - Michael Murphy
- Department of Psychiatry, McLean Hospital, Harvard Medical School; Boston, USA
| | - Shengying Qin
- Bio-X Institutes, Shanghai Jiao Tong University; Shanghai China
| | - Wei Zhu
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University; Wuxi, China
| | - Zhenhe Zhou
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University; Wuxi, China
| | - Robert Stickgold
- Beth Israel Deaconess Medical Center; Boston, USA
- Department of Psychiatry, Harvard Medical School; Boston, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Boston, USA
- ATGU, MGH, Harvard Medical School; Boston, USA
| | - Shuping Tan
- Huilong Guan Hospital, Beijing University; Beijing China
| | - Dara S. Manoach
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School; Boston, USA
| | - Jun Wang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University; Wuxi, China
| | - Mei-Hua Hall
- Department of Psychiatry, McLean Hospital, Harvard Medical School; Boston, USA
| | - Jen Q. Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Boston, USA
| | - Shaun M. Purcell
- Department of Psychiatry, Brigham and Women’s Hospital, Harvard Medical School; Boston, USA
- Department of Psychiatry, Harvard Medical School; Boston, USA
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5
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Goodman MO, Dashti HS, Lane JM, Windred DP, Burns A, Jones SE, Sofer T, Purcell SM, Zhu X, Ollila HM, Kyle SD, Spiegelhalder K, Peker Y, Huang T, Cain SW, Phillips AJK, Saxena R, Rutter MK, Redline S, Wang H. Causal Association Between Subtypes of Excessive Daytime Sleepiness and Risk of Cardiovascular Diseases. J Am Heart Assoc 2023; 12:e030568. [PMID: 38084713 PMCID: PMC10863774 DOI: 10.1161/jaha.122.030568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/03/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Excessive daytime sleepiness (EDS), experienced in 10% to 20% of the population, has been associated with cardiovascular disease and death. However, the condition is heterogeneous and is prevalent in individuals having short and long sleep duration. We sought to clarify the relationship between sleep duration subtypes of EDS with cardiovascular outcomes, accounting for these subtypes. METHODS AND RESULTS We defined 3 sleep duration subtypes of excessive daytime sleepiness: normal (6-9 hours), short (<6 hours), and long (>9 hours), and compared these with a nonsleepy, normal-sleep-duration reference group. We analyzed their associations with incident myocardial infarction (MI) and stroke using medical records of 355 901 UK Biobank participants and performed 2-sample Mendelian randomization for each outcome. Compared with healthy sleep, long-sleep EDS was associated with an 83% increased rate of MI (hazard ratio, 1.83 [95% CI, 1.21-2.77]) during 8.2-year median follow-up, adjusting for multiple health and sociodemographic factors. Mendelian randomization analysis provided supporting evidence of a causal role for a genetic long-sleep EDS subtype in MI (inverse-variance weighted β=1.995, P=0.001). In contrast, we did not find evidence that other subtypes of EDS were associated with incident MI or any associations with stroke (P>0.05). CONCLUSIONS Our study suggests the previous evidence linking EDS with increased cardiovascular disease risk may be primarily driven by the effect of its long-sleep subtype on higher risk of MI. Underlying mechanisms remain to be investigated but may involve sleep irregularity and circadian disruption, suggesting a need for novel interventions in this population.
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Affiliation(s)
- Matthew O. Goodman
- Division of Sleep and Circadian DisordersBrigham and Women’s HospitalBostonMA
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
- Broad InstituteCambridgeMA
| | - Hassan S. Dashti
- Broad InstituteCambridgeMA
- Center for Genomic MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMA
- Department of Anesthesia, Critical Care and Pain MedicineMassachusetts General HospitalBostonMA
| | - Jacqueline M. Lane
- Division of Sleep and Circadian DisordersBrigham and Women’s HospitalBostonMA
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
- Broad InstituteCambridgeMA
- Center for Genomic MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMA
| | - Daniel P. Windred
- School of Psychological SciencesTurner Institute for Brain and Mental Health, Monash UniversityMelbourneVictoriaAustralia
| | - Angus Burns
- Broad InstituteCambridgeMA
- Center for Genomic MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMA
- School of Psychological SciencesTurner Institute for Brain and Mental Health, Monash UniversityMelbourneVictoriaAustralia
| | - Samuel E. Jones
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
- University of Exeter Medical SchoolExeterUnited Kingdom
| | - Tamar Sofer
- Division of Sleep and Circadian DisordersBrigham and Women’s HospitalBostonMA
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
- Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMA
| | - Shaun M. Purcell
- Division of Sleep and Circadian DisordersBrigham and Women’s HospitalBostonMA
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
- Broad InstituteCambridgeMA
- Department of PsychiatryBrigham and Women’s HospitalBostonMA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health SciencesCase Western Reserve UniversityClevelandOH
| | - Hanna M. Ollila
- Broad InstituteCambridgeMA
- Center for Genomic MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMA
- Department of Anesthesia, Critical Care and Pain MedicineMassachusetts General HospitalBostonMA
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
| | - Simon D. Kyle
- Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical NeurosciencesUniversity of OxfordUnited Kingdom
| | - Kai Spiegelhalder
- Department of Psychiatry and PsychotherapyMedical Centre–University of Freiburg, Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Yuksel Peker
- Division of Sleep and Circadian DisordersBrigham and Women’s HospitalBostonMA
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
- Department of Pulmonary MedicineKoç University School of MedicineIstanbulTurkey
- Sahlgrenska AcademyUniversity of GothenburgSweden
- Department of Clinical Sciences, Respiratory Medicine and Allergology, Faculty of MedicineLund UniversityLundSweden
- Division of Pulmonary, Allergy, and Critical Care MedicineUniversity of Pittsburgh School of MedicinePittsburghPA
| | - Tianyi Huang
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
- Channing Division of Network MedicineBrigham and Women’s Hospital, Harvard Medical SchoolBostonMA
| | - Sean W. Cain
- School of Psychological SciencesTurner Institute for Brain and Mental Health, Monash UniversityMelbourneVictoriaAustralia
| | - Andrew J. K. Phillips
- School of Psychological SciencesTurner Institute for Brain and Mental Health, Monash UniversityMelbourneVictoriaAustralia
| | - Richa Saxena
- Broad InstituteCambridgeMA
- Center for Genomic MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMA
- Department of Anesthesia, Critical Care and Pain MedicineMassachusetts General HospitalBostonMA
| | - Martin K. Rutter
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUnited Kingdom
- Diabetes, Endocrinology and Metabolism CentreManchester University NHS Foundation Trust, NIHR Manchester Biomedical Research Centre, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Susan Redline
- Division of Sleep and Circadian DisordersBrigham and Women’s HospitalBostonMA
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
| | - Heming Wang
- Division of Sleep and Circadian DisordersBrigham and Women’s HospitalBostonMA
- Department of Neurology and MedicineHarvard Medical School, Brigham and Women’s HospitalBostonMA
- Broad InstituteCambridgeMA
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6
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Kozhemiako N, Buckley AW, Chervin RD, Redline S, Purcell SM. Mapping neurodevelopment with sleep macro- and micro-architecture across multiple pediatric populations. Neuroimage Clin 2023; 41:103552. [PMID: 38150746 PMCID: PMC10788305 DOI: 10.1016/j.nicl.2023.103552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/30/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023]
Abstract
Profiles of sleep duration and timing and corresponding electroencephalographic activity reflect brain changes that support cognitive and behavioral maturation and may provide practical markers for tracking typical and atypical neurodevelopment. To build and evaluate a sleep-based, quantitative metric of brain maturation, we used whole-night polysomnography data, initially from two large National Sleep Research Resource samples, spanning childhood and adolescence (total N = 4,013, aged 2.5 to 17.5 years): the Childhood Adenotonsillectomy Trial (CHAT), a research study of children with snoring without neurodevelopmental delay, and Nationwide Children's Hospital (NCH) Sleep Databank, a pediatric sleep clinic cohort. Among children without neurodevelopmental disorders (NDD), sleep metrics derived from the electroencephalogram (EEG) displayed robust age-related changes consistently across datasets. During non-rapid eye movement (NREM) sleep, spindles and slow oscillations further exhibited characteristic developmental patterns, with respect to their rate of occurrence, temporal coupling and morphology. Based on these metrics in NCH, we constructed a model to predict an individual's chronological age. The model performed with high accuracy (r = 0.93 in the held-out NCH sample and r = 0.85 in a second independent replication sample - the Pediatric Adenotonsillectomy Trial for Snoring (PATS)). EEG-based age predictions reflected clinically meaningful neurodevelopmental differences; for example, children with NDD showed greater variability in predicted age, and children with Down syndrome or intellectual disability had significantly younger brain age predictions (respectively, 2.1 and 0.8 years less than their chronological age) compared to age-matched non-NDD children. Overall, our results indicate that sleep architectureoffers a sensitive window for characterizing brain maturation, suggesting the potential for scalable, objective sleep-based biomarkers to measure neurodevelopment.
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Affiliation(s)
- N Kozhemiako
- Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - A W Buckley
- Sleep & Neurodevelopment Core, National Institute of Mental Health, NIH, Bethesda, MD, USA
| | - R D Chervin
- Sleep Disorders Center and Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - S Redline
- Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA; Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - S M Purcell
- Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
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7
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Pase MP, Harrison S, Misialek JR, Kline CE, Cavuoto M, Baril AA, Yiallourou S, Bisson A, Himali D, Leng Y, Yang Q, Seshadri S, Beiser A, Gottesman RF, Redline S, Lopez O, Lutsey PL, Yaffe K, Stone KL, Purcell SM, Himali JJ. Sleep Architecture, Obstructive Sleep Apnea, and Cognitive Function in Adults. JAMA Netw Open 2023; 6:e2325152. [PMID: 37462968 PMCID: PMC10354680 DOI: 10.1001/jamanetworkopen.2023.25152] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/07/2023] [Indexed: 07/21/2023] Open
Abstract
Importance Good sleep is essential for health, yet associations between sleep and dementia risk remain incompletely understood. The Sleep and Dementia Consortium was established to study associations between polysomnography (PSG)-derived sleep and the risk of dementia and related cognitive and brain magnetic resonance imaging endophenotypes. Objective To investigate association of sleep architecture and obstructive sleep apnea (OSA) with cognitive function in the Sleep and Dementia Consortium. Design, Setting, and Participants The Sleep and Dementia Consortium curated data from 5 population-based cohorts across the US with methodologically consistent, overnight, home-based type II PSG and neuropsychological assessments over 5 years of follow-up: the Atherosclerosis Risk in Communities study, Cardiovascular Health Study, Framingham Heart Study (FHS), Osteoporotic Fractures in Men Study, and Study of Osteoporotic Fractures. Sleep metrics were harmonized centrally and then distributed to participating cohorts for cohort-specific analysis using linear regression; study-level estimates were pooled in random effects meta-analyses. Results were adjusted for demographic variables, the time between PSG and neuropsychological assessment (0-5 years), body mass index, antidepressant use, and sedative use. There were 5946 participants included in the pooled analyses without stroke or dementia. Data were analyzed from March 2020 to June 2023. Exposures Measures of sleep architecture and OSA derived from in-home PSG. Main Outcomes and Measures The main outcomes were global cognitive composite z scores derived from principal component analysis, with cognitive domains investigated as secondary outcomes. Higher scores indicated better performance. Results Across cohorts, 5946 adults (1875 females [31.5%]; mean age range, 58-89 years) were included. The median (IQR) wake after sleep onset time ranged from 44 (27-73) to 101 (66-147) minutes, and the prevalence of moderate to severe OSA ranged from 16.9% to 28.9%. Across cohorts, higher sleep maintenance efficiency (pooled β per 1% increase, 0.08; 95% CI, 0.03 to 0.14; P < .01) and lower wake after sleep onset (pooled β per 1-min increase, -0.07; 95% CI, -0.13 to -0.01 per 1-min increase; P = .02) were associated with better global cognition. Mild to severe OSA (apnea-hypopnea index [AHI] ≥5) was associated with poorer global cognition (pooled β, -0.06; 95% CI, -0.11 to -0.01; P = .01) vs AHI less than 5; comparable results were found for moderate to severe OSA (pooled β, -0.06; 95% CI, -0.11 to -0.01; P = .02) vs AHI less than 5. Differences in sleep stages were not associated with cognition. Conclusions and Relevance This study found that better sleep consolidation and the absence of OSA were associated with better global cognition over 5 years of follow-up. These findings suggest that the role of interventions to improve sleep for maintaining cognitive function requires investigation.
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Affiliation(s)
- Matthew P. Pase
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, Victoria, Australia
- Harvard T.H. Chan School of Public Health, Massachusetts
- Framingham Heart Study, Framingham, Massachusetts
| | | | - Jeffrey R. Misialek
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis
| | - Christopher E. Kline
- Department of Health and Human Development, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marina Cavuoto
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, Victoria, Australia
| | - Andree-Ann Baril
- Framingham Heart Study, Framingham, Massachusetts
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
| | - Stephanie Yiallourou
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, Victoria, Australia
| | - Alycia Bisson
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Dibya Himali
- Framingham Heart Study, Framingham, Massachusetts
| | - Yue Leng
- Department of Psychiatry and Behavioral Sciences, University of California
| | - Qiong Yang
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Science Center San Antonio
| | - Alexa Beiser
- Framingham Heart Study, Framingham, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Rebecca F. Gottesman
- National Institute of Neurological Disorders and Stroke Intramural Research Program, Bethesda, Maryland
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Oscar Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis
| | - Kristine Yaffe
- Department of Psychiatry, University of California, San Francisco
- Department of Neurology, University of California, San Francisco
- Department of Epidemiology, University of California, San Francisco
| | - Katie L. Stone
- California Pacific Medical Center, Research Institute, San Francisco
- Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Shaun M. Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Jayandra J. Himali
- Framingham Heart Study, Framingham, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Science Center San Antonio
- Department of Population Health Sciences, University of Texas Health Science Center, San Antonio
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8
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Song TA, Chowdhury SR, Malekzadeh M, Harrison S, Hoge TB, Redline S, Stone KL, Saxena R, Purcell SM, Dutta J. AI-Driven sleep staging from actigraphy and heart rate. PLoS One 2023; 18:e0285703. [PMID: 37195925 PMCID: PMC10191307 DOI: 10.1371/journal.pone.0285703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/02/2023] [Indexed: 05/19/2023] Open
Abstract
Sleep is an important indicator of a person's health, and its accurate and cost-effective quantification is of great value in healthcare. The gold standard for sleep assessment and the clinical diagnosis of sleep disorders is polysomnography (PSG). However, PSG requires an overnight clinic visit and trained technicians to score the obtained multimodality data. Wrist-worn consumer devices, such as smartwatches, are a promising alternative to PSG because of their small form factor, continuous monitoring capability, and popularity. Unlike PSG, however, wearables-derived data are noisier and far less information-rich because of the fewer number of modalities and less accurate measurements due to their small form factor. Given these challenges, most consumer devices perform two-stage (i.e., sleep-wake) classification, which is inadequate for deep insights into a person's sleep health. The challenging multi-class (three, four, or five-class) staging of sleep using data from wrist-worn wearables remains unresolved. The difference in the data quality between consumer-grade wearables and lab-grade clinical equipment is the motivation behind this study. In this paper, we present an artificial intelligence (AI) technique termed sequence-to-sequence LSTM for automated mobile sleep staging (SLAMSS), which can perform three-class (wake, NREM, REM) and four-class (wake, light, deep, REM) sleep classification from activity (i.e., wrist-accelerometry-derived locomotion) and two coarse heart rate measures-both of which can be reliably obtained from a consumer-grade wrist-wearable device. Our method relies on raw time-series datasets and obviates the need for manual feature selection. We validated our model using actigraphy and coarse heart rate data from two independent study populations: the Multi-Ethnic Study of Atherosclerosis (MESA; N = 808) cohort and the Osteoporotic Fractures in Men (MrOS; N = 817) cohort. SLAMSS achieves an overall accuracy of 79%, weighted F1 score of 0.80, 77% sensitivity, and 89% specificity for three-class sleep staging and an overall accuracy of 70-72%, weighted F1 score of 0.72-0.73, 64-66% sensitivity, and 89-90% specificity for four-class sleep staging in the MESA cohort. It yielded an overall accuracy of 77%, weighted F1 score of 0.77, 74% sensitivity, and 88% specificity for three-class sleep staging and an overall accuracy of 68-69%, weighted F1 score of 0.68-0.69, 60-63% sensitivity, and 88-89% specificity for four-class sleep staging in the MrOS cohort. These results were achieved with feature-poor inputs with a low temporal resolution. In addition, we extended our three-class staging model to an unrelated Apple Watch dataset. Importantly, SLAMSS predicts the duration of each sleep stage with high accuracy. This is especially significant for four-class sleep staging, where deep sleep is severely underrepresented. We show that, by appropriately choosing the loss function to address the inherent class imbalance, our method can accurately estimate deep sleep time (SLAMSS/MESA: 0.61±0.69 hours, PSG/MESA ground truth: 0.60±0.60 hours; SLAMSS/MrOS: 0.53±0.66 hours, PSG/MrOS ground truth: 0.55±0.57 hours;). Deep sleep quality and quantity are vital metrics and early indicators for a number of diseases. Our method, which enables accurate deep sleep estimation from wearables-derived data, is therefore promising for a variety of clinical applications requiring long-term deep sleep monitoring.
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Affiliation(s)
- Tzu-An Song
- University of Massachusetts Amherst, Amherst, MA, United States of America
| | | | - Masoud Malekzadeh
- University of Massachusetts Amherst, Amherst, MA, United States of America
| | - Stephanie Harrison
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Terri Blackwell Hoge
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Susan Redline
- Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Katie L. Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Richa Saxena
- Massachusetts General Hospital, Boston, MA, United States of America
| | - Shaun M. Purcell
- Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Joyita Dutta
- University of Massachusetts Amherst, Amherst, MA, United States of America
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9
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Kozhemiako N, Mylonas D, Pan JQ, Prerau MJ, Redline S, Purcell SM. Sources of Variation in the Spectral Slope of the Sleep EEG. eNeuro 2022; 9:ENEURO.0094-22.2022. [PMID: 36123117 PMCID: PMC9512622 DOI: 10.1523/eneuro.0094-22.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/01/2022] [Accepted: 07/30/2022] [Indexed: 11/21/2022] Open
Abstract
The 1/f spectral slope of the electroencephalogram (EEG) estimated in the γ frequency range has been proposed as an arousal marker that differentiates wake, nonrapid eye movement (NREM) sleep, and rapid eye movement (REM) sleep. Here, we sought to replicate and extend these findings in a large sample, providing a comprehensive characterization of how slope changes with age, sex, and its test-retest reliability as well as potential confounds that could affect the slope estimation. We used 10,255 whole-night polysomnograms (PSGs) from the National Sleep Research Resource (NSRR). All preprocessing steps were performed using an open-source Luna package and the spectral slope was estimated by fitting log-log linear regression models on the absolute power from 30 to 45 Hz separately for wake, NREM, and REM stages. We confirmed that the mean spectral slope grows steeper going from wake to NREM to REM sleep. We found that the choice of mastoid referencing scheme modulated the extent to which electromyogenic, or electrocardiographic artifacts were likely to bias 30- to 45-Hz slope estimates, as well as other sources of technical, device-specific bias. Nonetheless, within individuals, slope estimates were relatively stable over time. Both cross-sectionally and longitudinal, slopes tended to become shallower with increasing age, particularly for REM sleep; males tended to show flatter slopes than females across all states. Our findings support that spectral slope can be a valuable arousal marker for both clinical and research endeavors but also underscore the importance of considering interindividual variation and multiple methodological aspects related to its estimation.
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Affiliation(s)
- Nataliia Kozhemiako
- Department of Psychiatry, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Dimitris Mylonas
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02142
| | - Michael J Prerau
- Department of Psychiatry, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Susan Redline
- Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Shaun M Purcell
- Department of Psychiatry, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115
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10
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Kozhemiako N, Wang J, Jiang C, Wang LA, Gai G, Zou K, Wang Z, Yu X, Zhou L, Li S, Guo Z, Law R, Coleman J, Mylonas D, Shen L, Wang G, Tan S, Qin S, Huang H, Murphy M, Stickgold R, Manoach D, Zhou Z, Zhu W, Hal MH, Purcell SM, Pan JQ. Non-rapid eye movement sleep and wake neurophysiology in schizophrenia. eLife 2022; 11:76211. [PMID: 35578829 PMCID: PMC9113745 DOI: 10.7554/elife.76211] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/11/2022] [Indexed: 12/29/2022] Open
Abstract
Motivated by the potential of objective neurophysiological markers to index thalamocortical function in patients with severe psychiatric illnesses, we comprehensively characterized key non-rapid eye movement (NREM) sleep parameters across multiple domains, their interdependencies, and their relationship to waking event-related potentials and symptom severity. In 72 schizophrenia (SCZ) patients and 58 controls, we confirmed a marked reduction in sleep spindle density in SCZ and extended these findings to show that fast and slow spindle properties were largely uncorrelated. We also describe a novel measure of slow oscillation and spindle interaction that was attenuated in SCZ. The main sleep findings were replicated in a demographically distinct sample, and a joint model, based on multiple NREM components, statistically predicted disease status in the replication cohort. Although also altered in patients, auditory event-related potentials elicited during wake were unrelated to NREM metrics. Consistent with a growing literature implicating thalamocortical dysfunction in SCZ, our characterization identifies independent NREM and wake EEG biomarkers that may index distinct aspects of SCZ pathophysiology and point to multiple neural mechanisms underlying disease heterogeneity. This study lays the groundwork for evaluating these neurophysiological markers, individually or in combination, to guide efforts at treatment and prevention as well as identifying individuals most likely to benefit from specific interventions.
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Affiliation(s)
- Nataliia Kozhemiako
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Jun Wang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Chenguang Jiang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Lei A Wang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Guanchen Gai
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Kai Zou
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Zhe Wang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Xiaoman Yu
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Lin Zhou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Shen Li
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, United States
| | - Zhenglin Guo
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Robert Law
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - James Coleman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Dimitrios Mylonas
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Lu Shen
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Guoqiang Wang
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Shuping Tan
- Huilong Guan Hospital, Beijing University, Beijing, China
| | - Shengying Qin
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Michael Murphy
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, United States
| | - Robert Stickgold
- Beth Israel Deaconess Medical Center, Boston, United States.,Department of Psychiatry, Harvard Medical School, Boston, United States
| | - Dara Manoach
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Zhenhe Zhou
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Wei Zhu
- The Affiliated Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - Mei-Hua Hal
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, United States
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Psychiatry, Harvard Medical School, Boston, United States
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
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11
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Xin Q, Yuan RK, Zitting KM, Wang W, Purcell SM, Vujovic N, Ronda JM, Quan SF, Williams JS, Buxton OM, Duffy JF, Czeisler CA. Impact of chronic sleep restriction on sleep continuity, sleep structure, and neurobehavioral performance. Sleep 2022; 45:6537622. [PMID: 35218665 PMCID: PMC9272266 DOI: 10.1093/sleep/zsac046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic sleep restriction (CSR) has been associated with adverse effects including cognitive impairment and increased risk of diabetes and cardiovascular disease. Yet, sleep restriction therapy is an essential component of most behavioral treatments for insomnia. Moreover, little is known about the impact of CSR on sleep continuity and structure in healthy people whose need for sleep is satiated. We investigated the impact of CSR on sleep continuity and structure in nine healthy participants. They had 4 nights of sleep extension, 2 nights of post-extension sleep, 21 nights of CSR (5/5.6-hour time-in-bed), and 9 nights of recovery sleep. Compared to postextension sleep, during CSR sleep duration was reduced by 95.4 ± 21.2 min per night, Slow-Wave Activity was significantly increased, and sleep was more consolidated. During recovery, sleep duration was increased by 103.3 ± 23.8 min compared to CSR, and the CSR-induced increase in Slow-Wave Activity persisted, particularly after the 5-hour exposure. Yet, we found that sustained vigilant attention was not fully recovered even after nine nights of recovery sleep. Our results suggest that CSR improves traditional metrics of sleep quality and may have a persistent impact on sleep depth, which is consistent with the reported benefits on sleep continuity and structure of sleep restriction therapy. However, these improvements in traditional metrics of sleep quality were associated with deterioration rather than improvement in neurobehavioral performance, demonstrating that sleep duration should be included in assessments of sleep quality. These results have implications for the long-term use of sleep restriction in the behavioral treatment of insomnia. Clinical Trial Registration: Impact of Chronic Circadian Disruption vs. Chronic Sleep Restriction on Metabolism (https://clinicaltrials.gov/ct2/show/; #NCT02171273).
