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Canning J, Strawbridge RJ, Miedzybrodzka Z, Marioni RE, Melbye M, Porteous DJ, Hurles ME, Sattar N, Sudlow CLM, Collins R, Padmanabhan S, Pell JP. Methods applied to neonatal dried blood spot samples for secondary research purposes: a scoping review. Crit Rev Clin Lab Sci 2024:1-24. [PMID: 38855982 DOI: 10.1080/10408363.2024.2360996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
This scoping review aimed to synthesize the analytical techniques used and methodological limitations encountered when undertaking secondary research using residual neonatal dried blood spot (DBS) samples. Studies that used residual neonatal DBS samples for secondary research (i.e. research not related to newborn screening for inherited genetic and metabolic disorders) were identified from six electronic databases: Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Embase, Medline, PubMed and Scopus. Inclusion was restricted to studies published from 1973 and written in or translated into English that reported the storage, extraction and testing of neonatal DBS samples. Sixty-seven studies were eligible for inclusion. Included studies were predominantly methodological in nature and measured various analytes, including nucleic acids, proteins, metabolites, environmental pollutants, markers of prenatal substance use and medications. Neonatal DBS samples were stored over a range of temperatures (ambient temperature, cold storage or frozen) and durations (two weeks to 40.5 years), both of which impacted the recovery of some analytes, particularly amino acids, antibodies and environmental pollutants. The size of DBS sample used and potential contamination were also cited as methodological limitations. Residual neonatal DBS samples retained by newborn screening programs are a promising resource for secondary research purposes, with many studies reporting the successful measurement of analytes even from neonatal DBS samples stored for long periods of time in suboptimal temperatures and conditions.
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Affiliation(s)
- Jordan Canning
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
| | - Rona J Strawbridge
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
- Division of Cardiovascular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Zosia Miedzybrodzka
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, UK
- Medical Genetics Group, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Aberdeen, UK
| | - Riccardo E Marioni
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Mads Melbye
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - David J Porteous
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Naveed Sattar
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Cathie L M Sudlow
- Usher Institute, University of Edinburgh, Edinburgh, UK
- Health Data Research UK, London, UK
| | - Rory Collins
- Clinical Trial Service Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sandosh Padmanabhan
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow, UK
| | - Jill P Pell
- School of Health & Wellbeing, University of Glasgow, Glasgow, UK
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2
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Liu X, Trinh NT, Wray NR, Lupattelli A, Albiñana C, Agerbo E, Vilhjálmsson BJ, Bergink V, Munk-Olsen T. Impact of genetic, sociodemographic, and clinical features on antidepressant treatment trajectories in the perinatal period. Eur Neuropsychopharmacol 2024; 81:20-27. [PMID: 38310717 DOI: 10.1016/j.euroneuro.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/06/2024]
Abstract
Pregnant women on antidepressants must balance potential fetal harm with the relapse risk. While various clinical and sociodemographic factors are known to influence treatment decisions, the impact of genetic factors remains unexplored. We conducted a cohort study among 2,316 women with diagnosed affective disorders who had redeemed antidepressant prescriptions six months before pregnancy, identified from the Danish Integrated Psychiatric Research study. We calculated polygenic risk scores (PGSs) for major depression (MDD), bipolar disorder (BD), and schizophrenia (SCZ) using individual-level genetic data and summary statistics from genome-wide association studies. We retrieved data on sociodemographic and clinical features from national registers. Applying group-based trajectory modeling, we identified four treatment trajectories across pregnancy and postpartum: Continuers (38.2 %), early discontinuers (22.7 %), late discontinuers (23.8 %), and interrupters (15.3 %). All three PGSs were not associated with treatment trajectories; for instance, the relative risk ratio for continuers versus early discontinuers was 0.93 (95 % CI: 0.81-1.06), 0.98 (0.84-1.13), 1.09 (0.95-1.27) for per 1-SD increase in PGS for MDD, BD, and SCZ, respectively. Sociodemographic factors were generally not associated with treatment trajectories, except for the association between primiparity and continuing antidepressant use. Women who received ≥2 classes or a higher dose of antidepressants had a higher probability of being late discontinuers, interrupters, and continuers. The likelihood of continuing antidepressants or restarting antidepressants postpartum increased with the previous antidepressant treatment duration. Our findings indicate that continued antidepressant use during pregnancy is influenced by the severity of the disease rather than genetic predisposition as measured by PGSs.