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Affiliation(s)
- Qilong Xin
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Robin K Yuan
- Corresponding author. Robin K. Yuan, RF386D, Division of Sleep and Circadian Disorders, 221 Longwood Avenue, Boston, MA 02115, USA.
| | - Kirsi-Marja Zitting
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Wang
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Nina Vujovic
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph M Ronda
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart F Quan
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan S Williams
- Department of Medicine, Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Orfeu M Buxton
- Department of Biobehavioral Health, Pennsylvania State University, University Park PA 16802, USA
| | - Jeanne F Duffy
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Charles A Czeisler
- Department of Medicine and Neurology, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
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12
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Wang H, Kurniansyah N, Cade BE, Goodman MO, Chen H, Gottlieb DJ, Gharib SA, Purcell SM, Lin X, Saxena R, Zhu X, Durda P, Tracy R, Liu Y, Taylor KD, Johnson WC, Gabriel S, Smith JD, Aguet F, Ardlie K, Blackwell T, Reiner AP, Rotter JI, Rich SS, Redline S, Sofer T. Upregulated heme biosynthesis increases obstructive sleep apnea severity: a pathway-based Mendelian randomization study. Sci Rep 2022; 12:1472. [PMID: 35087136 PMCID: PMC8795126 DOI: 10.1038/s41598-022-05415-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022] Open
Abstract
Obstructive sleep apnea (OSA) is a common disorder associated with increased risk of cardiovascular disease and mortality. Iron and heme metabolism, implicated in ventilatory control and OSA comorbidities, was associated with OSA phenotypes in recent admixture mapping and gene enrichment analyses. However, its causal contribution was unclear. In this study, we performed pathway-level transcriptional Mendelian randomization (MR) analysis to investigate the causal relationships between iron and heme related pathways and OSA. In primary analysis, we examined the expression level of four iron/heme Reactome pathways as exposures and four OSA traits as outcomes using cross-tissue cis-eQTLs from the Genotype-Tissue Expression portal and published genome-wide summary statistics of OSA. We identify a significant putative causal association between up-regulated heme biosynthesis pathway with higher sleep time percentage of hypoxemia (p = 6.14 × 10-3). This association is supported by consistency of point estimates in one-sample MR in the Multi-Ethnic Study of Atherosclerosis using high coverage DNA and RNA sequencing data generated by the Trans-Omics for Precision Medicine project. Secondary analysis for 37 additional iron/heme Gene Ontology pathways did not reveal any significant causal associations. This study suggests a causal association between increased heme biosynthesis and OSA severity.
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Affiliation(s)
- Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Nuzulul Kurniansyah
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Matthew O Goodman
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Han Chen
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- School of Biomedical Informatics, Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Daniel J Gottlieb
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Sina A Gharib
- Department of Medicine, Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, University of Washington, Seattle, WA, USA
| | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Xihong Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Richa Saxena
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Massachusetts General Hospital, Center for Genomic Medicine, Harvard Medical School, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, The Robert Larner, M.D. College of Medicine at the University of Vermont, Burlington, VT, 05446, USA
| | - Russel Tracy
- Department of Pathology and Laboratory Medicine, The Robert Larner, M.D. College of Medicine at the University of Vermont, Burlington, VT, 05446, USA
| | - Yongmei Liu
- Divisions of Cardiology and Neurology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Joshua D Smith
- Northwest Genomic Center, University of Washington, Seattle, WA, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kirstin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tom Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave BLI 252, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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13
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Cade BE, Lee J, Sofer T, Wang H, Zhang M, Chen H, Gharib SA, Gottlieb DJ, Guo X, Lane JM, Liang J, Lin X, Mei H, Patel SR, Purcell SM, Saxena R, Shah NA, Evans DS, Hanis CL, Hillman DR, Mukherjee S, Palmer LJ, Stone KL, Tranah GJ, Abecasis GR, Boerwinkle EA, Correa A, Cupples LA, Kaplan RC, Nickerson DA, North KE, Psaty BM, Rotter JI, Rich SS, Tracy RP, Vasan RS, Wilson JG, Zhu X, Redline S. Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program. Genome Med 2021; 13:136. [PMID: 34446064 PMCID: PMC8394596 DOI: 10.1186/s13073-021-00917-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/28/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Sleep-disordered breathing is a common disorder associated with significant morbidity. The genetic architecture of sleep-disordered breathing remains poorly understood. Through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program, we performed the first whole-genome sequence analysis of sleep-disordered breathing. METHODS The study sample was comprised of 7988 individuals of diverse ancestry. Common-variant and pathway analyses included an additional 13,257 individuals. We examined five complementary traits describing different aspects of sleep-disordered breathing: the apnea-hypopnea index, average oxyhemoglobin desaturation per event, average and minimum oxyhemoglobin saturation across the sleep episode, and the percentage of sleep with oxyhemoglobin saturation < 90%. We adjusted for age, sex, BMI, study, and family structure using MMSKAT and EMMAX mixed linear model approaches. Additional bioinformatics analyses were performed with MetaXcan, GIGSEA, and ReMap. RESULTS We identified a multi-ethnic set-based rare-variant association (p = 3.48 × 10-8) on chromosome X with ARMCX3. Additional rare-variant associations include ARMCX3-AS1, MRPS33, and C16orf90. Novel common-variant loci were identified in the NRG1 and SLC45A2 regions, and previously associated loci in the IL18RAP and ATP2B4 regions were associated with novel phenotypes. Transcription factor binding site enrichment identified associations with genes implicated with respiratory and craniofacial traits. Additional analyses identified significantly associated pathways. CONCLUSIONS We have identified the first gene-based rare-variant associations with objectively measured sleep-disordered breathing traits. Our results increase the understanding of the genetic architecture of sleep-disordered breathing and highlight associations in genes that modulate lung development, inflammation, respiratory rhythmogenesis, and HIF1A-mediated hypoxic response.
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Affiliation(s)
- Brian E. Cade
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA
| | - Jiwon Lee
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA
| | - Tamar Sofer
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Heming Wang
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA
| | - Man Zhang
- grid.411024.20000 0001 2175 4264Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Han Chen
- grid.267308.80000 0000 9206 2401Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Sina A. Gharib
- grid.34477.330000000122986657Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA 98195 USA
| | - Daniel J. Gottlieb
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.410370.10000 0004 4657 1992VA Boston Healthcare System, Boston, MA 02132 USA
| | - Xiuqing Guo
- grid.239844.00000 0001 0157 6501The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jacqueline M. Lane
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Jingjing Liang
- grid.67105.350000 0001 2164 3847Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Xihong Lin
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Hao Mei
- grid.410721.10000 0004 1937 0407Department of Data Science, University of Mississippi Medical Center, Jackson, MS 29216 USA
| | - Sanjay R. Patel
- grid.21925.3d0000 0004 1936 9000Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213 USA
| | - Shaun M. Purcell
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA
| | - Richa Saxena
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.66859.34Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Neomi A. Shah
- grid.59734.3c0000 0001 0670 2351Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Daniel S. Evans
- grid.17866.3e0000000098234542California Pacific Medical Center Research Institute, San Francisco, CA 94107 USA
| | - Craig L. Hanis
- grid.267308.80000 0000 9206 2401Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - David R. Hillman
- grid.3521.50000 0004 0437 5942Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia 6009 Australia
| | - Sutapa Mukherjee
- Sleep Health Service, Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, South Australia Australia ,grid.1014.40000 0004 0367 2697Adelaide Institute for Sleep Health, Flinders University, Adelaide, South Australia Australia
| | - Lyle J. Palmer
- grid.1010.00000 0004 1936 7304School of Public Health, University of Adelaide, Adelaide, South Australia 5000 Australia
| | - Katie L. Stone
- grid.17866.3e0000000098234542California Pacific Medical Center Research Institute, San Francisco, CA 94107 USA
| | - Gregory J. Tranah
- grid.17866.3e0000000098234542California Pacific Medical Center Research Institute, San Francisco, CA 94107 USA
| | | | - Gonçalo R. Abecasis
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Eric A. Boerwinkle
- grid.267308.80000 0000 9206 2401Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Adolfo Correa
- grid.410721.10000 0004 1937 0407Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216 USA ,Jackson Heart Study, Jackson, MS 39216 USA
| | - L. Adrienne Cupples
- grid.189504.10000 0004 1936 7558Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118 USA ,grid.510954.c0000 0004 0444 3861Framingham Heart Study, Framingham, MA 01702 USA
| | - Robert C. Kaplan
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, 10461 USA
| | - Deborah A. Nickerson
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA ,grid.34477.330000000122986657Northwest Genomics Center, Seattle, WA 98105 USA
| | - Kari E. North
- grid.410711.20000 0001 1034 1720Department of Epidemiology and Carolina Center of Genome Sciences, University of North Carolina, Chapel Hill, NC 27514 USA
| | - Bruce M. Psaty
- grid.34477.330000000122986657Cardiovascular Health Study, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA 98101 USA ,grid.488833.c0000 0004 0615 7519Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101 USA
| | - Jerome I. Rotter
- grid.239844.00000 0001 0157 6501The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Stephen S. Rich
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Russell P. Tracy
- grid.59062.380000 0004 1936 7689Department of Pathology, University of Vermont, Colchester, VT 05405 USA
| | - Ramachandran S. Vasan
- grid.510954.c0000 0004 0444 3861Framingham Heart Study, Framingham, MA 01702 USA ,grid.189504.10000 0004 1936 7558Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA 02118 USA ,grid.189504.10000 0004 1936 7558Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118 USA
| | - James G. Wilson
- grid.410721.10000 0004 1937 0407Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216 USA
| | - Xiaofeng Zhu
- grid.67105.350000 0001 2164 3847Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Susan Redline
- grid.38142.3c000000041936754XDivision of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDivision of Sleep Medicine, Harvard Medical School, Boston, MA 02115 USA ,grid.239395.70000 0000 9011 8547Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
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14
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Redline S, Purcell SM. Sleep and Big Data: harnessing data, technology, and analytics for monitoring sleep and improving diagnostics, prediction, and interventions-an era for Sleep-Omics? Sleep 2021; 44:6248627. [PMID: 33893509 DOI: 10.1093/sleep/zsab107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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15
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Djonlagic I, Mariani S, Fitzpatrick AL, Van Der Klei VMGTH, Johnson DA, Wood AC, Seeman T, Nguyen HT, Prerau MJ, Luchsinger JA, Dzierzewski JM, Rapp SR, Tranah GJ, Yaffe K, Burdick KE, Stone KL, Redline S, Purcell SM. Macro and micro sleep architecture and cognitive performance in older adults. Nat Hum Behav 2021; 5:123-145. [PMID: 33199858 PMCID: PMC9881675 DOI: 10.1038/s41562-020-00964-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 09/15/2020] [Indexed: 01/31/2023]
Abstract
We sought to determine which facets of sleep neurophysiology were most strongly linked to cognitive performance in 3,819 older adults from two independent cohorts, using whole-night electroencephalography. From over 150 objective sleep metrics, we identified 23 that predicted cognitive performance, and processing speed in particular, with effects that were broadly independent of gross changes in sleep quality and quantity. These metrics included rapid eye movement duration, features of the electroencephalography power spectra derived from multivariate analysis, and spindle and slow oscillation morphology and coupling. These metrics were further embedded within broader associative networks linking sleep with aging and cardiometabolic disease: individuals who, compared with similarly aged peers, had better cognitive performance tended to have profiles of sleep metrics more often seen in younger, healthier individuals. Taken together, our results point to multiple facets of sleep neurophysiology that track coherently with underlying, age-dependent determinants of cognitive and physical health trajectories in older adults.
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Affiliation(s)
- Ina Djonlagic
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sara Mariani
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Alexis C Wood
- USDA/ARS Children's Nutrition Center, Baylor College of Medicine, Houston, TX, USA
| | - Teresa Seeman
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Ha T Nguyen
- Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Michael J Prerau
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Stephen R Rapp
- Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Kristine Yaffe
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine E Burdick
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Katie L Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Susan Redline
- Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Shaun M Purcell
- Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Boston, MA, USA.
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16
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Bigdeli TB, Genovese G, Georgakopoulos P, Meyers JL, Peterson RE, Iyegbe CO, Medeiros H, Valderrama J, Achtyes ED, Kotov R, Stahl EA, Abbott C, Azevedo MH, Belliveau RA, Bevilacqua E, Bromet EJ, Byerley W, Carvalho CB, Chapman SB, DeLisi LE, Dumont AL, O’Dushlaine C, Evgrafov OV, Fochtmann LJ, Gage D, Kennedy JL, Kinkead B, Macedo A, Moran JL, Morley CP, Dewan MJ, Nemesh J, Perkins DO, Purcell SM, Rakofsky JJ, Scolnick EM, Sklar BM, Sklar P, Smoller JW, Sullivan PF, Macciardi F, Marder SR, Gur RC, Gur RE, Braff DL, Nicolini H, Escamilla MA, Vawter MP, Sobell JL, Malaspina D, Lehrer DS, Buckley PF, Rapaport MH, Knowles JA, Fanous AH, Pato MT, McCarroll SA, Pato CN. Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry. Mol Psychiatry 2020; 25:2455-2467. [PMID: 31591465 PMCID: PMC7515843 DOI: 10.1038/s41380-019-0517-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/01/2019] [Accepted: 04/24/2019] [Indexed: 11/10/2022]
Abstract
Schizophrenia is a common, chronic and debilitating neuropsychiatric syndrome affecting tens of millions of individuals worldwide. While rare genetic variants play a role in the etiology of schizophrenia, most of the currently explained liability is within common variation, suggesting that variation predating the human diaspora out of Africa harbors a large fraction of the common variant attributable heritability. However, common variant association studies in schizophrenia have concentrated mainly on cohorts of European descent. We describe genome-wide association studies of 6152 cases and 3918 controls of admixed African ancestry, and of 1234 cases and 3090 controls of Latino ancestry, representing the largest such study in these populations to date. Combining results from the samples with African ancestry with summary statistics from the Psychiatric Genomics Consortium (PGC) study of schizophrenia yielded seven newly genome-wide significant loci, and we identified an additional eight loci by incorporating the results from samples with Latino ancestry. Leveraging population differences in patterns of linkage disequilibrium, we achieve improved fine-mapping resolution at 22 previously reported and 4 newly significant loci. Polygenic risk score profiling revealed improved prediction based on trans-ancestry meta-analysis results for admixed African (Nagelkerke's R2 = 0.032; liability R2 = 0.017; P < 10-52), Latino (Nagelkerke's R2 = 0.089; liability R2 = 0.021; P < 10-58), and European individuals (Nagelkerke's R2 = 0.089; liability R2 = 0.037; P < 10-113), further highlighting the advantages of incorporating data from diverse human populations.
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Affiliation(s)
- Tim B. Bigdeli
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,Department of Psychiatry, Veterans Affairs New York Harbor Healthcare System, Brooklyn, NY USA
| | - Giulio Genovese
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA USA
| | - Penelope Georgakopoulos
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Jacquelyn L. Meyers
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Roseann E. Peterson
- grid.224260.00000 0004 0458 8737Department of Psychiatry, Virginia Commonwealth University, Richmond, VA USA
| | - Conrad O. Iyegbe
- grid.13097.3c0000 0001 2322 6764Department of Psychosis Studies, King’s College London, London, UK
| | - Helena Medeiros
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Jorge Valderrama
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Eric D. Achtyes
- grid.17088.360000 0001 2150 1785Cherry Health and Michigan State University College of Human Medicine, Grand Rapids, MI USA
| | - Roman Kotov
- grid.36425.360000 0001 2216 9681Department of Psychiatry, Stony Brook University, Stony Brook, NY USA
| | - Eli A. Stahl
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics & Genomics, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA
| | - Colony Abbott
- grid.42505.360000 0001 2156 6853Department of Psychiatry & Behavioral Sciences, University of Southern California, Los Angeles, CA USA
| | - Maria Helena Azevedo
- grid.8051.c0000 0000 9511 4342Institute of Medical Psychology, Faculty of Medicine, University of Coimbra, Coimbra, PT Portugal
| | - Richard A. Belliveau
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | | | - Evelyn J. Bromet
- grid.36425.360000 0001 2216 9681Department of Psychiatry, Stony Brook University, Stony Brook, NY USA
| | - William Byerley
- grid.266102.10000 0001 2297 6811Department of Psychiatry, University of California, San Francisco, CA USA
| | - Celia Barreto Carvalho
- grid.7338.f0000 0001 2096 9474Faculty of Social and Human Sciences, University of Azores, Ponta Delgada, Portugal
| | - Sinéad B. Chapman
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Lynn E. DeLisi
- grid.410370.10000 0004 4657 1992VA Boston Healthcare System, Brockton, MA USA ,grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA
| | - Ashley L. Dumont
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Colm O’Dushlaine
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Oleg V. Evgrafov
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Laura J. Fochtmann
- grid.36425.360000 0001 2216 9681Department of Psychiatry, Stony Brook University, Stony Brook, NY USA
| | - Diane Gage
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - James L. Kennedy
- grid.17063.330000 0001 2157 2938Neurogenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health; Department of Psychiatry, University of Toronto, Toronto, ON Canada
| | - Becky Kinkead
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - Antonio Macedo
- grid.8051.c0000 0000 9511 4342Institute of Medical Psychology, Faculty of Medicine, University of Coimbra, Coimbra, PT Portugal
| | - Jennifer L. Moran
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Christopher P. Morley
- grid.411023.50000 0000 9159 4457Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, NY USA ,grid.411023.50000 0000 9159 4457Department of Family Medicine, State University of New York, Upstate Medical University, Syracuse, NY USA ,grid.411023.50000 0000 9159 4457Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY USA
| | - Mantosh J. Dewan
- grid.411023.50000 0000 9159 4457Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY USA
| | - James Nemesh
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Diana O. Perkins
- grid.410711.20000 0001 1034 1720Department of Psychiatry, University of North Carolina, Chapel Hill, NC USA
| | - Shaun M. Purcell
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.62560.370000 0004 0378 8294Department of Psychiatry, Brigham and Women’s Hospital, Boston, MA USA
| | - Jeffrey J. Rakofsky
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - Edward M. Scolnick
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Brooke M. Sklar
- grid.42505.360000 0001 2156 6853Department of Psychiatry & Behavioral Sciences, University of Southern California, Los Angeles, CA USA
| | - Pamela Sklar
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics & Genomics, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA
| | - Jordan W. Smoller
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA ,grid.32224.350000 0004 0386 9924Department of Psychiatry, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Patrick F. Sullivan
- grid.410711.20000 0001 1034 1720Department of Psychiatry, University of North Carolina, Chapel Hill, NC USA ,grid.465198.7Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, SE Sweden
| | - Fabio Macciardi
- grid.266093.80000 0001 0668 7243Department of Psychiatry and Human Behavior, University of California, Irvine, CA USA
| | - Stephen R. Marder
- grid.19006.3e0000 0000 9632 6718Department of Psychiatry and Biobehavioral Sciences, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Semel Institute for Neuroscience and Human Behavior, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Ruben C. Gur
- grid.25879.310000 0004 1936 8972Department of Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Child & Adolescent Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Lifespan Brain Institute, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Raquel E. Gur
- grid.25879.310000 0004 1936 8972Department of Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Child & Adolescent Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Lifespan Brain Institute, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - David L. Braff
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California, La Jolla, San Diego, CA USA ,grid.410371.00000 0004 0419 2708VISN-22 Mental Illness, Research, Education and Clinical Center (MIRECC), VA San Diego Healthcare System, San Diego, CA USA
| | | | | | - Michael A. Escamilla
- grid.416992.10000 0001 2179 3554Department of Psychiatry, Texas Tech University Health Sciences Center, El Paso, TX USA
| | - Marquis P. Vawter
- grid.266093.80000 0001 0668 7243Department of Psychiatry and Human Behavior, University of California, Irvine, CA USA
| | - Janet L. Sobell
- grid.42505.360000 0001 2156 6853Department of Psychiatry & Behavioral Sciences, University of Southern California, Los Angeles, CA USA
| | - Dolores Malaspina
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics & Genomics, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA
| | - Douglas S. Lehrer
- grid.268333.f0000 0004 1936 7937Department of Psychiatry, Wright State University, Dayton, OH USA
| | - Peter F. Buckley
- grid.224260.00000 0004 0458 8737School of Medicine, Virginia Commonwealth University, Richmond, VA USA
| | - Mark H. Rapaport
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - James A. Knowles
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY USA
| | | | - Ayman H. Fanous
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,Department of Psychiatry, Veterans Affairs New York Harbor Healthcare System, Brooklyn, NY USA
| | - Michele T. Pato
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Steven A. McCarroll
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA USA
| | - Carlos N. Pato
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
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17
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Nguyen TH, Dobbyn A, Brown RC, Riley BP, Buxbaum JD, Pinto D, Purcell SM, Sullivan PF, He X, Stahl EA. mTADA is a framework for identifying risk genes from de novo mutations in multiple traits. Nat Commun 2020; 11:2929. [PMID: 32522981 PMCID: PMC7287090 DOI: 10.1038/s41467-020-16487-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 05/06/2020] [Indexed: 11/12/2022] Open
Abstract
Joint analysis of multiple traits can result in the identification of associations not found through the analysis of each trait in isolation. Studies of neuropsychiatric disorders and congenital heart disease (CHD) which use de novo mutations (DNMs) from parent-offspring trios have reported multiple putatively causal genes. However, a joint analysis method designed to integrate DNMs from multiple studies has yet to be implemented. We here introduce multiple-trait TADA (mTADA) which jointly analyzes two traits using DNMs from non-overlapping family samples. We first demonstrate that mTADA is able to leverage genetic overlaps to increase the statistical power of risk-gene identification. We then apply mTADA to large datasets of >13,000 trios for five neuropsychiatric disorders and CHD. We report additional risk genes for schizophrenia, epileptic encephalopathies and CHD. We outline some shared and specific biological information of intellectual disability and CHD by conducting systems biology analyses of genes prioritized by mTADA.
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Affiliation(s)
- Tan-Hoang Nguyen
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA.
| | - Amanda Dobbyn
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth C Brown
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Brien P Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Joseph D Buxbaum
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalila Pinto
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shaun M Purcell
- Sleep Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, USA.
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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18
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Szatkiewicz JP, Fromer M, Nonneman RJ, Ancalade N, Johnson JS, Stahl EA, Rees E, Bergen SE, Hultman CM, Kirov G, O'Donovan M, Owen M, Holmans P, Sklar P, Sullivan PF, Purcell SM, Crowley JJ, Ruderfer DM. Characterization of Single Gene Copy Number Variants in Schizophrenia. Biol Psychiatry 2020; 87:736-744. [PMID: 31767120 PMCID: PMC7103483 DOI: 10.1016/j.biopsych.2019.09.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Genetic studies of schizophrenia have implicated numerous risk loci including several copy number variants (CNVs) of large effect and hundreds of loci of small effect. In only a few cases has a specific gene been clearly identified. Rare CNVs affecting a single gene offer a potential avenue to discovering schizophrenia risk genes. METHODS CNVs were generated from exome sequencing of 4913 schizophrenia cases and 6188 control subjects from Sweden. We integrated two CNV calling methods (XHMM and ExomeDepth) to expand our set of single-gene CNVs and leveraged two different approaches for validating these variants (quantitative polymerase chain reaction and NanoString). RESULTS We found a significant excess of all rare CNVs (deletions: p = .0004, duplications: p = .0006) and single-gene CNVs (deletions: p = .04, duplications: p = .03) in schizophrenia cases compared with control subjects. An expanded set of CNVs generated from integrating multiple approaches showed a significant burden of deletions in 11 of 21 gene sets previously implicated in schizophrenia and across all genes in those sets (p = .008), although no tests survived correction. We performed an extensive validation of all deletions in the significant set of voltage-gated calcium channels among CNVs called from both exome sequencing and genotyping arrays. In total, 4 exonic, single-gene deletions were validated in schizophrenia cases and none in control subjects (p = .039), of which all were identified by exome sequencing. CONCLUSIONS These results point to the potential contribution of single-gene CNVs to schizophrenia, indicate that the utility of exome sequencing for CNV calling has yet to be maximized, and note that single-gene CNVs should be included in gene-focused studies using other classes of variation.
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Affiliation(s)
- Jin P Szatkiewicz
- Center for Psychiatric Genomics, Department of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - Menachem Fromer
- Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Randal J Nonneman
- Center for Psychiatric Genomics, Department of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - NaEshia Ancalade
- Center for Psychiatric Genomics, Department of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - Jessica S Johnson
- Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elliott Rees
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sarah E Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - George Kirov
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Peter Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Patrick F Sullivan
- Center for Psychiatric Genomics, Department of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - James J Crowley
- Center for Psychiatric Genomics, Department of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Douglas M Ruderfer
- Division of Genetic Medicine, Departments of Medicine, Psychiatry, and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee.
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19
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Ghoshal A, Uygun DS, Yang L, McNally JM, Lopez-Huerta VG, Arias-Garcia MA, Baez-Nieto D, Allen A, Fitzgerald M, Choi S, Zhang Q, Hope JM, Yan K, Mao X, Nicholson TB, Imaizumi K, Fu Z, Feng G, Brown RE, Strecker RE, Purcell SM, Pan JQ. Effects of a patient-derived de novo coding alteration of CACNA1I in mice connect a schizophrenia risk gene with sleep spindle deficits. Transl Psychiatry 2020; 10:29. [PMID: 32066662 PMCID: PMC7026444 DOI: 10.1038/s41398-020-0685-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/25/2019] [Accepted: 11/06/2019] [Indexed: 11/09/2022] Open
Abstract
CACNA1I, a schizophrenia risk gene, encodes a subtype of voltage-gated T-type calcium channel CaV3.3. We previously reported that a patient-derived missense de novo mutation (R1346H) of CACNA1I impaired CaV3.3 channel function. Here, we generated CaV3.3-RH knock-in animals, along with mice lacking CaV3.3, to investigate the biological impact of R1346H (RH) variation. We found that RH mutation altered cellular excitability in the thalamic reticular nucleus (TRN), where CaV3.3 is abundantly expressed. Moreover, RH mutation produced marked deficits in sleep spindle occurrence and morphology throughout non-rapid eye movement (NREM) sleep, while CaV3.3 haploinsufficiency gave rise to largely normal spindles. Therefore, mice harboring the RH mutation provide a patient derived genetic model not only to dissect the spindle biology but also to evaluate the effects of pharmacological reagents in normalizing sleep spindle deficits. Importantly, our analyses highlighted the significance of characterizing individual spindles and strengthen the inferences we can make across species over sleep spindles. In conclusion, this study established a translational link between a genetic allele and spindle deficits during NREM observed in schizophrenia patients, representing a key step toward testing the hypothesis that normalizing spindles may be beneficial for schizophrenia patients.
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Affiliation(s)
- Ayan Ghoshal
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
| | - David S. Uygun
- Department of Psychiatry, VA Boston Healthcare System & Harvard Medical School, Boston, MA USA
| | - Lingling Yang
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
| | - James M. McNally
- Department of Psychiatry, VA Boston Healthcare System & Harvard Medical School, Boston, MA USA
| | - Violeta G. Lopez-Huerta
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
- Present Address: Department of Neurodevelopment and Physiology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - Mario A. Arias-Garcia
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
- Present Address: Department of Neurodevelopment and Physiology, Institute of Cellular Physiology, National Autonomous University of Mexico, Mexico City, Mexico
| | - David Baez-Nieto
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
| | - Andrew Allen
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
| | - Megan Fitzgerald
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
| | - Soonwook Choi
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
| | - Qiangge Zhang
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
| | - Jen M. Hope
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
| | - Karena Yan
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
| | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139 USA
| | - Thomas B. Nicholson
- Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139 USA
| | | | - Zhanyan Fu
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
| | - Ritchie E. Brown
- Department of Psychiatry, VA Boston Healthcare System & Harvard Medical School, Boston, MA USA
| | - Robert E. Strecker
- Department of Psychiatry, VA Boston Healthcare System & Harvard Medical School, Boston, MA USA
| | - Shaun M. Purcell
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Jen Q. Pan
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA USA
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20
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Wang H, Lane JM, Jones SE, Dashti HS, Ollila HM, Wood AR, van Hees VT, Brumpton B, Winsvold BS, Kantojärvi K, Palviainen T, Cade BE, Sofer T, Song Y, Patel K, Anderson SG, Bechtold DA, Bowden J, Emsley R, Kyle SD, Little MA, Loudon AS, Scheer FAJL, Purcell SM, Richmond RC, Spiegelhalder K, Tyrrell J, Zhu X, Hublin C, Kaprio JA, Kristiansson K, Sulkava S, Paunio T, Hveem K, Nielsen JB, Willer CJ, Zwart JA, Strand LB, Frayling TM, Ray D, Lawlor DA, Rutter MK, Weedon MN, Redline S, Saxena R. Genome-wide association analysis of self-reported daytime sleepiness identifies 42 loci that suggest biological subtypes. Nat Commun 2019; 10:3503. [PMID: 31409809 PMCID: PMC6692391 DOI: 10.1038/s41467-019-11456-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 06/27/2019] [Indexed: 01/12/2023] Open
Abstract
Excessive daytime sleepiness (EDS) affects 10-20% of the population and is associated with substantial functional deficits. Here, we identify 42 loci for self-reported daytime sleepiness in GWAS of 452,071 individuals from the UK Biobank, with enrichment for genes expressed in brain tissues and in neuronal transmission pathways. We confirm the aggregate effect of a genetic risk score of 42 SNPs on daytime sleepiness in independent Scandinavian cohorts and on other sleep disorders (restless legs syndrome, insomnia) and sleep traits (duration, chronotype, accelerometer-derived sleep efficiency and daytime naps or inactivity). However, individual daytime sleepiness signals vary in their associations with objective short vs long sleep, and with markers of sleep continuity. The 42 sleepiness variants primarily cluster into two predominant composite biological subtypes - sleep propensity and sleep fragmentation. Shared genetic links are also seen with obesity, coronary heart disease, psychiatric diseases, cognitive traits and reproductive ageing.
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Affiliation(s)
- Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Jacqueline M Lane
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel E Jones
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, United Kingdom
| | - Hassan S Dashti
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanna M Ollila
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, United Kingdom
| | | | - Ben Brumpton
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Department of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Bendik S Winsvold
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Division of Clinical Neuroscience, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Katri Kantojärvi
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Teemu Palviainen
- Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Yanwei Song
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Northeastern University College of Science, Boston, MA, USA
| | - Krunal Patel
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Northeastern University College of Science, Boston, MA, USA
| | - Simon G Anderson
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The George Alleyne Chronic Disease Research Centre, Caribbean Institute for Health Research, University of the West Indies, Cave Hill, Barbados
| | - David A Bechtold
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jack Bowden
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard Emsley
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Simon D Kyle
- Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Max A Little
- Department of Mathematics, Aston University, Birmingham, UK
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew S Loudon
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Frank A J L Scheer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Kai Spiegelhalder
- Clinic for Psychiatry and Psychotherapy, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, United Kingdom
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Christer Hublin
- Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko A Kaprio
- Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Kati Kristiansson
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Sonja Sulkava
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Tiina Paunio
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristian Hveem
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - John-Anker Zwart
- Division of Clinical Neuroscience, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Linn B Strand
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, United Kingdom
| | - David Ray
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX39DU, UK
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Martin K Rutter
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Diabetes Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Michael N Weedon
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, United Kingdom
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Richa Saxena
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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21
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Charney AW, Stahl EA, Green EK, Chen CY, Moran JL, Chambert K, Belliveau RA, Forty L, Gordon-Smith K, Lee PH, Bromet EJ, Buckley PF, Escamilla MA, Fanous AH, Fochtmann LJ, Lehrer DS, Malaspina D, Marder SR, Morley CP, Nicolini H, Perkins DO, Rakofsky JJ, Rapaport MH, Medeiros H, Sobell JL, Backlund L, Bergen SE, Juréus A, Schalling M, Lichtenstein P, Knowles JA, Burdick KE, Jones I, Jones LA, Hultman CM, Perlis R, Purcell SM, McCarroll SA, Pato CN, Pato MT, Florio AD, Craddock N, Landén M, Smoller JW, Ruderfer DM, Sklar P. Contribution of Rare Copy Number Variants to Bipolar Disorder Risk Is Limited to Schizoaffective Cases. Biol Psychiatry 2019; 86:110-119. [PMID: 30686506 PMCID: PMC6586545 DOI: 10.1016/j.biopsych.2018.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 12/12/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Genetic risk for bipolar disorder (BD) is conferred through many common alleles, while a role for rare copy number variants (CNVs) is less clear. Subtypes of BD including schizoaffective disorder bipolar type (SAB), bipolar I disorder (BD I), and bipolar II disorder (BD II) differ according to the prominence and timing of psychosis, mania, and depression. The genetic factors contributing to the combination of symptoms among these subtypes are poorly understood. METHODS Rare large CNVs were analyzed in 6353 BD cases (3833 BD I [2676 with psychosis, 850 without psychosis, and 307 with unknown psychosis history], 1436 BD II, 579 SAB, and 505 BD not otherwise specified) and 8656 controls. CNV burden and a polygenic risk score (PRS) for schizophrenia were used to evaluate the relative contributions of rare and common variants to risk of BD, BD subtypes, and psychosis. RESULTS CNV burden did not differ between BD and controls when treated as a single diagnostic entity. However, burden in SAB was increased relative to controls (p = .001), BD I (p = .0003), and BD II (p = .0007). Burden and schizophrenia PRSs were increased in SAB compared with BD I with psychosis (CNV p = .0007, PRS p = .004), and BD I without psychosis (CNV p = .0004, PRS p = 3.9 × 10-5). Within BD I, psychosis was associated with increased schizophrenia PRSs (p = .005) but not CNV burden. CONCLUSIONS CNV burden in BD is limited to SAB. Rare and common genetic variants may contribute differently to risk for psychosis and perhaps other classes of psychiatric symptoms.
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Affiliation(s)
- Alexander W. Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA,Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Eli A. Stahl
- Icahn Institute of Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Elaine K. Green
- School of Biomedical and Health Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth University, Portland Square, Plymouth, PL4 8AA, UK
| | - Chia-Yen Chen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge St., Boston, MA, 02114, USA
| | - Jennifer L. Moran
- Department of Psychiatry, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Richard A. Belliveau
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Liz Forty
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff Unviersity, Hadyn Ellis Building, Maindy Road, Cardiff, CF14 4HQ, UK
| | - Katherine Gordon-Smith
- Department of Psychiatry, University of Birmingham, 25 Vincent Drive, Birmingham, B15 2FG, UK
| | - Phil H. Lee
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.,Department of Psychiatry, Harvard Medical School, 77 Avenue Louis Pasteur, Boston MA 02115,Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
| | - Evelyn J Bromet
- Department of Psychiatry, Stony Brook University, HSC, Level T-10, Room 020, Stony Brook, NY, 11794, USA
| | - Peter F Buckley
- School of Medicine, Virginia Commonwealth University, 1201 E Marshall St., Richmond, VA, 23298, USA.,Department of Psychiatry, Georgia Regents University Medical Center, 1120 15th Street, Augusta, GA, 30912, USA
| | - Michael A Escamilla
- Center of Excellence in Neuroscience, Department of Psychiatry, Texas Tech University Health Sciences Center at El Paso, 800 N. Mesa, Suite 200, El Paso, TX, 79902, USA
| | - Ayman H. Fanous
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, 450 Clarkson Ave., Brooklyn, NY, 11203, USA.,Department of Psychiatry, VA New York Harbor Healthcare System, 800 Poly Pl., Brooklyn, NY, 11209, USA
| | - Laura J Fochtmann
- Department of Psychiatry, Stony Brook University, HSC, Level T-10, Room 020, Stony Brook, NY, 11794, USA
| | - Douglas S. Lehrer
- Department of Psychiatry, Wright State University, 3640 Colonel Gleen Hwy, Dayton, OH, 45435, USA
| | - Dolores Malaspina
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA,Department of Psychiatry, New York University, 550 First Ave., New York, NY, 10016, USA
| | - Stephen R. Marder
- Semel Institute for Neuroscience, University of California, Los Angeles, 11301 Wilshire Blvd, Los Angeles, CA, 90073, USA
| | - Christopher P. Morley
- Department of Psychiatry and Behavioral Science, State University of New York, Upstate Medical University, 750 East Adams St, MIMC 200, Syracuse, NY, 13210, USA.,Department of Family Medicine, State University of New York, Upstate Medical University, 750 East Adams St, MIMC 200, Syracuse, NY, 13210, USA.,Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, 750 East Adams St, MIMC 200, Syracuse, NY, 13210, USA
| | - Humberto Nicolini
- Center for Genomic Sciences, Universidad Autónoma de la Ciudad de México, Dr. García Diego # 168, Col. Doctores, Del., Mexico City, Mexico,Department of Psychiatry, Carracci Medical Group, 107 Carracci Street, Mexico City, Mexico
| | - Diana O. Perkins
- Department of Psychiatry, University of North Carolina at Chapel Hill, 321 S. Columbia Street, Chapel Hill, NC, 27516, USA
| | - Jeffrey J. Rakofsky
- Department of Psychiatry and Behavioral Sciences, Emory University, 101 Woodruff Circle Suite 4000, Atlanta, GA, 30322, USA
| | - Mark H. Rapaport
- Department of Psychiatry and Behavioral Sciences, Emory University, 101 Woodruff Circle Suite 4000, Atlanta, GA, 30322, USA
| | - Helena Medeiros
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, 450 Clarkson Ave., Brooklyn, NY, 11203, USA
| | - Janet L. Sobell
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Keck School of Medicine, 2250 Alcazar Street, Los Angeles, CA, 90033, USA
| | - Lena Backlund
- Department of Clinical Neuroscience, Karolinska Institutet, Vårdvägen 3, Stockholm, 11281, Sweden
| | - Sarah E. Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12 A, Stockholm, 17177, Sweden
| | - Anders Juréus
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12 A, Stockholm, 17177, Sweden
| | - Martin Schalling
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Cmm (L8:00), Stockholm, 17176, Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12 A, Stockholm, 17177, Sweden
| | - James A. Knowles
- Department of Cell Biology, State University of New York, Downstate Medical Center, 450 Clarkson Ave., Brooklyn, NY, 11203, USA
| | - Katherine E. Burdick
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Psychiatry, Harvard Medical School, 77 Avenue Louis Pasteur, Boston MA 02115,Department of Psychiatry, Brigham and Women’s Hospital, 221 Longwood Ave Boston MA, 02115, USA
| | - Ian Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff Unviersity, Hadyn Ellis Building, Maindy Road, Cardiff, CF14 4HQ, UK
| | - Lisa A Jones
- Department of Psychiatry, University of Birmingham, 25 Vincent Drive, Birmingham, B15 2FG, UK
| | - Christina M. Hultman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12 A, Stockholm, 17177, Sweden
| | - Roy Perlis
- Center for Experimental Therapeutics, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
| | - Shaun M. Purcell
- Department of Psychiatry, Harvard Medical School, 77 Avenue Louis Pasteur, Boston MA 02115,Department of Psychiatry, Brigham and Women’s Hospital, 221 Longwood Ave Boston MA, 02115, USA
| | - Steven A. McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Carlos N. Pato
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, 450 Clarkson Ave., Brooklyn, NY, 11203, USA
| | - Michele T. Pato
- Department of Psychiatry and the Behavioral Sciences, State University of New York, Downstate Medical Center, 450 Clarkson Ave., Brooklyn, NY, 11203, USA
| | - Ariana Di Florio
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff Unviersity, Hadyn Ellis Building, Maindy Road, Cardiff, CF14 4HQ, UK.,Department of Psychiatry, University of North Carolina at Chapel Hill, 321 S. Columbia Street, Chapel Hill, NC, 27516, USA
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff Unviersity, Hadyn Ellis Building, Maindy Road, Cardiff, CF14 4HQ, UK
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12 A, Stockholm, 17177, Sweden,Institute of neuroscience and physiology, Sahlgenska academy at the Gothenburg university, Blå Sträket 15, Gothenburg, 41345, Sweden
| | - Jordan W. Smoller
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge St., Boston, MA, 02114, USA
| | - Douglas M. Ruderfer
- Division of Genetic Medicine, Departments of Medicine, Biomedical Informatics and Psychiatry, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Pamela Sklar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Icahn Institute of Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA.,Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
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22
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Wang H, Cade BE, Sofer T, Sands SA, Chen H, Browning SR, Stilp AM, Louie TL, Thornton TA, Johnson WC, Below JE, Conomos MP, Evans DS, Gharib SA, Guo X, Wood AC, Mei H, Yaffe K, Loredo JS, Ramos AR, Barrett-Connor E, Ancoli-Israel S, Zee PC, Arens R, Shah NA, Taylor KD, Tranah GJ, Stone KL, Hanis CL, Wilson JG, Gottlieb DJ, Patel SR, Rice K, Post WS, Rotter JI, Sunyaev SR, Cai J, Lin X, Purcell SM, Laurie CC, Saxena R, Redline S, Zhu X. Admixture mapping identifies novel loci for obstructive sleep apnea in Hispanic/Latino Americans. Hum Mol Genet 2019; 28:675-687. [PMID: 30403821 DOI: 10.1093/hmg/ddy387] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/05/2018] [Indexed: 01/11/2023] Open
Abstract
Obstructive sleep apnea (OSA) is a common disorder associated with increased risk of cardiovascular disease and mortality. Its prevalence and severity vary across ancestral background. Although OSA traits are heritable, few genetic associations have been identified. To identify genetic regions associated with OSA and improve statistical power, we applied admixture mapping on three primary OSA traits [the apnea hypopnea index (AHI), overnight average oxyhemoglobin saturation (SaO2) and percentage time SaO2 < 90%] and a secondary trait (respiratory event duration) in a Hispanic/Latino American population study of 11 575 individuals with significant variation in ancestral background. Linear mixed models were performed using previously inferred African, European and Amerindian local genetic ancestry markers. Global African ancestry was associated with a lower AHI, higher SaO2 and shorter event duration. Admixture mapping analysis of the primary OSA traits identified local African ancestry at the chromosomal region 2q37 as genome-wide significantly associated with AHI (P < 5.7 × 10-5), and European and Amerindian ancestries at 18q21 suggestively associated with both AHI and percentage time SaO2 < 90% (P < 10-3). Follow-up joint ancestry-SNP association analyses identified novel variants in ferrochelatase (FECH), significantly associated with AHI and percentage time SaO2 < 90% after adjusting for multiple tests (P < 8 × 10-6). These signals contributed to the admixture mapping associations and were replicated in independent cohorts. In this first admixture mapping study of OSA, novel associations with variants in the iron/heme metabolism pathway suggest a role for iron in influencing respiratory traits underlying OSA.
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Affiliation(s)
- Heming Wang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.,Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Scott A Sands
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Precision Health, School of Public Health & School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Tin L Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alexis C Wood
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kristine Yaffe
- Departments of Psychiatry and Neurology, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Jose S Loredo
- Division of Pulmonary Critical Care and Sleep Medicine, Department of Medicine, UC San Diego School of Medicine, La Jolla, CA, USA
| | - Alberto R Ramos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Sonia Ancoli-Israel
- Departments of Medicine and Psychiatry, University of California, San Diego, CA, USA.,Department of Veterans Affairs, San Diego Center of Excellence for Stress and Mental Health, San Diego, CA, USA
| | - Phyllis C Zee
- Department of Neurology and Sleep Medicine Center, Northwestern University, Chicago, IL, USA
| | - Raanan Arens
- The Children's Hospital at Montefiore, Division of Respiratory and Sleep Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Neomi A Shah
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Katie L Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Craig L Hanis
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - James G Wilson
- Physiology and Biophysics, University of Mississippi, Jackson, MS, USA
| | - Daniel J Gottlieb
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,VA Boston Healthcare System, Boston, MA, USA
| | - Sanjay R Patel
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Wendy S Post
- Division of Cardiology, Johns Hopkins University, Baltimore, MD, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Shamil R Sunyaev
- Broad Institute, Cambridge, MA 02142, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.,Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA.,Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Richa Saxena
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Broad Institute, Cambridge, MA 02142, USA.,Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
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23
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Stahl EA, Breen G, Forstner AJ, McQuillin A, Ripke S, Trubetskoy V, Mattheisen M, Wang Y, Coleman JRI, Gaspar HA, de Leeuw CA, Steinberg S, Pavlides JMW, Trzaskowski M, Byrne EM, Pers TH, Holmans PA, Richards AL, Abbott L, Agerbo E, Akil H, Albani D, Alliey-Rodriguez N, Als TD, Anjorin A, Antilla V, Awasthi S, Badner JA, Bækvad-Hansen M, Barchas JD, Bass N, Bauer M, Belliveau R, Bergen SE, Pedersen CB, Bøen E, Boks MP, Boocock J, Budde M, Bunney W, Burmeister M, Bybjerg-Grauholm J, Byerley W, Casas M, Cerrato F, Cervantes P, Chambert K, Charney AW, Chen D, Churchhouse C, Clarke TK, Coryell W, Craig DW, Cruceanu C, Curtis D, Czerski PM, Dale AM, de Jong S, Degenhardt F, Del-Favero J, DePaulo JR, Djurovic S, Dobbyn AL, Dumont A, Elvsåshagen T, Escott-Price V, Fan CC, Fischer SB, Flickinger M, Foroud TM, Forty L, Frank J, Fraser C, Freimer NB, Frisén L, Gade K, Gage D, Garnham J, Giambartolomei C, Pedersen MG, Goldstein J, Gordon SD, Gordon-Smith K, Green EK, Green MJ, Greenwood TA, Grove J, Guan W, Guzman-Parra J, Hamshere ML, Hautzinger M, Heilbronner U, Herms S, Hipolito M, Hoffmann P, Holland D, Huckins L, Jamain S, Johnson JS, Juréus A, Kandaswamy R, Karlsson R, Kennedy JL, Kittel-Schneider S, Knowles JA, Kogevinas M, Koller AC, Kupka R, Lavebratt C, Lawrence J, Lawson WB, Leber M, Lee PH, Levy SE, Li JZ, Liu C, Lucae S, Maaser A, MacIntyre DJ, Mahon PB, Maier W, Martinsson L, McCarroll S, McGuffin P, McInnis MG, McKay JD, Medeiros H, Medland SE, Meng F, Milani L, Montgomery GW, Morris DW, Mühleisen TW, Mullins N, Nguyen H, Nievergelt CM, Adolfsson AN, Nwulia EA, O'Donovan C, Loohuis LMO, Ori APS, Oruc L, Ösby U, Perlis RH, Perry A, Pfennig A, Potash JB, Purcell SM, Regeer EJ, Reif A, Reinbold CS, Rice JP, Rivas F, Rivera M, Roussos P, Ruderfer DM, Ryu E, Sánchez-Mora C, Schatzberg AF, Scheftner WA, Schork NJ, Shannon Weickert C, Shehktman T, Shilling PD, Sigurdsson E, Slaney C, Smeland OB, Sobell JL, Søholm Hansen C, Spijker AT, St Clair D, Steffens M, Strauss JS, Streit F, Strohmaier J, Szelinger S, Thompson RC, Thorgeirsson TE, Treutlein J, Vedder H, Wang W, Watson SJ, Weickert TW, Witt SH, Xi S, Xu W, Young AH, Zandi P, Zhang P, Zöllner S, Adolfsson R, Agartz I, Alda M, Backlund L, Baune BT, Bellivier F, Berrettini WH, Biernacka JM, Blackwood DHR, Boehnke M, Børglum AD, Corvin A, Craddock N, Daly MJ, Dannlowski U, Esko T, Etain B, Frye M, Fullerton JM, Gershon ES, Gill M, Goes F, Grigoroiu-Serbanescu M, Hauser J, Hougaard DM, Hultman CM, Jones I, Jones LA, Kahn RS, Kirov G, Landén M, Leboyer M, Lewis CM, Li QS, Lissowska J, Martin NG, Mayoral F, McElroy SL, McIntosh AM, McMahon FJ, Melle I, Metspalu A, Mitchell PB, Morken G, Mors O, Mortensen PB, Müller-Myhsok B, Myers RM, Neale BM, Nimgaonkar V, Nordentoft M, Nöthen MM, O'Donovan MC, Oedegaard KJ, Owen MJ, Paciga SA, Pato C, Pato MT, Posthuma D, Ramos-Quiroga JA, Ribasés M, Rietschel M, Rouleau GA, Schalling M, Schofield PR, Schulze TG, Serretti A, Smoller JW, Stefansson H, Stefansson K, Stordal E, Sullivan PF, Turecki G, Vaaler AE, Vieta E, Vincent JB, Werge T, Nurnberger JI, Wray NR, Di Florio A, Edenberg HJ, Cichon S, Ophoff RA, Scott LJ, Andreassen OA, Kelsoe J, Sklar P. Genome-wide association study identifies 30 loci associated with bipolar disorder. Nat Genet 2019; 51:793-803. [PMID: 31043756 PMCID: PMC6956732 DOI: 10.1038/s41588-019-0397-8] [Citation(s) in RCA: 879] [Impact Index Per Article: 175.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 03/18/2019] [Indexed: 12/18/2022]
Abstract
Bipolar disorder is a highly heritable psychiatric disorder. We performed a genome-wide association study (GWAS) including 20,352 cases and 31,358 controls of European descent, with follow-up analysis of 822 variants with P < 1 × 10-4 in an additional 9,412 cases and 137,760 controls. Eight of the 19 variants that were genome-wide significant (P < 5 × 10-8) in the discovery GWAS were not genome-wide significant in the combined analysis, consistent with small effect sizes and limited power but also with genetic heterogeneity. In the combined analysis, 30 loci were genome-wide significant, including 20 newly identified loci. The significant loci contain genes encoding ion channels, neurotransmitter transporters and synaptic components. Pathway analysis revealed nine significantly enriched gene sets, including regulation of insulin secretion and endocannabinoid signaling. Bipolar I disorder is strongly genetically correlated with schizophrenia, driven by psychosis, whereas bipolar II disorder is more strongly correlated with major depressive disorder. These findings address key clinical questions and provide potential biological mechanisms for bipolar disorder.