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Affiliation(s)
- Xiaoqin Liu
- NCRR-The National Centre for Register-based Research, Aarhus University, Denmark; CIRRAU-Centre for Integrated Register-base Research, Aarhus University, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark.
| | - Nhung Th Trinh
- PharmacoEpidemiology and Drug Safety Research Group, Department of Pharmacy, University of Oslo, Norway
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Angela Lupattelli
- PharmacoEpidemiology and Drug Safety Research Group, Department of Pharmacy, University of Oslo, Norway
| | - Clara Albiñana
- NCRR-The National Centre for Register-based Research, Aarhus University, Denmark; CIRRAU-Centre for Integrated Register-base Research, Aarhus University, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Esben Agerbo
- NCRR-The National Centre for Register-based Research, Aarhus University, Denmark; CIRRAU-Centre for Integrated Register-base Research, Aarhus University, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Bjarni J Vilhjálmsson
- NCRR-The National Centre for Register-based Research, Aarhus University, Denmark; CIRRAU-Centre for Integrated Register-base Research, Aarhus University, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Bioinformatics Research Centre, Aarhus University, Denmark
| | - Veerle Bergink
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Trine Munk-Olsen
- NCRR-The National Centre for Register-based Research, Aarhus University, Denmark; CIRRAU-Centre for Integrated Register-base Research, Aarhus University, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Clinical Research, University of Southern Denmark, Denmark
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Woon ST, Tjandra F, Mackay J, Lumley T, Grainger P, Wood A, Hsiao KC, Ameratunga R. Detection of interferon alpha and beta receptor subunit 1 (IFNAR1) loss-of-function Glu386∗ variant by tri-allelic genotyping. Pathology 2024; 56:92-97. [PMID: 37973454 DOI: 10.1016/j.pathol.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/27/2023] [Accepted: 09/11/2023] [Indexed: 11/19/2023]
Abstract
Mutations of the human interferon alpha and beta receptor subunit 1 (IFNAR1) gene are associated with severe viral infections. Individuals homozygous for the Glu386∗ variant have impaired type I interferon signalling and can suffer severe illness when exposed to certain viruses and live attenuated virus vaccines. Glu386∗ heterozygotes are clinically unaffected, but can pass the variant allele to their descendants. We aimed to develop an assay that can identify IFNAR1 Glu386∗ homozygotes and heterozygotes to support urgent clinical diagnosis, and that can use dried blood spots (DBS) sent at ambient temperature to overcome geographical logistical challenges in the South Pacific region. The tri-allelic genotyping assay interrogates a single nucleotide polymorphism (rs201609461) located in IFNAR1. The reference allele G encodes for wild-type IFNAR1. Minor alleles A (c.1156G>A) and T (c.1156G>T) encode for Glu386Lys and a truncated IFNAR1 protein (p.Glu386∗), respectively. Synthetic oligonucleotides were mixed in equal molar ratio to create six different genotypes which were randomly assigned to 960 genotyping reactions by R software. Three different fluorescence probes were designed to discriminate the three alleles (G, T and A) within a pair of flanking primers in a single genotyping reaction. The assay discriminated all three alleles using DBS from Guthrie cards randomly spiked with synthetic oligonucleotides. We correctly identified all the different genotypes in 960 reactions in these blinded experiments. These findings validate the genotyping assay for rapidly identifying the IFNAR1 Glu386∗ variant from DBS.