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Affiliation(s)
- Eli A Stahl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Andreas J Forstner
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Psychiatry (UPK), University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Stephan Ripke
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Vassily Trubetskoy
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Manuel Mattheisen
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital Würzburg, Würzburg, Germany
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Yunpeng Wang
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jonathan R I Coleman
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Héléna A Gaspar
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | | | - Maciej Trzaskowski
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Enda M Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tune H Pers
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Peter A Holmans
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Alexander L Richards
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Liam Abbott
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-based Research and Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Huda Akil
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Diego Albani
- Department of Neuroscience, Istituto Di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Ney Alliey-Rodriguez
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Thomas D Als
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Adebayo Anjorin
- Department of Psychiatry, Berkshire Healthcare NHS Foundation Trust, Bracknell, UK
| | - Verneri Antilla
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Swapnil Awasthi
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Judith A Badner
- Department of Psychiatry, Rush University Medical Center, Chicago, IL, USA
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jack D Barchas
- Department of Psychiatry, Weill Cornell Medical College, New York, NY, USA
| | - Nicholas Bass
- Division of Psychiatry, University College London, London, UK
| | - Michael Bauer
- Department of Psychiatry and Psychotherapy, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Richard Belliveau
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Sarah E Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Carsten Bøcker Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-based Research and Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Erlend Bøen
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Marco P Boks
- Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - James Boocock
- Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Monika Budde
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Munich, Germany
| | - William Bunney
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - Margit Burmeister
- Molecular & Behavioral Neuroscience Institute and Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - William Byerley
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Miquel Casas
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Felecia Cerrato
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Pablo Cervantes
- Department of Psychiatry, Mood Disorders Program, McGill University Health Center, Montreal, Quebec, Canada
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danfeng Chen
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Claire Churchhouse
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Edinburgh, Scotland
| | - William Coryell
- University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | | | - Cristiana Cruceanu
- Department of Psychiatry, Mood Disorders Program, McGill University Health Center, Montreal, Quebec, Canada
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - David Curtis
- Centre for Psychiatry, Queen Mary University of London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Piotr M Czerski
- Department of Psychiatry, Laboratory of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Anders M Dale
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Simone de Jong
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jurgen Del-Favero
- Applied Molecular Genomics Unit, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
| | - J Raymond DePaulo
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital Ullevål, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amanda L Dobbyn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashley Dumont
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Torbjørn Elvsåshagen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Oslo University Hospital, Oslo, Norway
| | - Valentina Escott-Price
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Chun Chieh Fan
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Sascha B Fischer
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Matthew Flickinger
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Tatiana M Foroud
- Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN, USA
| | - Liz Forty
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christine Fraser
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Louise Frisén
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Neuroscience, Karolinska Institutet and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
- Child and Adolescent Psychiatry Research Center, Stockholm, Sweden
| | - Katrin Gade
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Diane Gage
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Julie Garnham
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marianne Giørtz Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-based Research and Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Jaqueline Goldstein
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Scott D Gordon
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Elaine K Green
- School of Biomedical Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, University of Plymouth, Plymouth, UK
| | - Melissa J Green
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuroscience Research Australia, Sydney, New South Wales, Australia
| | - Tiffany A Greenwood
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Jakob Grove
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Weihua Guan
- Biostatistics, University of Minnesota System, Minneapolis, MN, USA
| | - José Guzman-Parra
- Mental Health Department, University Regional Hospital, Biomedicine Institute (IBIMA), Málaga, Spain
| | - Marian L Hamshere
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Martin Hautzinger
- Department of Psychology, Eberhard Karls Universität Tübingen, Tubingen, Germany
| | - Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Munich, Germany
| | - Stefan Herms
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Maria Hipolito
- Department of Psychiatry and Behavioral Sciences, Howard University Hospital, Washington, DC, USA
| | - Per Hoffmann
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Dominic Holland
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA, USA
| | - Laura Huckins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stéphane Jamain
- Psychiatrie Translationnelle, Inserm U955, Créteil, France
- Faculté de Médecine, Université Paris Est, Créteil, France
| | - Jessica S Johnson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anders Juréus
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Radhika Kandaswamy
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - James L Kennedy
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Onatario, Canada
- Neurogenetics Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Sarah Kittel-Schneider
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - James A Knowles
- Cell Biology, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | | | - Anna C Koller
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Ralph Kupka
- Psychiatry, Altrecht, Utrecht, the Netherlands
- Psychiatry, GGZ inGeest, Amsterdam, the Netherlands
- Psychiatry, VU Medisch Centrum, Amsterdam, the Netherlands
| | - Catharina Lavebratt
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jacob Lawrence
- Department of, rth East London NHS Foundation Trust, Ilford, UK
| | - William B Lawson
- Department of Psychiatry and Behavioral Sciences, Howard University Hospital, Washington, DC, USA
| | - Markus Leber
- Department of Neurodegenerative Diseases and Geropsychiatry, University Hospital Bonn, Bonn, Germany
| | - Phil H Lee
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Chunyu Liu
- Department of Psychiatry, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | | | - Anna Maaser
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Donald J MacIntyre
- Mental Health, NHS 24, Glasgow, UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Pamela B Mahon
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
| | - Wolfgang Maier
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Lina Martinsson
- Department of Clinical Neuroscience, Karolinska Institutet and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Steve McCarroll
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Peter McGuffin
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - James D McKay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Helena Medeiros
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - Sarah E Medland
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Fan Meng
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Derek W Morris
- Discipline of Biochemistry, Neuroimaging and Cognitive Genomics (NICOG) Centre, National University of Ireland, Galway, Galway, Ireland
- Neuropsychiatric Genetics Research Group, Department of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Thomas W Mühleisen
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Niamh Mullins
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Hoang Nguyen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Research/Psychiatry, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | | | - Evaristus A Nwulia
- Department of Psychiatry and Behavioral Sciences, Howard University Hospital, Washington, DC, USA
| | - Claire O'Donovan
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anil P S Ori
- Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lilijana Oruc
- Department of Clinical Psychiatry, Psychiatry Clinic, Clinical Center University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Urban Ösby
- Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Roy H Perlis
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, MA, USA
| | - Amy Perry
- Department of Psychological Medicine, University of Worcester, Worcester, UK
| | - Andrea Pfennig
- Department of Psychiatry and Psychotherapy, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - James B Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shaun M Purcell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
| | - Eline J Regeer
- Outpatient Clinic for Bipolar Disorder, Altrecht, Utrecht, the Netherlands
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Céline S Reinbold
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - John P Rice
- Department of Psychiatry, Washington University in Saint Louis, Saint Louis, MO, USA
| | - Fabio Rivas
- Mental Health Department, University Regional Hospital, Biomedicine Institute (IBIMA), Málaga, Spain
| | - Margarita Rivera
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- Department of Biochemistry and Molecular Biology II, Institute of Neurosciences, Center for Biomedical Research, University of Granada, Granada, Spain
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas M Ruderfer
- Medicine, Psychiatry, Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Cristina Sánchez-Mora
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelona, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alan F Schatzberg
- Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Cynthia Shannon Weickert
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuroscience Research Australia, Sydney, New South Wales, Australia
| | - Tatyana Shehktman
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Paul D Shilling
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Engilbert Sigurdsson
- Faculty of Medicine, Department of Psychiatry, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Claire Slaney
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Olav B Smeland
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- NORMENT, University of Oslo, Oslo, Norway
| | - Janet L Sobell
- Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Christine Søholm Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | - David St Clair
- Institute for Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - John S Strauss
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, Toronto, Onatario, Canada
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Robert C Thompson
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | | | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Helmut Vedder
- Department of Psychiatry, Psychiatrisches Zentrum Nordbaden, Wiesloch, Germany
| | - Weiqing Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stanley J Watson
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Thomas W Weickert
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuroscience Research Australia, Sydney, New South Wales, Australia
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Simon Xi
- Computational Sciences Center of Emphasis, Pfizer Global Research and Development, Cambridge, MA, USA
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Onatario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Allan H Young
- Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Peter Zandi
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Peng Zhang
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sebastian Zöllner
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Rolf Adolfsson
- Department of Clinical Sciences, Psychiatry, Umeå University Medical Faculty, Umeå, Sweden
| | - Ingrid Agartz
- Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Institute of Clinical Medicine and Diakonhjemmet Hospital, University of Oslo, Oslo, Norway
| | - Martin Alda
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
- National Institute of Mental Health, Klecany, Czech Republic
| | - Lena Backlund
- Department of Clinical Neuroscience, Karolinska Institutet and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Bernhard T Baune
- Department of Psychiatry, University of Melbourne, Melbourne, Victoria, Australia
- Department of Psychiatry, University of Munster, Munster, Germany
| | - Frank Bellivier
- Department of Psychiatry and Addiction Medicine, Assistance Publique-Hopitaux de Paris, Paris, France
- Paris Bipolar and TRD Expert Centres, FondaMental Foundation, Paris, France
- UMR-S1144 Team 1: Biomarkers of relapse and therapeutic response in addiction and mood disorders, INSERM, Paris, France
- Department of Psychiatry, Université Paris Diderot, Paris, France
| | - Wade H Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Michael Boehnke
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Anders D Børglum
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Nicholas Craddock
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Udo Dannlowski
- Department of Psychiatry, University of Munster, Munster, Germany
| | - Tõnu Esko
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Division of Endocrinology, Children's Hospital Boston, Boston, MA, USA
| | - Bruno Etain
- Department of Psychiatry and Addiction Medicine, Assistance Publique-Hopitaux de Paris, Paris, France
- UMR-S1144 Team 1: Biomarkers of relapse and therapeutic response in addiction and mood disorders, INSERM, Paris, France
- Department of Psychiatry, Université Paris Diderot, Paris, France
- Centre for Affective Disorders, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Mark Frye
- Department of Psychiatry & Psychology, Mayo Clinic, Rochester, MN, USA
| | - Janice M Fullerton
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Michael Gill
- Neuropsychiatric Genetics Research Group, Department of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Fernando Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maria Grigoroiu-Serbanescu
- Biometric Psychiatric Genetics Research Unit, Alexandru Obregia Clinical Psychiatric Hospital, Bucharest, Romania
| | - Joanna Hauser
- Department of Psychiatry, Laboratory of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ian Jones
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Lisa A Jones
- Department of Psychological Medicine, University of Worcester, Worcester, UK
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - George Kirov
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Marion Leboyer
- Faculté de Médecine, Université Paris Est, Créteil, France
- Department of Psychiatry and Addiction Medicine, Assistance Publique-Hopitaux de Paris, Paris, France
- INSERM, Paris, France
| | - Cathryn M Lewis
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Qingqin S Li
- Neuroscience Therapeutic Area, Janssen Research and Development, LLC, Titusville, NJ, USA
| | - Jolanta Lissowska
- Cancer Epidemiology and Prevention, M. Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Nicholas G Martin
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Psychology, The University of Queensland, Brisbane, Queensland, Australia
| | - Fermin Mayoral
- Mental Health Department, University Regional Hospital, Biomedicine Institute (IBIMA), Málaga, Spain
| | | | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, Scotland
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Francis J McMahon
- Human Genetics Branch, Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Ingrid Melle
- Division of Mental Health and Addiction and Institute of Clinical Medicine, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Philip B Mitchell
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Gunnar Morken
- Mental Health, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology-NTNU, Trondheim, Norway
- Department of Psychiatry, St Olavs University Hospital, Trondheim, Norway
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Preben Bo Mortensen
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-based Research and Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- University of Liverpool, Liverpool, UK
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Benjamin M Neale
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Michael C O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Ketil J Oedegaard
- Division of Psychiatry, Haukeland Universitetssjukehus, Bergen, Norway
- Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Michael J Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
| | - Sara A Paciga
- Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Groton, CT, USA
| | - Carlos Pato
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
- College of Medicine Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - Michele T Pato
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, the Netherlands
| | - Josep Antoni Ramos-Quiroga
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelona, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Ribasés
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelona, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Guy A Rouleau
- Department of Neurology and Neurosurgery, McGill University, Faculty of Medicine, Montreal, Quebec, Canada
- Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | - Martin Schalling
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Peter R Schofield
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
- Human Genetics Branch, Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Alessandro Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy
| | - Jordan W Smoller
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, Department of Psychiatry, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Eystein Stordal
- Department of Psychiatry, Hospital Namsos, Namsos, Norway
- Department of Mental Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gustavo Turecki
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Arne E Vaaler
- Department of Psychiatry, Sankt Olavs Hospital Universitetssykehuset i Trondheim, Trondheim, Norway
| | - Eduard Vieta
- Clinical Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Spain
| | - John B Vincent
- Centre for Addiction and Mental Health, Toronto, Onatario, Canada
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Naomi R Wray
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Arianna Di Florio
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, England
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Howard J Edenberg
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sven Cichon
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Roel A Ophoff
- Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
- Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura J Scott
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Ole A Andreassen
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- NORMENT, University of Oslo, Oslo, Norway
| | - John Kelsoe
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
| | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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24
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Cade BE, Chen H, Stilp AM, Louie T, Ancoli-Israel S, Arens R, Barfield R, Below JE, Cai J, Conomos MP, Evans DS, Frazier-Wood AC, Gharib SA, Gleason KJ, Gottlieb DJ, Hillman DR, Johnson WC, Lederer DJ, Lee J, Loredo JS, Mei H, Mukherjee S, Patel SR, Post WS, Purcell SM, Ramos AR, Reid KJ, Rice K, Shah NA, Sofer T, Taylor KD, Thornton TA, Wang H, Yaffe K, Zee PC, Hanis CL, Palmer LJ, Rotter JI, Stone KL, Tranah GJ, Wilson JG, Sunyaev SR, Laurie CC, Zhu X, Saxena R, Lin X, Redline S. Associations of variants In the hexokinase 1 and interleukin 18 receptor regions with oxyhemoglobin saturation during sleep. PLoS Genet 2019; 15:e1007739. [PMID: 30990817 PMCID: PMC6467367 DOI: 10.1371/journal.pgen.1007739] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
Sleep disordered breathing (SDB)-related overnight hypoxemia is associated with cardiometabolic disease and other comorbidities. Understanding the genetic bases for variations in nocturnal hypoxemia may help understand mechanisms influencing oxygenation and SDB-related mortality. We conducted genome-wide association tests across 10 cohorts and 4 populations to identify genetic variants associated with three correlated measures of overnight oxyhemoglobin saturation: average and minimum oxyhemoglobin saturation during sleep and the percent of sleep with oxyhemoglobin saturation under 90%. The discovery sample consisted of 8,326 individuals. Variants with p < 1 × 10(-6) were analyzed in a replication group of 14,410 individuals. We identified 3 significantly associated regions, including 2 regions in multi-ethnic analyses (2q12, 10q22). SNPs in the 2q12 region associated with minimum SpO2 (rs78136548 p = 2.70 × 10(-10)). SNPs at 10q22 were associated with all three traits including average SpO2 (rs72805692 p = 4.58 × 10(-8)). SNPs in both regions were associated in over 20,000 individuals and are supported by prior associations or functional evidence. Four additional significant regions were detected in secondary sex-stratified and combined discovery and replication analyses, including a region overlapping Reelin, a known marker of respiratory complex neurons.These are the first genome-wide significant findings reported for oxyhemoglobin saturation during sleep, a phenotype of high clinical interest. Our replicated associations with HK1 and IL18R1 suggest that variants in inflammatory pathways, such as the biologically-plausible NLRP3 inflammasome, may contribute to nocturnal hypoxemia.
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Affiliation(s)
- Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX United States of America
- Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX United States of America
| | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - Sonia Ancoli-Israel
- Department of Psychiatry, University of California, San Diego, CA, United States of America
| | - Raanan Arens
- The Children’s Hospital at Montefiore, Division of Respiratory and Sleep Medicine, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Richard Barfield
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Jennifer E. Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Jianwen Cai
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States of America
| | - Matthew P. Conomos
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Alexis C. Frazier-Wood
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States of America
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle WA, United States of America
| | - Kevin J. Gleason
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Department of Public Health Sciences, University of Chicago, Chicago, IL, United States of America
| | - Daniel J. Gottlieb
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States of America
- VA Boston Healthcare System, Boston, MA, United States of America
| | - David R. Hillman
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - David J. Lederer
- Departments of Medicine and Epidemiology, Columbia University, New York, NY, United States of America
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Jose S. Loredo
- Division of Pulmonary Critical Care and Sleep Medicine, Department of Medicine, UC San Diego School of Medicine, La Jolla, CA, United States of America
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Sutapa Mukherjee
- Sleep Health Service, Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, South Australia
- Adelaide Institute for Sleep Health, Flinders University, Adelaide, South Australia
| | - Sanjay R. Patel
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Wendy S. Post
- Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Shaun M. Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Alberto R. Ramos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States of America
| | - Kathryn J. Reid
- Department of Neurology, Center for Circadian and Sleep Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - Neomi A. Shah
- Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
| | - Kristine Yaffe
- Department of Psychiatry, Neurology, and Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, United States of America
- San Francisco VA Medical Center, San Francisco, CA, United States of America
| | - Phyllis C. Zee
- Department of Neurology, Center for Circadian and Sleep Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - Craig L. Hanis
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX United States of America
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, South Australia, Australia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Katie L. Stone
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Gregory J. Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson MS, United States of America
| | - Shamil R. Sunyaev
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, United States of America
- Division of Medical Sciences, Harvard Medical School, Boston, MA, United States of America
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA United States of America
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Richa Saxena
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States of America
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, United States of America
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States of America
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25
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Dashti HS, Jones SE, Wood AR, Lane JM, van Hees VT, Wang H, Rhodes JA, Song Y, Patel K, Anderson SG, Beaumont RN, Bechtold DA, Bowden J, Cade BE, Garaulet M, Kyle SD, Little MA, Loudon AS, Luik AI, Scheer FAJL, Spiegelhalder K, Tyrrell J, Gottlieb DJ, Tiemeier H, Ray DW, Purcell SM, Frayling TM, Redline S, Lawlor DA, Rutter MK, Weedon MN, Saxena R. Genome-wide association study identifies genetic loci for self-reported habitual sleep duration supported by accelerometer-derived estimates. Nat Commun 2019; 10:1100. [PMID: 30846698 PMCID: PMC6405943 DOI: 10.1038/s41467-019-08917-4] [Citation(s) in RCA: 297] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Sleep is an essential state of decreased activity and alertness but molecular factors regulating sleep duration remain unknown. Through genome-wide association analysis in 446,118 adults of European ancestry from the UK Biobank, we identify 78 loci for self-reported habitual sleep duration (p < 5 × 10−8; 43 loci at p < 6 × 10−9). Replication is observed for PAX8, VRK2, and FBXL12/UBL5/PIN1 loci in the CHARGE study (n = 47,180; p < 6.3 × 10−4), and 55 signals show sign-concordant effects. The 78 loci further associate with accelerometer-derived sleep duration, daytime inactivity, sleep efficiency and number of sleep bouts in secondary analysis (n = 85,499). Loci are enriched for pathways including striatum and subpallium development, mechanosensory response, dopamine binding, synaptic neurotransmission and plasticity, among others. Genetic correlation indicates shared links with anthropometric, cognitive, metabolic, and psychiatric traits and two-sample Mendelian randomization highlights a bidirectional causal link with schizophrenia. This work provides insights into the genetic basis for inter-individual variation in sleep duration implicating multiple biological pathways. Sleep is essential for homeostasis and insufficient or excessive sleep are associated with adverse outcomes. Here, the authors perform GWAS for self-reported habitual sleep duration in adults, supported by accelerometer-derived measures, and identify genetic correlation with psychiatric and metabolic traits
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Affiliation(s)
- Hassan S Dashti
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.,Broad Institute, Cambridge, 02142, MA, USA
| | - Samuel E Jones
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Jacqueline M Lane
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.,Broad Institute, Cambridge, 02142, MA, USA.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA
| | | | - Heming Wang
- Broad Institute, Cambridge, 02142, MA, USA.,Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, 02115, MA, USA
| | - Jessica A Rhodes
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.,Broad Institute, Cambridge, 02142, MA, USA
| | - Yanwei Song
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.,Northeastern University College of Science, 176 Mugar Life Sciences, 360 Huntington Avenue, Boston, MA, 02015, USA
| | - Krunal Patel
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.,Northeastern University College of Science, 176 Mugar Life Sciences, 360 Huntington Avenue, Boston, MA, 02015, USA
| | - Simon G Anderson
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Robin N Beaumont
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - David A Bechtold
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Jack Bowden
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Brian E Cade
- Broad Institute, Cambridge, 02142, MA, USA.,Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, 02115, MA, USA
| | - Marta Garaulet
- Department of Physiology, University of Murcia, Murcia, 30100, Spain.,IMIB-Arrixaca, Murcia, 30120, Spain
| | - Simon D Kyle
- Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 7LF, UK
| | - Max A Little
- Department of Mathematics, Aston University, Birmingham, B4 7ET, UK.,Media Lab, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
| | - Andrew S Loudon
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Annemarie I Luik
- Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 7LF, UK
| | - Frank A J L Scheer
- Broad Institute, Cambridge, 02142, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, 02115, MA, USA.,Medical Chronobiology Program, Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, 02115, MA, USA
| | - Kai Spiegelhalder
- Clinic for Psychiatry and Psychotherapy, Medical Centre - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Daniel J Gottlieb
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, 02115, MA, USA.,VA Boston Healthcare System, Boston, 02132, MA, USA
| | - Henning Tiemeier
- Deprtment of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, 02115, MA, USA.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, 3015, The Netherlands
| | - David W Ray
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Shaun M Purcell
- Department of Psychiatry, Brigham & Women's Hospital, Harvard Medical School, 02115, Boston, MA, USA
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Susan Redline
- Departments of Medicine, Brigham and Women's Hospital and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, 02115, MA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Martin K Rutter
- Division of Endocrinology, Diabetes & Gastroenterology, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.,Manchester Diabetes Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Michael N Weedon
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Richa Saxena
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA. .,Broad Institute, Cambridge, 02142, MA, USA. .,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, MA, USA.
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26
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Mariani S, Tarokh L, Djonlagic I, Cade BE, Morrical MG, Yaffe K, Stone KL, Loparo KA, Purcell SM, Redline S, Aeschbach D. Evaluation of an automated pipeline for large-scale EEG spectral analysis: the National Sleep Research Resource. Sleep Med 2018; 47:126-136. [PMID: 29803181 PMCID: PMC5976521 DOI: 10.1016/j.sleep.2017.11.1128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022]
Abstract
STUDY OBJECTIVES We present an automated sleep electroencephalogram (EEG) spectral analysis pipeline that includes an automated artifact detection step, and we test the hypothesis that spectral power density estimates computed with this pipeline are comparable to those computed with a commercial method preceded by visual artifact detection by a sleep expert (standard approach). METHODS EEG data were analyzed from the C3-A2 lead in a sample of polysomnograms from 161 older women participants in a community-based cohort study. We calculated the sensitivity, specificity, accuracy, and Cohen's kappa measures from epoch-by-epoch comparisons of automated to visual-based artifact detection results; then we computed the average EEG spectral power densities in six commonly used EEG frequency bands and compared results from the two methods using correlation analysis and Bland-Altman plots. RESULTS Assessment of automated artifact detection showed high specificity [96.8%-99.4% in non-rapid eye movement (NREM), 96.9%-99.1% in rapid eye movement (REM) sleep] but low sensitivity (26.7%-38.1% in NREM, 9.1-27.4% in REM sleep). However, large artifacts (total power > 99th percentile) were removed with sensitivity up to 87.7% in NREM and 90.9% in REM, with specificities of 96.9% and 96.6%, respectively. Mean power densities computed with the two approaches for all EEG frequency bands showed very high correlation (≥0.99). The automated pipeline allowed for a 100-fold reduction in analysis time with regard to the standard approach. CONCLUSION Despite low sensitivity for artifact rejection, the automated pipeline generated results comparable to those obtained with a standard method that included manual artifact detection. Automated pipelines can enable practical analyses of recordings from thousands of individuals, allowing for use in genetics and epidemiological research requiring large samples.
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Affiliation(s)
- Sara Mariani
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA.
| | - Leila Tarokh
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland; Chronobiology and Sleep Research, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Ina Djonlagic
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA; Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael G Morrical
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Kristine Yaffe
- University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Katie L Stone
- Research Institute, California Pacific Medical Center, Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | - Shaun M Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA; Case Western Reserve University, Cleveland, OH, USA
| | - Daniel Aeschbach
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA; Division of Sleep and Human Factors Research, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
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27
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Fernández E, Collins MO, Frank RAW, Zhu F, Kopanitsa MV, Nithianantharajah J, Lemprière SA, Fricker D, Elsegood KA, McLaughlin CL, Croning MDR, Mclean C, Armstrong JD, Hill WD, Deary IJ, Cencelli G, Bagni C, Fromer M, Purcell SM, Pocklington AJ, Choudhary JS, Komiyama NH, Grant SGN. Arc Requires PSD95 for Assembly into Postsynaptic Complexes Involved with Neural Dysfunction and Intelligence. Cell Rep 2018; 21:679-691. [PMID: 29045836 PMCID: PMC5656750 DOI: 10.1016/j.celrep.2017.09.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 08/03/2017] [Accepted: 09/13/2017] [Indexed: 12/12/2022] Open
Abstract
Arc is an activity-regulated neuronal protein, but little is known about its interactions, assembly into multiprotein complexes, and role in human disease and cognition. We applied an integrated proteomic and genetic strategy by targeting a tandem affinity purification (TAP) tag and Venus fluorescent protein into the endogenous Arc gene in mice. This allowed biochemical and proteomic characterization of native complexes in wild-type and knockout mice. We identified many Arc-interacting proteins, of which PSD95 was the most abundant. PSD95 was essential for Arc assembly into 1.5-MDa complexes and activity-dependent recruitment to excitatory synapses. Integrating human genetic data with proteomic data showed that Arc-PSD95 complexes are enriched in schizophrenia, intellectual disability, autism, and epilepsy mutations and normal variants in intelligence. We propose that Arc-PSD95 postsynaptic complexes potentially affect human cognitive function. TAP tag and purification of endogenous Arc protein complexes from the mouse brain PSD95 is the major Arc binding protein, and both assemble into 1.5-MDa supercomplexes PSD95 is essential for recruitment of Arc to synapses Mutations and genetic variants in Arc-PSD95 are linked to cognition
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Affiliation(s)
- Esperanza Fernández
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; KU Leuven, Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), and VIB Center for the Biology of Disease, Leuven, Belgium
| | - Mark O Collins
- Proteomic Mass Spectrometry, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - René A W Frank
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fei Zhu
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK
| | - Maksym V Kopanitsa
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Synome Ltd., Moneta Building, Babraham Research Campus, Cambridge, UK
| | - Jess Nithianantharajah
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK
| | - Sarah A Lemprière
- Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK
| | - David Fricker
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Synome Ltd., Moneta Building, Babraham Research Campus, Cambridge, UK
| | - Kathryn A Elsegood
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK
| | - Catherine L McLaughlin
- Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK
| | - Mike D R Croning
- Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK
| | - Colin Mclean
- School of Informatics, Institute for Adaptive and Neural Computation, University of Edinburgh, UK
| | - J Douglas Armstrong
- School of Informatics, Institute for Adaptive and Neural Computation, University of Edinburgh, UK
| | - W David Hill
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, UK
| | - Giulia Cencelli
- KU Leuven, Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), and VIB Center for the Biology of Disease, Leuven, Belgium; Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Bagni
- KU Leuven, Center for Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), and VIB Center for the Biology of Disease, Leuven, Belgium; Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Menachem Fromer
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew J Pocklington
- Institute of Psychological Medicine & Clinical Neurosciences, University of Cardiff, Cardiff, Wales, UK
| | - Jyoti S Choudhary
- Proteomic Mass Spectrometry, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Noboru H Komiyama
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK
| | - Seth G N Grant
- Genes to Cognition Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK; Genes to Cognition Programme, Centre for Clinical Brain Science, University of Edinburgh, Edinburgh, UK.
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28
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Özbek U, Lin HM, Lin Y, Weeks DE, Chen W, Shaffer JR, Purcell SM, Feingold E. Statistics for X-chromosome associations. Genet Epidemiol 2018; 42:539-550. [PMID: 29900581 DOI: 10.1002/gepi.22132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 03/14/2018] [Accepted: 04/30/2018] [Indexed: 01/26/2023]
Abstract
In a genome-wide association study (GWAS), association between genotype and phenotype at autosomal loci is generally tested by regression models. However, X-chromosome data are often excluded from published analyses of autosomes because of the difference between males and females in number of X chromosomes. Failure to analyze X-chromosome data at all is obviously less than ideal, and can lead to missed discoveries. Even when X-chromosome data are included, they are often analyzed with suboptimal statistics. Several mathematically sensible statistics for X-chromosome association have been proposed. The optimality of these statistics, however, is based on very specific simple genetic models. In addition, while previous simulation studies of these statistics have been informative, they have focused on single-marker tests and have not considered the types of error that occur even under the null hypothesis when the entire X chromosome is scanned. In this study, we comprehensively tested several X-chromosome association statistics using simulation studies that include the entire chromosome. We also considered a wide range of trait models for sex differences and phenotypic effects of X inactivation. We found that models that do not incorporate a sex effect can have large type I error in some cases. We also found that many of the best statistics perform well even when there are modest deviations, such as trait variance differences between the sexes or small sex differences in allele frequencies, from assumptions.
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Affiliation(s)
- Umut Özbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hui-Min Lin
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yan Lin
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Daniel E Weeks
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Wei Chen
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania
| | - John R Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eleanor Feingold
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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29
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Ni G, Moser G, Wray NR, Lee SH, Ripke S, Neale BM, Corvin A, Walters JT, Farh KH, Holmans PA, Lee P, Bulik-Sullivan B, Collier DA, Huang H, Pers TH, Agartz I, Agerbo E, Albus M, Alexander M, Amin F, Bacanu SA, Begemann M, Belliveau RA, Bene J, Bergen SE, Bevilacqua E, Bigdeli TB, Black DW, Bruggeman R, Buccola NG, Buckner RL, Byerley W, Cahn W, Cai G, Campion D, Cantor RM, Carr VJ, Carrera N, Catts SV, Chambert KD, Chan RC, Chen RY, Chen EY, Cheng W, Cheung EF, Chong SA, Cloninger CR, Cohen D, Cohen N, Cormican P, Craddock N, Crowley JJ, Curtis D, Davidson M, Davis KL, Degenhardt F, Del Favero J, Demontis D, Dikeos D, Dinan T, Djurovic S, Donohoe G, Drapeau E, Duan J, Dudbridge F, Durmishi N, Eichhammer P, Eriksson J, Escott-Price V, Essioux L, Fanous AH, Farrell MS, Frank J, Franke L, Freedman R, Freimer NB, Friedl M, Friedman JI, Fromer M, Genovese G, Georgieva L, Giegling I, Giusti-Rodríguez P, Godard S, Goldstein JI, Golimbet V, Gopal S, Gratten J, de Haan L, Hammer C, Hamshere ML, Hansen M, Hansen T, Haroutunian V, Hartmann AM, Henskens FA, Herms S, Hirschhorn JN, Hoffmann P, Hofman A, Hollegaard MV, Hougaard DM, Ikeda M, Joa I, Juliá A, Kahn RS, Kalaydjieva L, Karachanak-Yankova S, Karjalainen J, Kavanagh D, Keller MC, Kennedy JL, Khrunin A, Kim Y, Klovins J, Knowles JA, Konte B, Kucinskas V, Kucinskiene ZA, Kuzelova-Ptackova H, Kähler AK, Laurent C, Keong JLC, Legge SE, Lerer B, Li M, Li T, Liang KY, Lieberman J, Limborska S, Loughland CM, Lubinski J, Lönnqvist J, Macek M, Magnusson PK, Maher BS, Maier W, Mallet J, Marsal S, Mattheisen M, Mattingsda M, McCarley RW, McDonald C, McIntosh AM, Meier S, Meijer CJ, Melegh B, Melle I, Mesholam-Gately RI, Metspalu A, Michie PT, Milani L, Milanova V, Mokrab Y, Morris DW, Mors O, Murphy KC, Murray RM, Myin-Germeys I, Müller-Myhsok B, Nelis M, Nenadic I, Nertney DA, Nestadt G, Nicodemus KK, Nikitina-Zake L, Nisenbaum L, Nordin A, O’Callaghan E, O’Dushlaine C, O’Neill FA, Oh SY, Olinc A, Olsen L, Van Os J, Pantelis C, Papadimitriou GN, Papio S, Parkhomenko E, Pato MT, Paunio T, Pejovic-Milovancevic M, Perkins DO, Pietiläinenl O, Pimm J, Pocklington AJ, Powell J, Price A, Pulver AE, Purcell SM, Quested D, Rasmussen HB, Reichenberg A, Reimers MA, Richards AL, Roffman JL, Roussos P, Ruderfer DM, Salomaa V, Sanders AR, Schall U, Schubert CR, Schulze TG, Schwab SG, Scolnick EM, Scott RJ, Seidman LJ, Shi J, Sigurdsson E, Silagadze T, Silverman JM, Sim K, Slominsky P, Smoller JW, So HC, Spencer CC, Stah EA, Stefansson H, Steinberg S, Stogmann E, Straub RE, Strengman E, Strohmaier J, Stroup TS, Subramaniam M, Suvisaari J, Svrakic DM, Szatkiewicz JP, Söderman E, Thirumalai S, Toncheva D, Tosato S, Veijola J, Waddington J, Walsh D, Wang D, Wang Q, Webb BT, Weiser M, Wildenauer DB, Williams NM, Williams S, Witt SH, Wolen AR, Wong EH, Wormley BK, Xi HS, Zai CC, Zheng X, Zimprich F, Stefansson K, Visscher PM, Adolfsson R, Andreassen OA, Blackwood DH, Bramon E, Buxbaum JD, Børglum AD, Cichon S, Darvasi A, Domenici E, Ehrenreich H, Esko T, Gejman PV, Gill M, Gurling H, Hultman CM, Iwata N, Jablensky AV, Jönsson EG, Kendler KS, Kirov G, Knight J, Lencz T, Levinson DF, Li QS, Liu J, Malhotra AK, McCarrol SA, McQuillin A, Moran JL, Mortensen PB, Mowry BJ, Nöthen MM, Ophoff RA, Owen MJ, Palotie A, Pato CN, Petryshen TL, Posthuma D, Rietsche M, Riley BP, Rujescu D, Sham PC, Sklar P, St Clair D, Weinberger DR, Wendland JR, Werge T, Daly MJ, Sullivan PF, O’Donovan MC. Estimation of Genetic Correlation via Linkage Disequilibrium Score Regression and Genomic Restricted Maximum Likelihood. Am J Hum Genet 2018; 102:1185-1194. [PMID: 29754766 PMCID: PMC5993419 DOI: 10.1016/j.ajhg.2018.03.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/20/2018] [Indexed: 10/16/2022] Open
Abstract
Genetic correlation is a key population parameter that describes the shared genetic architecture of complex traits and diseases. It can be estimated by current state-of-art methods, i.e., linkage disequilibrium score regression (LDSC) and genomic restricted maximum likelihood (GREML). The massively reduced computing burden of LDSC compared to GREML makes it an attractive tool, although the accuracy (i.e., magnitude of standard errors) of LDSC estimates has not been thoroughly studied. In simulation, we show that the accuracy of GREML is generally higher than that of LDSC. When there is genetic heterogeneity between the actual sample and reference data from which LD scores are estimated, the accuracy of LDSC decreases further. In real data analyses estimating the genetic correlation between schizophrenia (SCZ) and body mass index, we show that GREML estimates based on ∼150,000 individuals give a higher accuracy than LDSC estimates based on ∼400,000 individuals (from combined meta-data). A GREML genomic partitioning analysis reveals that the genetic correlation between SCZ and height is significantly negative for regulatory regions, which whole genome or LDSC approach has less power to detect. We conclude that LDSC estimates should be carefully interpreted as there can be uncertainty about homogeneity among combined meta-datasets. We suggest that any interesting findings from massive LDSC analysis for a large number of complex traits should be followed up, where possible, with more detailed analyses with GREML methods, even if sample sizes are lesser.
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30
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Blokland GAM, del Re EC, Mesholam-Gately RI, Jovicich J, Trampush JW, Keshavan MS, DeLisi LE, Walters JTR, Turner JA, Malhotra AK, Lencz T, Shenton ME, Voineskos AN, Rujescu D, Giegling I, Kahn RS, Roffman JL, Holt DJ, Ehrlich S, Kikinis Z, Dazzan P, Murray RM, Di Forti M, Lee J, Sim K, Lam M, Wolthusen RPF, de Zwarte SMC, Walton E, Cosgrove D, Kelly S, Maleki N, Osiecki L, Picchioni MM, Bramon E, Russo M, David AS, Mondelli V, Reinders AATS, Falcone MA, Hartmann AM, Konte B, Morris DW, Gill M, Corvin AP, Cahn W, Ho NF, Liu JJ, Keefe RSE, Gollub RL, Manoach DS, Calhoun VD, Schulz SC, Sponheim SR, Goff DC, Buka SL, Cherkerzian S, Thermenos HW, Kubicki M, Nestor PG, Dickie EW, Vassos E, Ciufolini S, Marques TR, Crossley NA, Purcell SM, Smoller JW, van Haren NEM, Toulopoulou T, Donohoe G, Goldstein JM, Seidman LJ, McCarley RW, Petryshen TL. The Genetics of Endophenotypes of Neurofunction to Understand Schizophrenia (GENUS) consortium: A collaborative cognitive and neuroimaging genetics project. Schizophr Res 2018; 195:306-317. [PMID: 28982554 PMCID: PMC5882601 DOI: 10.1016/j.schres.2017.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Schizophrenia has a large genetic component, and the pathways from genes to illness manifestation are beginning to be identified. The Genetics of Endophenotypes of Neurofunction to Understand Schizophrenia (GENUS) Consortium aims to clarify the role of genetic variation in brain abnormalities underlying schizophrenia. This article describes the GENUS Consortium sample collection. METHODS We identified existing samples collected for schizophrenia studies consisting of patients, controls, and/or individuals at familial high-risk (FHR) for schizophrenia. Samples had single nucleotide polymorphism (SNP) array data or genomic DNA, clinical and demographic data, and neuropsychological and/or brain magnetic resonance imaging (MRI) data. Data were subjected to quality control procedures at a central site. RESULTS Sixteen research groups contributed data from 5199 psychosis patients, 4877 controls, and 725 FHR individuals. All participants have relevant demographic data and all patients have relevant clinical data. The sex ratio is 56.5% male and 43.5% female. Significant differences exist between diagnostic groups for premorbid and current IQ (both p<1×10-10). Data from a diversity of neuropsychological tests are available for 92% of participants, and 30% have structural MRI scans (half also have diffusion-weighted MRI scans). SNP data are available for 76% of participants. The ancestry composition is 70% European, 20% East Asian, 7% African, and 3% other. CONCLUSIONS The Consortium is investigating the genetic contribution to brain phenotypes in a schizophrenia sample collection of >10,000 participants. The breadth of data across clinical, genetic, neuropsychological, and MRI modalities provides an important opportunity for elucidating the genetic basis of neural processes underlying schizophrenia.
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Affiliation(s)
- Gabriëlla A. M. Blokland
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic
Medicine, Massachusetts General Hospital, Boston, MA, United States,Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Stanley Center for Psychiatric Research, Broad Institute of MIT and
Harvard, Cambridge, MA, United States
| | - Elisabetta C. del Re
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Department of Psychiatry, Veterans Affairs Boston Healthcare System,
Brockton, MA, United States,Psychiatry Neuroimaging Laboratory, Department of Psychiatry,
Brigham and Women’s Hospital, Boston, MA, United States
| | - Raquelle I. Mesholam-Gately
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Massachusetts Mental Health Center Public Psychiatry Division, Beth
Israel Deaconess Medical Center, Boston, MA, United States
| | - Jorge Jovicich
- Center for Mind/Brain Sciences (CiMEC), University of Trento,
Trento, Italy
| | - Joey W. Trampush
- Center for Psychiatric Neuroscience, The Feinstein Institute for
Medical Research, Division of Northwell Health, Manhasset, NY, United States;
Division of Psychiatry Research, The Zucker Hillside Hospital, Division of Northwell
Health, Glen Oaks, NY, United States; Hofstra Northwell School of Medicine,
Departments of Psychiatry and Molecular Medicine, Hempstead, NY, United States,BrainWorkup, LLC, Los Angeles, CA, United States
| | - Matcheri S. Keshavan
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Massachusetts Mental Health Center Public Psychiatry Division, Beth
Israel Deaconess Medical Center, Boston, MA, United States,University of Pittsburgh Medical Center, Pittsburgh, PA, United
States
| | - Lynn E. DeLisi
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Department of Psychiatry, Veterans Affairs Boston Healthcare System,
Brockton, MA, United States
| | - James T. R. Walters
- Department of Psychological Medicine, Cardiff University, Cardiff,
United Kingdom
| | - Jessica A. Turner
- The Mind Research Network, Albuquerque, NM, United States,Department of Psychology and Neuroscience Institute, Georgia State
University, GA, United States
| | - Anil K. Malhotra
- Center for Psychiatric Neuroscience, The Feinstein Institute for
Medical Research, Division of Northwell Health, Manhasset, NY, United States;
Division of Psychiatry Research, The Zucker Hillside Hospital, Division of Northwell
Health, Glen Oaks, NY, United States; Hofstra Northwell School of Medicine,
Departments of Psychiatry and Molecular Medicine, Hempstead, NY, United States
| | - Todd Lencz
- Center for Psychiatric Neuroscience, The Feinstein Institute for
Medical Research, Division of Northwell Health, Manhasset, NY, United States;
Division of Psychiatry Research, The Zucker Hillside Hospital, Division of Northwell
Health, Glen Oaks, NY, United States; Hofstra Northwell School of Medicine,
Departments of Psychiatry and Molecular Medicine, Hempstead, NY, United States
| | - Martha E. Shenton
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Department of Psychiatry, Veterans Affairs Boston Healthcare System,
Brockton, MA, United States,Psychiatry Neuroimaging Laboratory, Department of Psychiatry,
Brigham and Women’s Hospital, Boston, MA, United States,Department of Radiology, Brigham and Women’s Hospital,
Harvard Medical School, Boston, MA, United States
| | - Aristotle N. Voineskos
- Kimel Family Translational Imaging Genetics Laboratory, Research
Imaging Centre, Campbell Family Mental Health Institute, Centre for Addiction and
Mental Health, Department of Psychiatry, Faculty of Medicine, University of Toronto,
Toronto, ON, Canada,Department of Psychiatry and Institute of Medical Science,
University of Toronto, Toronto, ON, Canada
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics,
University of Halle-Wittenberg, Halle an der Saale, Germany,Department of Psychiatry, Ludwig Maximilians University, Munich,
Germany
| | - Ina Giegling
- Department of Psychiatry, Psychotherapy and Psychosomatics,
University of Halle-Wittenberg, Halle an der Saale, Germany
| | - René S. Kahn
- Brain Centre Rudolf Magnus, Department of Psychiatry, University
Medical Centre Utrecht, Utrecht, The Netherlands
| | - Joshua L. Roffman
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States
| | - Daphne J. Holt
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States
| | - Stefan Ehrlich
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States,Division of Psychological & Social Medicine and Developmental
Neurosciences, Faculty of Medicine, Technische Universität Dresden, Dresden,
Germany
| | - Zora Kikinis
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Psychiatry Neuroimaging Laboratory, Department of Psychiatry,
Brigham and Women’s Hospital, Boston, MA, United States
| | - Paola Dazzan
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Robin M. Murray
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Marta Di Forti
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Jimmy Lee
- Institute of Mental Health, Woodbridge Hospital, Singapore
| | - Kang Sim
- Institute of Mental Health, Woodbridge Hospital, Singapore
| | - Max Lam
- Institute of Mental Health, Woodbridge Hospital, Singapore
| | - Rick P. F. Wolthusen
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States,Division of Psychological & Social Medicine and Developmental
Neurosciences, Faculty of Medicine, Technische Universität Dresden, Dresden,
Germany
| | - Sonja M. C. de Zwarte
- Brain Centre Rudolf Magnus, Department of Psychiatry, University
Medical Centre Utrecht, Utrecht, The Netherlands
| | - Esther Walton
- Division of Psychological & Social Medicine and Developmental
Neurosciences, Faculty of Medicine, Technische Universität Dresden, Dresden,
Germany
| | - Donna Cosgrove
- The Cognitive Genetics and Cognitive Therapy Group, Department of
Psychology, National University of Ireland, Galway, Ireland
| | - Sinead Kelly
- Neuropsychiatric Genetics Research Group, Department of Psychiatry,
Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; Trinity
College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland,Laboratory of NeuroImaging, Keck School of Medicine, University of
Southern California, Los Angeles, CA, United States
| | - Nasim Maleki
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic
Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Marco M. Picchioni
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Elvira Bramon
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom,Mental Health Neuroscience Research Department, UCL Division of
Psychiatry, University College London, United Kingdom
| | - Manuela Russo
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Anthony S. David
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Valeria Mondelli
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Antje A. T. S. Reinders
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - M. Aurora Falcone
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Annette M. Hartmann
- Department of Psychiatry, Psychotherapy and Psychosomatics,
University of Halle-Wittenberg, Halle an der Saale, Germany
| | - Bettina Konte
- Department of Psychiatry, Psychotherapy and Psychosomatics,
University of Halle-Wittenberg, Halle an der Saale, Germany
| | - Derek W. Morris
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging and
Cognitive Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of
Psychology and Discipline of Biochemistry, National University of Ireland, Galway,
Ireland
| | - Michael Gill
- Neuropsychiatric Genetics Research Group, Department of Psychiatry,
Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; Trinity
College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Aiden P. Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry,
Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; Trinity
College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Wiepke Cahn
- Brain Centre Rudolf Magnus, Department of Psychiatry, University
Medical Centre Utrecht, Utrecht, The Netherlands
| | - New Fei Ho
- Institute of Mental Health, Woodbridge Hospital, Singapore
| | | | - Richard S. E. Keefe
- Department of Psychiatry and Behavioral Sciences, Duke University
Medical Center, Durham, NC, United States
| | - Randy L. Gollub
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States
| | - Dara S. Manoach
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States
| | - Vince D. Calhoun
- The Mind Research Network, Albuquerque, NM, United States,Department of Electrical and Computer Engineering, University of
New Mexico, Albuquerque, NM, United States
| | - S. Charles Schulz
- Department of Psychiatry, University of Minnesota, Minneapolis, MN,
United States
| | - Scott R. Sponheim
- Department of Psychiatry, University of Minnesota, Minneapolis, MN,
United States
| | - Donald C. Goff
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Nathan S. Kline Institute for Psychiatric Research, Department of
Psychiatry, New York University Langone Medical Center, New York, NY, United
States
| | - Stephen L. Buka
- Department of Epidemiology, Brown University, Providence, RI,
United States
| | - Sara Cherkerzian
- Department of Medicine, Division of Women’s Health, Brigham
and Women’s Hospital, Harvard Medical School, Boston, MA, United
States
| | - Heidi W. Thermenos
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Massachusetts Mental Health Center Public Psychiatry Division, Beth
Israel Deaconess Medical Center, Boston, MA, United States
| | - Marek Kubicki
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Psychiatry Neuroimaging Laboratory, Department of Psychiatry,
Brigham and Women’s Hospital, Boston, MA, United States,Department of Radiology, Brigham and Women’s Hospital,
Harvard Medical School, Boston, MA, United States,MGH/HST Athinoula A. Martinos Center for Biomedical Imaging,
Massachusetts General Hospital, Charlestown, MA, United States
| | - Paul G. Nestor
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Department of Psychiatry, Veterans Affairs Boston Healthcare System,
Brockton, MA, United States,Laboratory of Applied Neuropsychology, University of Massachusetts,
Boston, MA, United States
| | - Erin W. Dickie
- Kimel Family Translational Imaging Genetics Laboratory, Research
Imaging Centre, Campbell Family Mental Health Institute, Centre for Addiction and
Mental Health, Department of Psychiatry, Faculty of Medicine, University of Toronto,
Toronto, ON, Canada
| | - Evangelos Vassos
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Simone Ciufolini
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Tiago Reis Marques
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Nicolas A. Crossley
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,National Institute for Health Research (NIHR) Mental Health
Biomedical Research Centre at South London and Maudsley NHS Foundation Trust,
London, United Kingdom
| | - Shaun M. Purcell
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Stanley Center for Psychiatric Research, Broad Institute of MIT and
Harvard, Cambridge, MA, United States,Department of Psychiatry, Brigham and Women’s Hospital,
Boston, MA, United States,Division of Psychiatric Genomics, Departments of Psychiatry and
Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York,
NY, United States
| | - Jordan W. Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic
Medicine, Massachusetts General Hospital, Boston, MA, United States,Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Stanley Center for Psychiatric Research, Broad Institute of MIT and
Harvard, Cambridge, MA, United States
| | - Neeltje E. M. van Haren
- Brain Centre Rudolf Magnus, Department of Psychiatry, University
Medical Centre Utrecht, Utrecht, The Netherlands
| | - Timothea Toulopoulou
- Institute of Psychiatry, Psychology, and Neuroscience,
King’s College London, London, United Kingdom,Department of Psychology, Bilkent University, Bilkent, Ankara,
Turkey,Department of Psychology, The University of Hong Kong, Pokfulam,
Hong Kong, SAR, China
| | - Gary Donohoe
- Neuropsychiatric Genetics Research Group, Department of Psychiatry,
Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland; Trinity
College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland,Cognitive Genetics and Cognitive Therapy Group, Neuroimaging and
Cognitive Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of
Psychology and Discipline of Biochemistry, National University of Ireland, Galway,
Ireland
| | - Jill M. Goldstein
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Department of Medicine, Division of Women’s Health, Brigham
and Women’s Hospital, Harvard Medical School, Boston, MA, United
States,Department of Psychiatry, Brigham and Women’s Hospital,
Boston, MA, United States
| | - Larry J. Seidman
- Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Massachusetts Mental Health Center Public Psychiatry Division, Beth
Israel Deaconess Medical Center, Boston, MA, United States
| | - Robert W. McCarley
- Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Department of Psychiatry, Veterans Affairs Boston Healthcare System,
Brockton, MA, United States
| | - Tracey L. Petryshen
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic
Medicine, Massachusetts General Hospital, Boston, MA, United States,Department of Psychiatry, Massachusetts General Hospital, Boston,
MA, United States,Department of Psychiatry, Harvard Medical School, Boston, MA, United
States,Stanley Center for Psychiatric Research, Broad Institute of MIT and
Harvard, Cambridge, MA, United States
| |
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31
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Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF. Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nat Genet 2018; 50:668-681. [PMID: 29700475 PMCID: PMC5934326 DOI: 10.1038/s41588-018-0090-3] [Citation(s) in RCA: 1625] [Impact Index Per Article: 270.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/14/2018] [Indexed: 12/12/2022]
Abstract
Major depressive disorder (MDD) is a common illness accompanied by considerable morbidity, mortality, costs, and heightened risk of suicide. We conducted a genome-wide association meta-analysis based in 135,458 cases and 344,901 controls and identified 44 independent and significant loci. The genetic findings were associated with clinical features of major depression and implicated brain regions exhibiting anatomical differences in cases. Targets of antidepressant medications and genes involved in gene splicing were enriched for smaller association signal. We found important relationships of genetic risk for major depression with educational attainment, body mass, and schizophrenia: lower educational attainment and higher body mass were putatively causal, whereas major depression and schizophrenia reflected a partly shared biological etiology. All humans carry lesser or greater numbers of genetic risk factors for major depression. These findings help refine the basis of major depression and imply that a continuous measure of risk underlies the clinical phenotype.
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Affiliation(s)
- Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
| | - Stephan Ripke
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany
| | - Manuel Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Maciej Trzaskowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Enda M Byrne
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Abdel Abdellaoui
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Esben Agerbo
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Tracy M Air
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Till M F Andlauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Silviu-Alin Bacanu
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Marie Bækvad-Hansen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Aartjan F T Beekman
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Tim B Bigdeli
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Virginia Institute for Psychiatric and Behavior Genetics, Richmond, VA, USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henriette N Buttenschøn
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Na Cai
- Statistical Genomics and Systems Genetics, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Enrique Castelao
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Jane Hvarregaard Christensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Toni-Kim Clarke
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Jonathan I R Coleman
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Lucía Colodro-Conde
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Baptiste Couvy-Duchesne
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Nick Craddock
- Psychological Medicine, Cardiff University, Cardiff, UK
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Cheynna A Crowley
- Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hassan S Dashti
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
| | - Eske M Derks
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Nese Direk
- Psychiatry, Dokuz Eylul University School of Medicine, Izmir, Turkey
- Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Conor V Dolan
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erin C Dunn
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Thalia C Eley
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | | | | | | | - Hilary K Finucane
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
- Department of Psychiatry (UPK), University of Basel, Basel, Switzerland
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Héléna A Gaspar
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Michael Gill
- Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | | | - Fernando S Goes
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Scott D Gordon
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Lynsey S Hall
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | | | - Christine Søholm Hansen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas F Hansen
- Danish Headache Centre, Department of Neurology, Rigshospitalet, Glostrup, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Psychiatric Research, Copenhagen, Denmark
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ian B Hickie
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine and Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Carsten Horn
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Jouke-Jan Hottenga
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - David M Hougaard
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ming Hu
- Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Craig L Hyde
- Statistics, Pfizer Global Research and Development, Groton, CT, USA
| | - Marcus Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Rick Jansen
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Fulai Jin
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - James A Knowles
- Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, USA
| | - Isaac S Kohane
- Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Julia Kraft
- Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany
| | | | - Jesper Krogh
- Department of Endocrinology at Herlev University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine (IUMSP), University Hospital of Lausanne, Lausanne, Switzerland
| | - Jacqueline M Lane
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yihan Li
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yun Li
- Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Penelope A Lind
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Leina Lu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Donald J MacIntyre
- Mental Health, NHS 24, Glasgow, UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Dean F MacKinnon
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Robert M Maier
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Wolfgang Maier
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | | | - Hamdi Mbarek
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Patrick McGrath
- Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Peter McGuffin
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Sarah E Medland
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Divya Mehta
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- School of Psychology and Counseling, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Christel M Middeldorp
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Child and Youth Mental Health Service, Children's Health Queensland Hospital and Health Service, South Brisbane, Queensland, Australia
- Child Health Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | | | - Yuri Milaneschi
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Francis M Mondimore
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Sara Mostafavi
- Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Niamh Mullins
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, University Medicine, University Medicine Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Bernard Ng
- Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michel G Nivard
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dale R Nyholt
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Paul F O'Reilly
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | | | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Jodie N Painter
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Carsten Bøcker Pedersen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Marianne Giørtz Pedersen
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Roseann E Peterson
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Erik Pettersson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Wouter J Peyrot
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Giorgio Pistis
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Danielle Posthuma
- Complex Trait Genetics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Clinical Genetics, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Per Qvist
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - John P Rice
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Brien P Riley
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Margarita Rivera
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- Department of Biochemistry and Molecular Biology II, Institute of Neurosciences, Center for Biomedical Research, University of Granada, Granada, Spain
| | | | - Richa Saxena
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert Schoevers
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eva C Schulte
- Department of Psychiatry and Psychotherapy, Medical Center of the University of Munich, Campus Innenstadt, Munich, Germany
- Institute of Psychiatric Phenomics and Genomics (IPPG), Medical Center of the University of Munich, Campus Innenstadt, Munich, Germany
| | - Ling Shen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stanley I Shyn
- Behavioral Health Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Engilbert Sigurdsson
- Faculty of Medicine, Department of Psychiatry, University of Iceland, Reykjavik, Iceland
| | - Grant B C Sinnamon
- School of Medicine and Dentistry, James Cook University, Townsville, Queensland, Australia
| | - Johannes H Smit
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Daniel J Smith
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | | | | | - Craig A Stockmeier
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Katherine E Tansey
- College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Henning Teismann
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Wesley Thompson
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- KG Jebsen Centre for Psychosis Research, Norway Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Pippa A Thomson
- Medical Genetics Section, CGEM, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Chao Tian
- Research, 23andMe, Inc., Mountain View, CA, USA
| | - Matthew Traylor
- Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vassily Trubetskoy
- Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany
| | | | - Daniel Umbricht
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery and Translational Medicine Area, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd, Basel, Switzerland
| | - Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Albert M van Hemert
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander Viktorin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Yunpeng Wang
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- KG Jebsen Centre for Psychosis Research, Norway Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bradley T Webb
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Shantel Marie Weinsheimer
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
| | - Jürgen Wellmann
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Gonneke Willemsen
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Yang Wu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Hualin S Xi
- Computational Sciences Center of Emphasis, Pfizer Global Research and Development, Cambridge, MA, USA
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Volker Arolt
- Department of Psychiatry, University of Münster, Munster, Germany
| | - Bernhard T Baune
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Dorret I Boomsma
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Udo Dannlowski
- Department of Psychiatry, University of Münster, Munster, Germany
| | - E C J de Geus
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Institute, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - J Raymond DePaulo
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Enrico Domenici
- Centre for Integrative Biology, Università degli Studi di Trento, Trento, Italy
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tõnu Esko
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Steven P Hamilton
- Psychiatry, Kaiser Permanente Northern California, San Francisco, CA, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew C Heath
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | | | - Kenneth S Kendler
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Stefan Kloiber
- Max Planck Institute of Psychiatry, Munich, Germany
- Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Glyn Lewis
- Division of Psychiatry, University College London, London, UK
| | - Qingqin S Li
- Neuroscience Therapeutic Area, Janssen Research and Development, LLC, Titusville, NJ, USA
| | | | - Pamela F A Madden
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas G Martin
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Ole Mors
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - Preben Bo Mortensen
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Merete Nordentoft
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Sara A Paciga
- Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Groton, CT, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Brenda W J H Penninx
- Department of Psychiatry, Vrije Universiteit Medical Center and GGZ inGeest, Amsterdam, The Netherlands
| | - Roy H Perlis
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatry, Harvard Medical School, Boston, MA, USA
| | - David J Porteous
- Medical Genetics Section, CGEM, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Martin Preisig
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas G Schulze
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
- Institute of Psychiatric Phenomics and Genomics (IPPG), Medical Center of the University of Munich, Campus Innenstadt, Munich, Germany
- Human Genetics Branch, NIMH Division of Intramural Research Programs, Bethesda, MD, USA
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Jordan W Smoller
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Henning Tiemeier
- Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Child and Adolescent Psychiatry, Erasmus MC, Rotterdam, The Netherlands
- Psychiatry, Erasmus MC, Rotterdam, The Netherlands
| | - Rudolf Uher
- Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Myrna M Weissman
- Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY, USA
- Division of Epidemiology, New York State Psychiatric Institute, New York, NY, USA
| | - Thomas Werge
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ashley R Winslow
- Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Cambridge, MA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cathryn M Lewis
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Douglas F Levinson
- Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Gerome Breen
- MRC Social Genetic and Developmental Psychiatry Centre, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- iPSYCH, Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Stone KL, Peters KE, Redline S, Yaffe K, Purcell SM, Mariani S, Djonlagic I, Younes M. 1013 Novel Quantitative EEG Exposures and Risk of Incident MCI and Dementia in Older Women. Sleep 2018. [DOI: 10.1093/sleep/zsy061.1012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- K L Stone
- California Pacific Medical Center Research Institute, San Francisco, CA
| | - K E Peters
- California Pacific Medical Center Research Institute, San Francisco, CA
| | - S Redline
- Brigham and Women’s Hospital, Boston, MA
| | - K Yaffe
- University of California, San Francisco, San Francisco, CA
| | | | - S Mariani
- Brigham and Women’s Hospital, Boston, MA
| | | | - M Younes
- University of Manitoba, Winnipeg, MB, CANADA
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Smoll EJ, Tesa-Serrate MA, Purcell SM, D'Andrea L, Bruce DW, Slattery JM, Costen ML, Minton TK, McKendrick KG. Determining the composition of the vacuum-liquid interface in ionic-liquid mixtures. Faraday Discuss 2018; 206:497-522. [PMID: 28944811 DOI: 10.1039/c7fd00175d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vacuum-liquid interfaces of a number of ionic-liquid mixtures have been investigated using the combination of reactive-atom scattering with laser-induced fluorescence detection (RAS-LIF), selected surface tension measurements, and molecular dynamics (MD) simulations. The mixtures are based on the widespread 1-alkyl-3-methylimidazolium ([Cnmim]+) cation, including mixed cations which differ in chain length or chemical functionality with a common anion; and different anions for a common cation. RAS-LIF results imply that the surface compositions exhibit a general form of non-stoichiometric behaviour that mimics the well-known Henry's and Raoult's laws at low and high mole fraction, respectively. The extended Langmuir model provides a moderately good single-parameter fit, but higher-order terms are required for an accurate description. The quantitative relationship between RAS-LIF and surface tension, which probes the surface composition only indirectly, is explored for mixtures of [C2mim]+ and [C12mim]+ with a common bis(trifluoromethylsulfonyl)imide ([NTf2]-) anion. Extended Langmuir model fits to surface tension data are broadly consistent with those to RAS-LIF; however, several other common approaches to extracting surface compositions from measured surface tensions result in much larger discrepancies. MD simulations suggest that RAS-LIF faithfully reports on the alkyl-chain exposure at the surface, which is only subtly modified by composition-dependent structural reorganisation.
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Affiliation(s)
- E J Smoll
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA.
| | - M A Tesa-Serrate
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
| | - S M Purcell
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
| | - L D'Andrea
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - D W Bruce
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - J M Slattery
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - M L Costen
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
| | - T K Minton
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA.
| | - K G McKendrick
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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Nguyen HT, Bryois J, Kim A, Dobbyn A, Huckins LM, Munoz-Manchado AB, Ruderfer DM, Genovese G, Fromer M, Xu X, Pinto D, Linnarsson S, Verhage M, Smit AB, Hjerling-Leffler J, Buxbaum JD, Hultman C, Sklar P, Purcell SM, Lage K, He X, Sullivan PF, Stahl EA. Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders. Genome Med 2017; 9:114. [PMID: 29262854 PMCID: PMC5738153 DOI: 10.1186/s13073-017-0497-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/16/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Integrating rare variation from trio family and case-control studies has successfully implicated specific genes contributing to risk of neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD), intellectual disability (ID), developmental disorders (DDs), and epilepsy (EPI). For schizophrenia (SCZ), however, while sets of genes have been implicated through the study of rare variation, only two risk genes have been identified. METHODS We used hierarchical Bayesian modeling of rare-variant genetic architecture to estimate mean effect sizes and risk-gene proportions, analyzing the largest available collection of whole exome sequence data for SCZ (1,077 trios, 6,699 cases, and 13,028 controls), and data for four NDDs (ASD, ID, DD, and EPI; total 10,792 trios, and 4,058 cases and controls). RESULTS For SCZ, we estimate there are 1,551 risk genes. There are more risk genes and they have weaker effects than for NDDs. We provide power analyses to predict the number of risk-gene discoveries as more data become available. We confirm and augment prior risk gene and gene set enrichment results for SCZ and NDDs. In particular, we detected 98 new DD risk genes at FDR < 0.05. Correlations of risk-gene posterior probabilities are high across four NDDs (ρ>0.55), but low between SCZ and the NDDs (ρ<0.3). An in-depth analysis of 288 NDD genes shows there is highly significant protein-protein interaction (PPI) network connectivity, and functionally distinct PPI subnetworks based on pathway enrichment, single-cell RNA-seq cell types, and multi-region developmental brain RNA-seq. CONCLUSIONS We have extended a pipeline used in ASD studies and applied it to infer rare genetic parameters for SCZ and four NDDs ( https://github.com/hoangtn/extTADA ). We find many new DD risk genes, supported by gene set enrichment and PPI network connectivity analyses. We find greater similarity among NDDs than between NDDs and SCZ. NDD gene subnetworks are implicated in postnatally expressed presynaptic and postsynaptic genes, and for transcriptional and post-transcriptional gene regulation in prenatal neural progenitor and stem cells.
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Affiliation(s)
- Hoang T. Nguyen
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Surgery, Massachusetts General Hospital, Boston, 02114 MA USA
| | - Amanda Dobbyn
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Laura M. Huckins
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Ana B. Munoz-Manchado
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Douglas M. Ruderfer
- Division of Genetic Medicine, Departments of Medicine, Psychiatry and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, 37235 TN USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Genetics, Harvard Medical School, Cambridge, Massachusetts USA
| | - Menachem Fromer
- Verily Life Sciences, 269 E Grand Ave, South San Francisco, 94080 CA USA
| | - Xinyi Xu
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Dalila Pinto
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Matthijs Verhage
- Department of Functional Genomics, The Center for Neurogenomics and Cognitive Research, VU University and VU Medical Center, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, The Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Joseph D. Buxbaum
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Shaun M. Purcell
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Sleep Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Surgery, Massachusetts General Hospital, Boston, 02114 MA USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, 60637 IL USA
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, 27599-7264 North Carolina USA
| | - Eli A. Stahl
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
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35
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Direk N, Williams S, Smith JA, Ripke S, Air T, Amare AT, Amin N, Baune BT, Bennett DA, Blackwood DH, Boomsma D, Breen G, Buttenschøn HN, Byrne EM, Børglum AD, Castelao E, Cichon S, Clarke TK, Cornelis MC, Dannlowski U, De Jager PL, Demirkan A, Domenici E, van Duijn CM, Dunn EC, Eriksson JG, Esko T, Faul JD, Ferrucci L, Fornage M, de Geus E, Gill M, Gordon SD, Jörgen Grabe H, van Grootheest G, Hamilton SP, Hartman CA, Heath AC, Hek K, Hofman A, Homuth G, Horn C, Hottenga JJ, Kardia SL, Kloiber S, Koenen K, Kutalik Z, Ladwig KH, Lahti J, Levinson DF, Lewis CM, Lewis G, Li QS, Llewellyn DJ, Lucae S, Lunetta KL, MacIntyre DJ, Madden P, Martin NG, McIntosh AM, Metspalu A, Milaneschi Y, Montgomery GW, Mors O, Mosley TH, Murabito JM, Müller-Myhsok B, Nöthen MM, Nyholt DR, O’Donovan MC, Penninx BW, Pergadia ML, Perlis R, Potash JB, Preisig M, Purcell SM, Quiroz JA, Räikkönen K, Rice JP, Rietschel M, Rivera M, Schulze TG, Shi J, Shyn S, Sinnamon GC, Smit JH, Smoller JW, Snieder H, Tanaka T, Tansey KE, Teumer A, Uher R, Umbricht D, Van der Auwera S, Ware EB, Weir DR, Weissman MM, Willemsen G, Yang J, Zhao W, Tiemeier H, Sullivan PF. An Analysis of Two Genome-wide Association Meta-analyses Identifies a New Locus for Broad Depression Phenotype. Biol Psychiatry 2017; 82:322-329. [PMID: 28049566 PMCID: PMC5462867 DOI: 10.1016/j.biopsych.2016.11.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND The genetics of depression has been explored in genome-wide association studies that focused on either major depressive disorder or depressive symptoms with mostly negative findings. A broad depression phenotype including both phenotypes has not been tested previously using a genome-wide association approach. We aimed to identify genetic polymorphisms significantly associated with a broad phenotype from depressive symptoms to major depressive disorder. METHODS We analyzed two prior studies of 70,017 participants of European ancestry from general and clinical populations in the discovery stage. We performed a replication meta-analysis of 28,328 participants. Single nucleotide polymorphism (SNP)-based heritability and genetic correlations were calculated using linkage disequilibrium score regression. Discovery and replication analyses were performed using a p-value-based meta-analysis. Lifetime major depressive disorder and depressive symptom scores were used as the outcome measures. RESULTS The SNP-based heritability of major depressive disorder was 0.21 (SE = 0.02), the SNP-based heritability of depressive symptoms was 0.04 (SE = 0.01), and their genetic correlation was 1.001 (SE = 0.2). We found one genome-wide significant locus related to the broad depression phenotype (rs9825823, chromosome 3: 61,082,153, p = 8.2 × 10-9) located in an intron of the FHIT gene. We replicated this SNP in independent samples (p = .02) and the overall meta-analysis of the discovery and replication cohorts (1.0 × 10-9). CONCLUSIONS This large study identified a new locus for depression. Our results support a continuum between depressive symptoms and major depressive disorder. A phenotypically more inclusive approach may help to achieve the large sample sizes needed to detect susceptibility loci for depression.
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Affiliation(s)
- Nese Direk
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Psychiatry, Dokuz Eylul University, Izmir, Turkey
| | - Stephanie Williams
- Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - Jennifer A. Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Stephan Ripke
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA,Department of Psychiatry and Psychotherapy, Charité, Campus Mitte, Berlin, Germany
| | - Tracy Air
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Azmeraw T. Amare
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bernhard T. Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - David A. Bennett
- Rush Alzheimer's Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | | | - Dorret Boomsma
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Gerome Breen
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Henriette N. Buttenschøn
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Denmark,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
| | - Enda M. Byrne
- The University of Queensland, Queensland Brain Institute, St. Lucia, Queensland, Australia
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark,Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Denmark
| | - Enrique Castelao
- Departement of Psychiatry, Lausanne University Hospital, Switzerland
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany,Department of Genomics, Life & Brain Center, Bonn, Germany,Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany,Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Marilyn C. Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago IL, USA
| | - Udo Dannlowski
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Philip L. De Jager
- Department of Neurology, Program in Translational NeuroPsychiatric Genomics, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA,Harvard Medical School, Boston, Massachusetts, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Ayse Demirkan
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Enrico Domenici
- Centre for Integrative Biology, University of Trento, Trento, Italy,Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erin C. Dunn
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Johan G. Eriksson
- National Institute for Health and Welfare, Department of Chronic Disease Prevention, Helsinki, Finland,Department of General Practice and Primary Health Care, University of Helsinki, Finland,Unit of General Practice, Helsinki University Central Hospital, Finland,Folkhalsan Research Centre, Helsinki, Finland,Vasa Central Hospital, Vasa, Finland
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia,Division of Endocrinology, Boston Children's Hospital, Cambridge, MA, USA,Program in Medical and Populational Genetics, Broad Institute, Cambridge, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jessica D. Faul
- Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eco de Geus
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Michael Gill
- Department of Psychiatry, Trinity Centre for Health Science, Dublin, Ireland
| | - Scott D. Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Hans Jörgen Grabe
- Department of Psychiatry and Psychotherapy, Helios Hospital Stralsund, Germany,Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany,German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Germany
| | - Gerard van Grootheest
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Steven P. Hamilton
- Department of Psychiatry, Kaiser Permanente San Francisco Medical Center, CA, USA
| | - Catharina A. Hartman
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Andrew C. Heath
- Department of Psychiatry, Washington University St. Louis, Missouri, USA
| | - Karin Hek
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands,Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Germany
| | - Carsten Horn
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | | | | | - Karestan Koenen
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Karl-Heinz Ladwig
- Institute of Epidemiology II, Mental Health Research Unit, Helmholtz Zentrum München, German Research Center for Environmental Health, Germany,Department of Psychosomatic Medicine and Psychotherapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jari Lahti
- Folkhalsan Research Centre, Helsinki, Finland,Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - Douglas F. Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Cathryn M. Lewis
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Glyn Lewis
- Division of Psychiatry, University College London, London, UK
| | | | | | | | - Kathryn L. Lunetta
- Boston University School of Public Health, Department of Biostatistics, Boston, MA, USA,Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA
| | | | - Pamela Madden
- Department of Psychiatry, Washington University St. Louis, Missouri, USA
| | | | | | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark,Research Department P, Aarhus University Hospital, Risskov, Denmark
| | - Thomas H. Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne M. Murabito
- Boston University and NHLBI's Framingham Heart Study, Framingham, MA, USA,Boston University School of Medicine, Department of Medicine, Section of General Internal Medicine, Boston, MA, USA
| | - Bertram Müller-Myhsok
- Max Planck Institute of Psychiatry, Munich, Germany,University of Liverpool, Institute of Translational Medicine, Liverpool, L69 3BX, UK,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany,Department of Genomics, Life & Brain Center, Bonn, Germany
| | - Dale R. Nyholt
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Michael C. O’Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Brenda W. Penninx
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Michele L. Pergadia
- Department of Psychiatry, Washington University St. Louis, Missouri, USA,Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Roy Perlis
- Center for Experimental Drugs and Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - James B. Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Martin Preisig
- Departement of Psychiatry, Lausanne University Hospital, Switzerland
| | - Shaun M. Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jorge A. Quiroz
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland,Solid GT, Boston, MA, USA
| | - Katri Räikkönen
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - John P. Rice
- Department of Psychiatry, Washington University St. Louis, Missouri, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Margarita Rivera
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK,CIBERSAM-Universidad de Granada, Granada, Spain,Instituto de Investigación Biosanitaria ibs.GRANADA. Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
| | - Thomas G. Schulze
- Department of Psychiatry and Psychotherapy, University of Göttingen, Göttingen, Germany,Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University, Munich, 80336 Munich, Germany
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Grant C. Sinnamon
- Department of Psychiatry and Psychiatric Neuroscience, School of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
| | - Johannes H. Smit
- Department of Psychiatry, Neuroscience Campus Amsterdam and EMGO Institute of Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Jordan W. Smoller
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Harold Snieder
- Unit of Genetic Epidemiology & Bioinformatics, Department of Epidemiology, University Medical Center Groningen, Groningen, the Netherlands
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Katherine E. Tansey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - Rudolf Uher
- MRC SGDP Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK,Dalhousie University, 6299 South St, Halifax, Nova Scotia B3H 4R2, Canada
| | - Daniel Umbricht
- Roche Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology and Rare Diseases Discovery & Translational Medicine Area, Roche Innovation Center Basel, F Hoffman-La Roche Ltd., Switzerland
| | - Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany,German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Germany
| | - Erin B. Ware
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA,Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - David R. Weir
- Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Myrna M. Weissman
- College of Physicians and Surgeons and the Mailman School of Public Health, Columbia University and New York State Psychiatric Institute, New York, NY, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University, Amsterdam, The Netherlands
| | - Jingyun Yang
- Rush Alzheimer's Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam; Department of Psychiatry, Erasmus University Medical Center, Rotterdam.
| | - Patrick F. Sullivan
- Center for Psychiatric Genomics, Department of Genetics, Genomic Medicine, University of North Carolina, Chapel Hill, NC, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden
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Purcell SM, Manoach DS, Demanuele C, Cade BE, Mariani S, Cox R, Panagiotaropoulou G, Saxena R, Pan JQ, Smoller JW, Redline S, Stickgold R. Characterizing sleep spindles in 11,630 individuals from the National Sleep Research Resource. Nat Commun 2017. [PMID: 28649997 PMCID: PMC5490197 DOI: 10.1038/ncomms15930] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Sleep spindles are characteristic electroencephalogram (EEG) signatures of stage 2 non-rapid eye movement sleep. Implicated in sleep regulation and cognitive functioning, spindles may represent heritable biomarkers of neuropsychiatric disease. Here we characterize spindles in 11,630 individuals aged 4 to 97 years, as a prelude to future genetic studies. Spindle properties are highly reliable but exhibit distinct developmental trajectories. Across the night, we observe complex patterns of age- and frequency-dependent dynamics, including signatures of circadian modulation. We identify previously unappreciated correlates of spindle activity, including confounding by body mass index mediated by cardiac interference in the EEG. After taking account of these confounds, genetic factors significantly contribute to spindle and spectral sleep traits. Finally, we consider topographical differences and critical measurement issues. Taken together, our findings will lead to an increased understanding of the genetic architecture of sleep spindles and their relation to behavioural and health outcomes, including neuropsychiatric disorders. Sleep patterns vary and are associated with health and disease. Here Purcell et al characterize sleep spindle activity in 11,630 individuals and describe age-related changes, genetic influences, and possible confounding effects, serving as a resource for further understanding the physiology of sleep.
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Affiliation(s)
- S M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - D S Manoach
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, USA
| | - C Demanuele
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, USA
| | - B E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - S Mariani
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - R Cox
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - G Panagiotaropoulou
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts 02129, USA
| | - R Saxena
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - J Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - J W Smoller
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - S Redline
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - R Stickgold
- Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
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Panagiotaropoulou G, Cade B, Mariani S, Demanuale C, Cox R, Saxena R, Pan J, Smoller J, Stickgold R, Manoach D, Redline S, Purcell SM. 0001 GENOME-WIDE ANALYSES OF SLEEP SPINDLES IN THE NATIONAL SLEEP RESEARCH RESOURCE. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Charney AW, Ruderfer DM, Stahl EA, Moran JL, Chambert K, Belliveau RA, Forty L, Gordon-Smith K, Di Florio A, Lee PH, Bromet EJ, Buckley PF, Escamilla MA, Fanous AH, Fochtmann LJ, Lehrer DS, Malaspina D, Marder SR, Morley CP, Nicolini H, Perkins DO, Rakofsky JJ, Rapaport MH, Medeiros H, Sobell JL, Green EK, Backlund L, Bergen SE, Juréus A, Schalling M, Lichtenstein P, Roussos P, Knowles JA, Jones I, Jones LA, Hultman CM, Perlis RH, Purcell SM, McCarroll SA, Pato CN, Pato MT, Craddock N, Landén M, Smoller JW, Sklar P. Evidence for genetic heterogeneity between clinical subtypes of bipolar disorder. Transl Psychiatry 2017; 7:e993. [PMID: 28072414 PMCID: PMC5545718 DOI: 10.1038/tp.2016.242] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 01/12/2023] Open
Abstract
We performed a genome-wide association study of 6447 bipolar disorder (BD) cases and 12 639 controls from the International Cohort Collection for Bipolar Disorder (ICCBD). Meta-analysis was performed with prior results from the Psychiatric Genomics Consortium Bipolar Disorder Working Group for a combined sample of 13 902 cases and 19 279 controls. We identified eight genome-wide significant, associated regions, including a novel associated region on chromosome 10 (rs10884920; P=3.28 × 10-8) that includes the brain-enriched cytoskeleton protein adducin 3 (ADD3), a non-coding RNA, and a neuropeptide-specific aminopeptidase P (XPNPEP1). Our large sample size allowed us to test the heritability and genetic correlation of BD subtypes and investigate their genetic overlap with schizophrenia and major depressive disorder. We found a significant difference in heritability of the two most common forms of BD (BD I SNP-h2=0.35; BD II SNP-h2=0.25; P=0.02). The genetic correlation between BD I and BD II was 0.78, whereas the genetic correlation was 0.97 when BD cohorts containing both types were compared. In addition, we demonstrated a significantly greater load of polygenic risk alleles for schizophrenia and BD in patients with BD I compared with patients with BD II, and a greater load of schizophrenia risk alleles in patients with the bipolar type of schizoaffective disorder compared with patients with either BD I or BD II. These results point to a partial difference in the genetic architecture of BD subtypes as currently defined.
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Affiliation(s)
- A W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - D M Ruderfer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - E A Stahl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - J L Moran
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - K Chambert
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - R A Belliveau
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - L Forty
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff Unviersity, Cardiff, UK
| | - K Gordon-Smith
- Department of Psychological Medicine, University of Worcester, Worcester, UK
| | - A Di Florio
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff Unviersity, Cardiff, UK
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - P H Lee
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - E J Bromet
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, USA
| | - P F Buckley
- Department of Psychiatry, Georgia Regents University Medical Center, Augusta, GA, USA
| | - M A Escamilla
- Center of Excellence in Neuroscience, Department of Psychiatry, Texas Tech University Health Sciences Center at El Paso, El Paso, TX, USA
| | - A H Fanous
- Department of Psychiatry, Veterans Administration Medical Center, Washington, DC, USA
- Department of Psychiatry, Georgetown University, Washington, DC, USA
| | - L J Fochtmann
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, USA
| | - D S Lehrer
- Department of Psychiatry, Wright State University, Dayton, OH, USA
| | - D Malaspina
- Department of Psychiatry, New York University, New York, NY, USA
| | - S R Marder
- Department of Psychiatry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C P Morley
- Department of Psychiatry and Behavioral Science, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Departments of Family Medicine, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - H Nicolini
- Center for Genomic Sciences, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
- Department of Psychiatry, Carracci Medical Group, Mexico City, Mexico
| | - D O Perkins
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J J Rakofsky
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - M H Rapaport
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - H Medeiros
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - J L Sobell
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - E K Green
- School of Biomedical and Health Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, UK
| | - L Backlund
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - S E Bergen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - A Juréus
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - M Schalling
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - P Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - P Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - J A Knowles
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - I Jones
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff Unviersity, Cardiff, UK
| | - L A Jones
- Department of Psychological Medicine, University of Worcester, Worcester, UK
| | - C M Hultman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - R H Perlis
- Center for Experimental Therapeutics, Massachusetts General Hospital, Boston, MA, USA
| | - S M Purcell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
| | - S A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C N Pato
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - M T Pato
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
- Zilkha Neurogenetic Institute, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA
| | - N Craddock
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff Unviersity, Cardiff, UK
| | - M Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Neuroscience and Physiology, Sahlgenska Academy at the Gothenburg University, Gothenburg, Sweden
| | - J W Smoller
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - P Sklar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA
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39
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Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, McLean CY, Tung JY, Yu LPC, Gambetti P, Blevins J, Zhang S, Cohen Y, Chen W, Yamada M, Hamaguchi T, Sanjo N, Mizusawa H, Nakamura Y, Kitamoto T, Collins SJ, Boyd A, Will RG, Knight R, Ponto C, Zerr I, Kraus TFJ, Eigenbrod S, Giese A, Calero M, de Pedro-Cuesta J, Haïk S, Laplanche JL, Bouaziz-Amar E, Brandel JP, Capellari S, Parchi P, Poleggi A, Ladogana A, O'Donnell-Luria AH, Karczewski KJ, Marshall JL, Boehnke M, Laakso M, Mohlke KL, Kähler A, Chambert K, McCarroll S, Sullivan PF, Hultman CM, Purcell SM, Sklar P, van der Lee SJ, Rozemuller A, Jansen C, Hofman A, Kraaij R, van Rooij JGJ, Ikram MA, Uitterlinden AG, van Duijn CM, Daly MJ, MacArthur DG. Quantifying prion disease penetrance using large population control cohorts. Sci Transl Med 2016; 8:322ra9. [PMID: 26791950 DOI: 10.1126/scitranslmed.aad5169] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
More than 100,000 genetic variants are reported to cause Mendelian disease in humans, but the penetrance-the probability that a carrier of the purported disease-causing genotype will indeed develop the disease-is generally unknown. We assess the impact of variants in the prion protein gene (PRNP) on the risk of prion disease by analyzing 16,025 prion disease cases, 60,706 population control exomes, and 531,575 individuals genotyped by 23andMe Inc. We show that missense variants in PRNP previously reported to be pathogenic are at least 30 times more common in the population than expected on the basis of genetic prion disease prevalence. Although some of this excess can be attributed to benign variants falsely assigned as pathogenic, other variants have genuine effects on disease susceptibility but confer lifetime risks ranging from <0.1 to ~100%. We also show that truncating variants in PRNP have position-dependent effects, with true loss-of-function alleles found in healthy older individuals, a finding that supports the safety of therapeutic suppression of prion protein expression.
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Affiliation(s)
- Eric Vallabh Minikel
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA.
| | - Sonia M Vallabh
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA. Prion Alliance, Cambridge, MA 02139, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karol Estrada
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaitlin E Samocha
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | | | - Cory Y McLean
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Joyce Y Tung
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Linda P C Yu
- Research, 23andMe Inc., Mountain View, CA 94041, USA
| | - Pierluigi Gambetti
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Janis Blevins
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Shulin Zhang
- University Hospitals Case Medical Center, Cleveland, OH 44106, USA
| | - Yvonne Cohen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Wei Chen
- National Prion Disease Pathology Surveillance Center, Cleveland, OH 44106, USA
| | - Masahito Yamada
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Tsuyoshi Hamaguchi
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Nobuo Sanjo
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Hidehiro Mizusawa
- National Center Hospital, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan
| | - Yosikazu Nakamura
- Department of Public Health, Jichi Medical University, Shimotsuke 329-0498, Japan
| | - Tetsuyuki Kitamoto
- Department of Neurological Science, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Steven J Collins
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alison Boyd
- Australian National Creutzfeldt-Jakob Disease Registry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert G Will
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Richard Knight
- National Creutzfeldt-Jakob Disease Research & Surveillance Unit, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Claudia Ponto
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Inga Zerr
- National Reference Center for the Surveillance of Human Transmissible Spongiform Encephalopathies, Georg-August-University, Goettingen 37073, Germany
| | - Theo F J Kraus
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Sabina Eigenbrod
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University, Munich 81377, Germany
| | - Miguel Calero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Jesús de Pedro-Cuesta
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Stéphane Haïk
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Jean-Louis Laplanche
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Elodie Bouaziz-Amar
- AP-HP, Service de Biochimie et Biologie Moléculaire, Hôpital Lariboisière, 75010 Paris, France
| | - Jean-Philippe Brandel
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, Pierre and Marie Curie University Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
| | - Sabina Capellari
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Piero Parchi
- Istituto di Ricovero e Cura a Carattere Scientifico, Institute of Neurological Sciences, Bologna 40123, Italy. Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Anna Poleggi
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anna Ladogana
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Anne H O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jamie L Marshall
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio 70210, Finland
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Anna Kähler
- Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA. Karolinska Institutet, Stockholm SE-171 77, Sweden
| | | | - Shaun M Purcell
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Annemieke Rozemuller
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Casper Jansen
- Dutch Surveillance Centre for Prion Diseases, Department of Pathology, University Medical Center, Utrecht 3584 CX, Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | | | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands. Department of Internal Medicine, Erasmus MC, Rotterdam 3000 CA, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center (MC), Rotterdam 3000 CA, Netherlands
| | | | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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40
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Manoach DS, Pan JQ, Purcell SM, Stickgold R. Reduced Sleep Spindles in Schizophrenia: A Treatable Endophenotype That Links Risk Genes to Impaired Cognition? Biol Psychiatry 2016; 80:599-608. [PMID: 26602589 PMCID: PMC4833702 DOI: 10.1016/j.biopsych.2015.10.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/18/2015] [Accepted: 10/05/2015] [Indexed: 11/26/2022]
Abstract
Although schizophrenia (SZ) is defined by waking phenomena, abnormal sleep is a common feature. In particular, there is accumulating evidence of a sleep spindle deficit. Sleep spindles, a defining thalamocortical oscillation of non-rapid eye movement stage 2 sleep, correlate with IQ and are thought to promote long-term potentiation and enhance memory consolidation. We review evidence that reduced spindle activity in SZ is an endophenotype that impairs sleep-dependent memory consolidation, contributes to symptoms, and is a novel treatment biomarker. Studies showing that spindles can be pharmacologically enhanced in SZ and that increasing spindles improves memory in healthy individuals suggest that treating spindle deficits in patients with SZ may improve cognition. Spindle activity is highly heritable, and recent large-scale genome-wide association studies have identified SZ risk genes that may contribute to spindle deficits and illuminate their mechanisms. For example, the SZ risk gene CACNA1I encodes a calcium channel that is abundantly expressed in the thalamic spindle generator and plays a critical role in spindle activity based on a mouse knockout. Future genetic studies of animals and humans can delineate the role of this and other genes in spindles. Such cross-disciplinary research, by forging empirical links in causal chains from risk genes to proteins and cellular functions to endophenotypes, cognitive impairments, symptoms, and diagnosis, has the potential to advance the mechanistic understanding, treatment, and prevention of SZ. This review highlights the importance of deficient sleep-dependent memory consolidation among the cognitive deficits of SZ and implicates reduced sleep spindles as a potentially treatable mechanism.
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Affiliation(s)
- Dara S. Manoach
- Department of Psychiatry and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02215, USA,Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jen Q. Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Shaun M. Purcell
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02215, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA,Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Stickgold
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA,Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, MA 02215 Harvard Medical School, Boston, MA, 02215
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41
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Genovese G, Fromer M, Stahl EA, Ruderfer DM, Chambert K, Landén M, Moran JL, Purcell SM, Sklar P, Sullivan PF, Hultman CM, McCarroll SA. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. Nat Neurosci 2016; 19:1433-1441. [PMID: 27694994 PMCID: PMC5104192 DOI: 10.1038/nn.4402] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/06/2016] [Indexed: 12/15/2022]
Abstract
By analyzing the exomes of 12,332 unrelated Swedish individuals – including 4,877 affected with schizophrenia – in ways informed by exome sequences from 45,376 other individuals, we identified 244,246 coding-sequence and splice-site ultra-rare variants (URVs) that were unique to individual Swedes. We found that gene-disruptive and putatively protein-damaging URVs (but not synonymous URVs) were more abundant in schizophrenia cases than controls (P = 1.3 × 10−10). This elevation of protein-compromising URVs was several times larger than an analogously elevated rate for de novo mutations, suggesting that most rare-variant effects on schizophrenia risk are inherited. Among individuals with schizophrenia, the elevated frequency of protein-compromising URVs was concentrated in brain-expressed genes, particularly in neuronally expressed genes; most of this genetic signal arose from large sets of genes whose RNAs have been found to interact with synaptically localized proteins. Our results suggest that synaptic dysfunction may mediate a large fraction of strong, individually rare genetic influences on schizophrenia risk.
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Affiliation(s)
- Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Menachem Fromer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mikael Landén
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience a Physiology at Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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42
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Lee SH, Byrne EM, Hultman CM, Kähler A, Vinkhuyzen AAE, Ripke S, Andreassen OA, Frisell T, Gusev A, Hu X, Karlsson R, Mantzioris VX, McGrath JJ, Mehta D, Stahl EA, Zhao Q, Kendler KS, Sullivan PF, Price AL, O'Donovan M, Okada Y, Mowry BJ, Raychaudhuri S, Wray NR, Byerley W, Cahn W, Cantor RM, Cichon S, Cormican P, Curtis D, Djurovic S, Escott-Price V, Gejman PV, Georgieva L, Giegling I, Hansen TF, Ingason A, Kim Y, Konte B, Lee PH, McIntosh A, McQuillin A, Morris DW, Nöthen MM, O'Dushlaine C, Olincy A, Olsen L, Pato CN, Pato MT, Pickard BS, Posthuma D, Rasmussen HB, Rietschel M, Rujescu D, Schulze TG, Silverman JM, Thirumalai S, Werge T, Agartz I, Amin F, Azevedo MH, Bass N, Black DW, Blackwood DHR, Bruggeman R, Buccola NG, Choudhury K, Cloninger RC, Corvin A, Craddock N, Daly MJ, Datta S, Donohoe GJ, Duan J, Dudbridge F, Fanous A, Freedman R, Freimer NB, Friedl M, Gill M, Gurling H, De Haan L, Hamshere ML, Hartmann AM, Holmans PA, Kahn RS, Keller MC, Kenny E, Kirov GK, Krabbendam L, Krasucki R, Lawrence J, Lencz T, Levinson DF, Lieberman JA, Lin DY, Linszen DH, Magnusson PKE, Maier W, Malhotra AK, Mattheisen M, Mattingsdal M, McCarroll SA, Medeiros H, Melle I, Milanova V, Myin-Germeys I, Neale BM, Ophoff RA, Owen MJ, Pimm J, Purcell SM, Puri V, Quested DJ, Rossin L, Ruderfer D, Sanders AR, Shi J, Sklar P, St Clair D, Stroup TS, Van Os J, Visscher PM, Wiersma D, Zammit S, Bridges SL, Choi HK, Coenen MJH, de Vries N, Dieud P, Greenberg JD, Huizinga TWJ, Padyukov L, Siminovitch KA, Tak PP, Worthington J, De Jager PL, Denny JC, Gregersen PK, Klareskog L, Mariette X, Plenge RM, van Laar M, van Riel P. New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. Int J Epidemiol 2016; 44:1706-21. [PMID: 26286434 DOI: 10.1093/ije/dyv136] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND A long-standing epidemiological puzzle is the reduced rate of rheumatoid arthritis (RA) in those with schizophrenia (SZ) and vice versa. Traditional epidemiological approaches to determine if this negative association is underpinned by genetic factors would test for reduced rates of one disorder in relatives of the other, but sufficiently powered data sets are difficult to achieve. The genomics era presents an alternative paradigm for investigating the genetic relationship between two uncommon disorders. METHODS We use genome-wide common single nucleotide polymorphism (SNP) data from independently collected SZ and RA case-control cohorts to estimate the SNP correlation between the disorders. We test a genotype X environment (GxE) hypothesis for SZ with environment defined as winter- vs summer-born. RESULTS We estimate a small but significant negative SNP-genetic correlation between SZ and RA (-0.046, s.e. 0.026, P = 0.036). The negative correlation was stronger for the SNP set attributed to coding or regulatory regions (-0.174, s.e. 0.071, P = 0.0075). Our analyses led us to hypothesize a gene-environment interaction for SZ in the form of immune challenge. We used month of birth as a proxy for environmental immune challenge and estimated the genetic correlation between winter-born and non-winter born SZ to be significantly less than 1 for coding/regulatory region SNPs (0.56, s.e. 0.14, P = 0.00090). CONCLUSIONS Our results are consistent with epidemiological observations of a negative relationship between SZ and RA reflecting, at least in part, genetic factors. Results of the month of birth analysis are consistent with pleiotropic effects of genetic variants dependent on environmental context.
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43
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Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B, Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M, McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG. Analysis of protein-coding genetic variation in 60,706 humans. Nature 2016; 536:285-91. [PMID: 27535533 PMCID: PMC5018207 DOI: 10.1038/nature19057] [Citation(s) in RCA: 7269] [Impact Index Per Article: 908.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/24/2016] [Indexed: 02/02/2023]
Abstract
Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.
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Affiliation(s)
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,School of Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia,Institute for Neuroscience and Muscle Research, Childrens Hospital at Westmead, Sydney, NSW, Australia
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric V Minikel
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Kaitlin E Samocha
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy Fennell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - James S Ware
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA,National Heart and Lung Institute, Imperial College London, London, UK,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton Hospital, London, UK,MRC Clinical Sciences Centre, Imperial College London, London, UK
| | - Andrew J Hill
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beryl B Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel P Birnbaum
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack A Kosmicki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Laramie E Duncan
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karol Estrada
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fengmei Zhao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Zou
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joanne Berghout
- Mouse Genome Informatics, Jackson Laboratory, Bar Harbor, ME, USA,Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, AZ, USA
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | | | - Mark DePristo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA,The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Menachem Fromer
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jackie Goldstein
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Howrigan
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam Kiezun
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mitja I Kurki
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Disease Laboratory, Instituto Nacional de Medicina Gen—mica, Mexico City, Mexico
| | - Gina M Peloso
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan Poplin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manuel A Rivas
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Samuel A Rose
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Douglas M Ruderfer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Khalid Shakir
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Christine Stevens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brett P Thomas
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Grace Tiao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maria T Tusie-Luna
- Molecular Biology and Genomic Medicine Unit, Instituto Nacional de Ciencias M_dicas y Nutrici—n, Mexico City, Mexico
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University,Samsung Medical Center, Seoul, Republic of Korea
| | - Dongmei Yu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - David M Altshuler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Vertex Pharmaceuticals, Boston, MA, USA
| | | | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Danesh
- Department of Public Health and Primary Care, Strangeways Research Laboratory, Cambridge, UK
| | - Stacey Donnelly
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - Stacey B Gabriel
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen J Glatt
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory, State University of New York,Upstate Medical University, Syracuse, NY, USA,Department of Psychiatry and Behavioral Sciences, State University of New York,Upstate Medical University, Syracuse, NY, USA,Department of Neuroscience and Physiology, State University of New York,Upstate Medical University, Syracuse, NY, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Foundation Trust, Oxford, UK
| | - Dermot McGovern
- Inflammatory Bowel Disease and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruth McPherson
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON, Canada
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Shaun M Purcell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danish Saleheen
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,Center for Non-Communicable Diseases, Karachi, , Pakistan
| | - Jeremiah M Scharf
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jaakko Tuomilehto
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Ming T Tsuang
- Department of Psychiatry, University of California, San Diego, CA, USA
| | - Hugh C Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK,Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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44
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Goes FS, Pirooznia M, Parla JS, Kramer M, Ghiban E, Mavruk S, Chen YC, Monson ET, Willour VL, Karchin R, Flickinger M, Locke AE, Levy SE, Scott LJ, Boehnke M, Stahl E, Moran JL, Hultman CM, Landén M, Purcell SM, Sklar P, Zandi PP, McCombie WR, Potash JB. Exome Sequencing of Familial Bipolar Disorder. JAMA Psychiatry 2016; 73:590-7. [PMID: 27120077 PMCID: PMC5600716 DOI: 10.1001/jamapsychiatry.2016.0251] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
IMPORTANCE Complex disorders, such as bipolar disorder (BD), likely result from the influence of both common and rare susceptibility alleles. While common variation has been widely studied, rare variant discovery has only recently become feasible with next-generation sequencing. OBJECTIVE To utilize a combined family-based and case-control approach to exome sequencing in BD using multiplex families as an initial discovery strategy, followed by association testing in a large case-control meta-analysis. DESIGN, SETTING, AND PARTICIPANTS We performed exome sequencing of 36 affected members with BD from 8 multiplex families and tested rare, segregating variants in 3 independent case-control samples consisting of 3541 BD cases and 4774 controls. MAIN OUTCOMES AND MEASURES We used penalized logistic regression and 1-sided gene-burden analyses to test for association of rare, segregating damaging variants with BD. Permutation-based analyses were performed to test for overall enrichment with previously identified gene sets. RESULTS We found 84 rare (frequency <1%), segregating variants that were bioinformatically predicted to be damaging. These variants were found in 82 genes that were enriched for gene sets previously identified in de novo studies of autism (19 observed vs. 10.9 expected, P = .0066) and schizophrenia (11 observed vs. 5.1 expected, P = .0062) and for targets of the fragile X mental retardation protein (FMRP) pathway (10 observed vs. 4.4 expected, P = .0076). The case-control meta-analyses yielded 19 genes that were nominally associated with BD based either on individual variants or a gene-burden approach. Although no gene was individually significant after correction for multiple testing, this group of genes continued to show evidence for significant enrichment of de novo autism genes (6 observed vs 2.6 expected, P = .028). CONCLUSIONS AND RELEVANCE Our results are consistent with the presence of prominent locus and allelic heterogeneity in BD and suggest that very large samples will be required to definitively identify individual rare variants or genes conferring risk for this disorder. However, we also identify significant associations with gene sets composed of previously discovered de novo variants in autism and schizophrenia, as well as targets of the FRMP pathway, providing preliminary support for the overlap of potential autism and schizophrenia risk genes with rare, segregating variants in families with BD.
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Affiliation(s)
- Fernando S. Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jennifer S. Parla
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Melissa Kramer
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Elena Ghiban
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Senem Mavruk
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Yun-Ching Chen
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland4Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Eric T. Monson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City
| | - Virginia L. Willour
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City
| | - Rachel Karchin
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland4Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Matthew Flickinger
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor
| | - Adam E. Locke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor
| | - Shawn E. Levy
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor
| | - Eli Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York9Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jennifer L. Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden12Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Shaun M. Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York9Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York10Stanley Center for Psychiat
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York9Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York15Friedman Brain Institute, I
| | - Peter P. Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - W. Richard McCombie
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - James B. Potash
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City
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45
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Ruderfer DM, Charney AW, Readhead B, Kidd BA, Kähler AK, Kenny PJ, Keiser MJ, Moran JL, Hultman CM, Scott SA, Sullivan PF, Purcell SM, Dudley JT, Sklar P. Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. Lancet Psychiatry 2016; 3:350-7. [PMID: 26915512 PMCID: PMC4982509 DOI: 10.1016/s2215-0366(15)00553-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND Therapeutic treatments for schizophrenia do not alleviate symptoms for all patients and efficacy is limited by common, often severe, side-effects. Genetic studies of disease can identify novel drug targets, and drugs for which the mechanism has direct genetic support have increased likelihood of clinical success. Large-scale genetic studies of schizophrenia have increased the number of genes and gene sets associated with risk. We aimed to examine the overlap between schizophrenia risk loci and gene targets of a comprehensive set of medications to potentially inform and improve treatment of schizophrenia. METHODS We defined schizophrenia risk loci as genomic regions reaching genome-wide significance in the latest Psychiatric Genomics Consortium schizophrenia genome-wide association study (GWAS) of 36 989 cases and 113 075 controls and loss of function variants observed only once among 5079 individuals in an exome-sequencing study of 2536 schizophrenia cases and 2543 controls (Swedish Schizophrenia Study). Using two large and orthogonally created databases, we collated drug targets into 167 gene sets targeted by pharmacologically similar drugs and examined enrichment of schizophrenia risk loci in these sets. We further linked the exome-sequenced data with a national drug registry (the Swedish Prescribed Drug Register) to assess the contribution of rare variants to treatment response, using clozapine prescription as a proxy for treatment resistance. FINDINGS We combined results from testing rare and common variation and, after correction for multiple testing, two gene sets were associated with schizophrenia risk: agents against amoebiasis and other protozoal diseases (106 genes, p=0·00046, pcorrected =0·024) and antipsychotics (347 genes, p=0·00078, pcorrected=0·046). Further analysis pointed to antipsychotics as having independent enrichment after removing genes that overlapped these two target sets. We noted significant enrichment both in known targets of antipsychotics (70 genes, p=0·0078) and novel predicted targets (277 genes, p=0·019). Patients with treatment-resistant schizophrenia had an excess of rare disruptive variants in gene targets of antipsychotics (347 genes, p=0·0067) and in genes with evidence for a role in antipsychotic efficacy (91 genes, p=0·0029). INTERPRETATION Our results support genetic overlap between schizophrenia pathogenesis and antipsychotic mechanism of action. This finding is consistent with treatment efficacy being polygenic and suggests that single-target therapeutics might be insufficient. We provide evidence of a role for rare functional variants in antipsychotic treatment response, pointing to a subset of patients where their genetic information could inform treatment. Finally, we present a novel framework for identifying treatments from genetic data and improving our understanding of therapeutic mechanism. FUNDING US National Institutes of Health.
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Affiliation(s)
- Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, New York, NY, USA; Institute for Genomics and Multiscale Biology, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Alexander W Charney
- Division of Psychiatric Genomics, Department of Psychiatry, New York, NY, USA; Institute for Genomics and Multiscale Biology, New York, NY, USA
| | - Ben Readhead
- Institute for Genomics and Multiscale Biology, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Brian A Kidd
- Institute for Genomics and Multiscale Biology, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul J Kenny
- Department of Pharmacology and Systems Therapeutics, New York, NY, USA
| | - Michael J Keiser
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA; USA Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, CA, USA; Institute of Neurodegenerative Diseases, University of California, San Francisco, CA, USA
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, New York, NY, USA; Institute for Genomics and Multiscale Biology, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Joel T Dudley
- Institute for Genomics and Multiscale Biology, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, New York, NY, USA; Institute for Genomics and Multiscale Biology, New York, NY, USA; Department of Genetics and Genomic Sciences, New York, NY, USA; Friedman Brain Institute, New York, NY, USA
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Singh T, Kurki MI, Curtis D, Purcell SM, Crooks L, McRae J, Suvisaari J, Chheda H, Blackwood D, Breen G, Pietiläinen O, Gerety SS, Ayub M, Blyth M, Cole T, Collier D, Coomber EL, Craddock N, Daly MJ, Danesh J, DiForti M, Foster A, Freimer NB, Geschwind D, Johnstone M, Joss S, Kirov G, Körkkö J, Kuismin O, Holmans P, Hultman CM, Iyegbe C, Lönnqvist J, Männikkö M, McCarroll SA, McGuffin P, McIntosh AM, McQuillin A, Moilanen JS, Moore C, Murray RM, Newbury-Ecob R, Ouwehand W, Paunio T, Prigmore E, Rees E, Roberts D, Sambrook J, Sklar P, St Clair D, Veijola J, Walters JTR, Williams H, Sullivan PF, Hurles ME, O'Donovan MC, Palotie A, Owen MJ, Barrett JC. Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. Nat Neurosci 2016; 19:571-7. [PMID: 26974950 DOI: 10.1038/nn.4267] [Citation(s) in RCA: 297] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/11/2016] [Indexed: 12/17/2022]
Abstract
By analyzing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls and 1,077 trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in SETD1A and risk for schizophrenia (P = 3.3 × 10(-9)). We found only two heterozygous LoF variants in 45,376 exomes from individuals without a neuropsychiatric diagnosis, indicating that SETD1A is substantially depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying SETD1A LoF variants also had learning difficulties. We further identified four SETD1A LoF carriers among 4,281 children with severe developmental disorders and two more carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations indicate that LoF variants in SETD1A cause a range of neurodevelopmental disorders, including schizophrenia. Combining these data with previous common variant evidence, we suggest that epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, is an important mechanism in the pathogenesis of schizophrenia.
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Affiliation(s)
- Tarjinder Singh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David Curtis
- University College London Genetics Institute, University College London, London, UK
| | - Shaun M Purcell
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lucy Crooks
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Sheffield Diagnostic Genetics Service, Sheffield Childrens' NHS Foundation Trust, Sheffield, UK
| | - Jeremy McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jaana Suvisaari
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Himanshu Chheda
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Douglas Blackwood
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Gerome Breen
- Institute of Psychiatry, Kings College London, London, UK.,NIHR BRC for Mental Health, Institute of Psychiatry and SLaM NHS Trust, King's College London, London, UK
| | - Olli Pietiläinen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sebastian S Gerety
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Muhammad Ayub
- Division of Developmental Disabilities, Department of Psychiatry, Queen's University, Kingston, Ontario, Canada
| | - Moira Blyth
- Department of Clinical Genetics, Chapel Allerton Hospital, Chapeltown Road, Leeds, UK
| | - Trevor Cole
- Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - David Collier
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK.,Lilly Research Laboratories, Eli Lilly &Co. Ltd., Windlesham, Surrey, UK
| | - Eve L Coomber
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Mark J Daly
- Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John Danesh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marta DiForti
- Institute of Psychiatry, Kings College London, London, UK
| | - Alison Foster
- Clinical Genetics Unit, Birmingham Women's NHS Foundation Trust, Edgbaston, Birmingham, UK
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, USA
| | - Daniel Geschwind
- UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Mandy Johnstone
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Shelagh Joss
- West of Scotland Genetics Service, South Glasgow University Hospitals, Glasgow, UK
| | - Georg Kirov
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jarmo Körkkö
- Center for Intellectual Disability Care, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Outi Kuismin
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Conrad Iyegbe
- Institute of Psychiatry, Kings College London, London, UK
| | - Jouko Lönnqvist
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Minna Männikkö
- Center for Life Course Epidemiology and Systems Medicine, University of Oulu, Oulu, Finland
| | - Steve A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Peter McGuffin
- Institute of Psychiatry, Kings College London, London, UK
| | - Andrew M McIntosh
- Division of Psychiatry, The University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Andrew McQuillin
- University College London, Molecular Psychiatry Laboratory, Division of Psychiatry, London, UK
| | - Jukka S Moilanen
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Carmel Moore
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robin M Murray
- Institute of Psychiatry, Kings College London, London, UK.,NIHR BRC for Mental Health, Institute of Psychiatry and SLaM NHS Trust, King's College London, London, UK
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, St Michael's Hospital, Bristol, UK
| | - Willem Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Department of Haemotology, University of Cambridge, Cambridge, UK.,NHS Blood and Transplant, Cambridge, UK
| | - Tiina Paunio
- National Institute for Health and Welfare (THL), Helsinki, Finland.,University of Helsinki, Department of Psychiatry, Helsinki, Finland
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - David Roberts
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,NHS Blood and Transplant Oxford Centre, John Radcliffe Hospital, Oxford, UK.,Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jennifer Sambrook
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Department of Haemotology, University of Cambridge, Cambridge, UK
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Juha Veijola
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Hywel Williams
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | | | | | | | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics &Genomics, Institute of Psychological Medicine &Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Aarno Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael J Owen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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47
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Russo M, Mahon K, Shanahan M, Ramjas E, Solon C, Purcell SM, Burdick KE. The relationship between sleep quality and neurocognition in bipolar disorder. J Affect Disord 2015; 187:156-62. [PMID: 26339925 PMCID: PMC4598049 DOI: 10.1016/j.jad.2015.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/15/2015] [Accepted: 08/04/2015] [Indexed: 01/01/2023]
Abstract
BACKGROUNDS Sleep and circadian rhythm disruptions are prominent, trait-like features of bipolar disorder (BD) which precede the onset of mood episodes. Neurocognitive impairments also characterize BD not only during acute phases of the illness but also during remission. Although the relationship between these two debilitating aspects of the illness might seem intuitive, very little is known about their relationship. We examined the association between sleep dysfunction and neurocognition in BD. METHODS In a sample of 117 BD patients (mean age=45.0±10.7; 59.0% (n=69) male), neurocognitive functioning was assessed using the MATRICS Consensus Cognitive Battery (MCCB). Sleep quality data were collected using the Epworth Sleepiness Scale (ESS) and the Pittsburgh Sleep Quality Index (PSQI). Partial Pearson correlations tested for a relationship between sleep and neurocognition. Path analyses were conducted to examine the hypothesized direct influence of sleep disruption on neurocognition. RESULTS Higher levels of sleep disruptions were associated with a more severe clinical presentation and poorer performance in social cognition, visual learning and working memory. Social cognition and working memory were directly (negatively) predicted by sleep disruptions. LIMITATIONS The study was limited by a relatively small sample size and the lack of behavioral and biological objectives measure of activity/rest cycles. CONCLUSIONS Our study suggests that in patients with BD, sleep disruptions have a detrimental effect on general level of psychopathology and contribute directly to impaired cognitive functioning in the domains of social cognition and working memory. More research using objective measurement of sleep should be pursued to support these data and to further investigate the causal relationship between these disabling aspects of the illness.
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Affiliation(s)
- Manuela Russo
- Icahn School of Medicine at Mount Sinai; Departments of Psychiatry and Neuroscience
| | - Katie Mahon
- Icahn School of Medicine at Mount Sinai; Departments of Psychiatry and Neuroscience
| | - Megan Shanahan
- Icahn School of Medicine at Mount Sinai; Departments of Psychiatry and Neuroscience
| | - Elizabeth Ramjas
- Icahn School of Medicine at Mount Sinai; Departments of Psychiatry and Neuroscience
| | - Carly Solon
- Icahn School of Medicine at Mount Sinai; Departments of Psychiatry and Neuroscience
| | - Shaun M Purcell
- Icahn School of Medicine at Mount Sinai; Departments of Psychiatry and Neuroscience
| | - Katherine E Burdick
- Icahn School of Medicine at Mount Sinai, Departments of Psychiatry and Neuroscience, United States; James J Peters VA Medical Center Bronx, NY, United States.
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48
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Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 2015; 348:666-9. [PMID: 25954003 PMCID: PMC4537935 DOI: 10.1126/science.1261877] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Accurate prediction of the functional effect of genetic variation is critical for clinical genome interpretation. We systematically characterized the transcriptome effects of protein-truncating variants, a class of variants expected to have profound effects on gene function, using data from the Genotype-Tissue Expression (GTEx) and Geuvadis projects. We quantitated tissue-specific and positional effects on nonsense-mediated transcript decay and present an improved predictive model for this decay. We directly measured the effect of variants both proximal and distal to splice junctions. Furthermore, we found that robustness to heterozygous gene inactivation is not due to dosage compensation. Our results illustrate the value of transcriptome data in the functional interpretation of genetic variants.
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Affiliation(s)
- Manuel A Rivas
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
| | - Matti Pirinen
- FInstitute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Monkol Lek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Emily K Tsang
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA. Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Konrad J Karczewski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Julian B Maller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kimberly R Kukurba
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Menachem Fromer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. Department of Psychiatry, Mt. Sinai Hospital, NY, USA
| | - Pedro G Ferreira
- Department of Genetic Medicine and Development,University of Geneva, Geneva, Switzerland. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland. Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Kevin S Smith
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rui Zhang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Fengmei Zhao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Banks
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan Poplin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Douglas M Ruderfer
- Department of Psychiatry, Mt. Sinai Hospital, NY, USA. Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Shaun M Purcell
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. Department of Psychiatry, Mt. Sinai Hospital, NY, USA. Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Taru Tukiainen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric V Minikel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | | | | | - Jared Nedzel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Roderic Guigo
- Center for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. Department of Statistics, University of Oxford, Oxford, UK
| | | | - Michael Sammeth
- Center for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain. National Institute for Scientific Computing (LNCC), Petropolis, Rio de Janeiro, Brazil
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development,University of Geneva, Geneva, Switzerland. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland. Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. Oxford Center for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Pathology, Stanford University, Stanford, CA, USA
| | - Tuuli Lappalainen
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Genetic Medicine and Development,University of Geneva, Geneva, Switzerland. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland. Swiss Institute of Bioinformatics, Geneva, Switzerland. New York Genome Center, New York, NY, USA. Department of Systems Biology, Columbia University, New York, NY, USA.
| | - Daniel G MacArthur
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA. Department of Medicine, Harvard Medical School, Boston, MA, USA.
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49
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Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 2015. [PMID: 25722852 DOI: 10.1186/s13742-015–0047-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. FINDINGS To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, [Formula: see text]-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). CONCLUSIONS The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.
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Affiliation(s)
- Christopher C Chang
- Complete Genomics, 2071 Stierlin Court, Mountain View, 94043 CA USA ; BGI Cognitive Genomics Lab, Building No. 11, Bei Shan Industrial Zone, Yantian District, Shenzhen, 518083 China
| | - Carson C Chow
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, 20892 MD USA
| | - Laurent Cam Tellier
- BGI Cognitive Genomics Lab, Building No. 11, Bei Shan Industrial Zone, Yantian District, Shenzhen, 518083 China ; Bioinformatics Centre, University of Copenhagen, Copenhagen, 2200 Denmark
| | - Shashaank Vattikuti
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, 20892 MD USA
| | - Shaun M Purcell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA ; Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA ; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA ; Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, 02114 MA USA
| | - James J Lee
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, 20892 MD USA ; Department of Psychology, University of Minnesota Twin Cities, Minneapolis, 55455 MN USA
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Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 2015; 4:7. [PMID: 25722852 PMCID: PMC4342193 DOI: 10.1186/s13742-015-0047-8] [Citation(s) in RCA: 5827] [Impact Index Per Article: 647.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/26/2015] [Indexed: 11/10/2022] Open
Abstract
Background PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1’s primary data format. Findings To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, \documentclass[12pt]{minimal}
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\begin{document} $O\left (\sqrt {n}\right)$ \end{document}On-time/constant-space Hardy-Weinberg equilibrium and Fisher’s exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). Conclusions The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0047-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher C Chang
- Complete Genomics, 2071 Stierlin Court, Mountain View, 94043 CA USA ; BGI Cognitive Genomics Lab, Building No. 11, Bei Shan Industrial Zone, Yantian District, Shenzhen, 518083 China
| | - Carson C Chow
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, 20892 MD USA
| | - Laurent Cam Tellier
- BGI Cognitive Genomics Lab, Building No. 11, Bei Shan Industrial Zone, Yantian District, Shenzhen, 518083 China ; Bioinformatics Centre, University of Copenhagen, Copenhagen, 2200 Denmark
| | - Shashaank Vattikuti
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, 20892 MD USA
| | - Shaun M Purcell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, 02142 MA USA ; Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA ; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA ; Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, 02114 MA USA
| | - James J Lee
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, 20892 MD USA ; Department of Psychology, University of Minnesota Twin Cities, Minneapolis, 55455 MN USA
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