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Affiliation(s)
- See-Tarn Woon
- Molecular Immunology, LabPLUS, Te Whatu Ora, Health New Zealand Te Toka Tumai Auckland, New Zealand; Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
| | - Felicia Tjandra
- Molecular Immunology, LabPLUS, Te Whatu Ora, Health New Zealand Te Toka Tumai Auckland, New Zealand
| | - John Mackay
- dnature diagnostics and research Limited, Gisborne, New Zealand
| | - Thomas Lumley
- Statistics, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Pippa Grainger
- Diagnostic Genetics, LabPLUS, Te Whatu Ora, Health New Zealand Te Toka Tumai Auckland, New Zealand
| | - Andrew Wood
- Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Starship Children's Health, Te Whatu Ora, Health New Zealand Te Toka Tumai Auckland, New Zealand
| | - Kuang-Chih Hsiao
- Starship Children's Health, Te Whatu Ora, Health New Zealand Te Toka Tumai Auckland, New Zealand
| | - Rohan Ameratunga
- Molecular Immunology, LabPLUS, Te Whatu Ora, Health New Zealand Te Toka Tumai Auckland, New Zealand; Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; Clinical Immunology, Te Whatu Ora, Health New Zealand Te Toka Tumai Auckland, New Zealand
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4
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Munk-Olsen T, Di Florio A, Madsen KB, Albiñana C, Mægbæk ML, Bergink V, Frøkjær VG, Agerbo E, Vilhjálmsson BJ, Werge T, Nordentoft M, Hougaard DM, Børglum AD, Mors O, Mortensen PB, Liu X. Postpartum and non-postpartum depression: a population-based matched case-control study comparing polygenic risk scores for severe mental disorders. Transl Psychiatry 2023; 13:346. [PMID: 37953300 PMCID: PMC10641081 DOI: 10.1038/s41398-023-02649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/23/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023] Open
Abstract
It remains inconclusive whether postpartum depression (PPD) and depression with onset outside the postpartum period (MDD) are genetically distinct disorders. We aimed to investigate whether polygenic risk scores (PGSs) for major mental disorders differ between PPD cases and MDD cases in a nested case-control study of 50,057 women born from 1981 to 1997 in the iPSYCH2015 sample in Demark. We identified 333 women with first-onset postpartum depression (PPD group), who were matched with 993 women with first-onset depression diagnosed outside of postpartum (MDD group), and 999 female population controls. Data on genetics and depressive disorders were retrieved from neonatal biobanks and the Psychiatric Central Research Register. PGSs were calculated from both individual-level genetic data and meta-analysis summary statistics from the Psychiatric Genomics Consortium. Conditional logistic regression was used to calculate the odds ratio (OR), accounting for the selection-related reproductive behavior. After adjustment for covariates, higher PGSs for severe mental disorders were associated with increased ORs of both PPD and MDD. Compared with MDD cases, MDD PGS and attention-deficit/hyperactivity disorder PGS were marginally but not statistically higher for PPD cases, with the OR of PPD versus MDD being 1.12 (95% CI: 0 .97-1.29) and 1.11 (0.97-1.27) per-standard deviation increase, respectively. The ORs of PPD versus MDD did not statistically differ by PGSs of bipolar disorder, schizophrenia, or autism spectrum disorder. Our findings suggest that relying on PGS data, there was no clear evidence of distinct genetic make-up of women with depression occurring during or outside postpartum, after taking the selection-related reproductive behavior into account.
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Affiliation(s)
- Trine Munk-Olsen
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Arianna Di Florio
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Kathrine B Madsen
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Clara Albiñana
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Merete L Mægbæk
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Veerle Bergink
- Department of Psychiatry, Erasmus Medical Centre Rotterdam, Rotterdam, The Netherlands
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Vibe G Frøkjær
- Department of Neurology and Neurobiology Research Unit, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Esben Agerbo
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU-Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Bjarni J Vilhjálmsson
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU-Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - 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
| | - Merete Nordentoft
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Clinical Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
- CORE- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - David M Hougaard
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Anders D Børglum
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, CGPM, Aarhus University, Aarhus, Denmark
| | - Ole Mors
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Risskov, Denmark
| | - Preben Bo Mortensen
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- CIRRAU-Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Xiaoqin Liu
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.
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5
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Ersig AL, Jaja C, Tluczek A. Call to Action for Advancing Equitable Genomic Newborn Screening. Public Health Genomics 2023; 26:188-193. [PMID: 37848010 PMCID: PMC10664321 DOI: 10.1159/000534648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Affiliation(s)
- Anne L. Ersig
- School of Nursing, University of Wisconsin-Madison, Madison, WI, USA
| | - Cheedy Jaja
- College of Nursing, University of South Florida, Tampa, FL, USA
| | - Audrey Tluczek
- School of Nursing, University of Wisconsin-Madison, Madison, WI, USA
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6
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Vaez M, Montalbano S, Sánchez XC, Georgii Hellberg KL, Rasekhi Dehkordi S, Dybdahl Krebs M, Meijsen J, Shorter J, Byberg-Grauholm J, Mortensen PB, Børglum AD, Hougaard DM, Nordentoft M, Geschwind DH, Buil A, Schork AJ, Helenius D, Raznahan A, Thompson WK, Werge T, Ingason A. Population-based Risk of Psychiatric Disorders Associated with Recurrent CNVs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.04.23294975. [PMID: 37886536 PMCID: PMC10602037 DOI: 10.1101/2023.09.04.23294975] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Recurrent copy number variants (rCNVs) are associated with increased risk of neuropsychiatric disorders but their pathogenic population-level impact is unknown. We provide population-based estimates of rCNV-associated risk of neuropsychiatric disorders for 34 rCNVs in the iPSYCH2015 case-cohort sample (n=120,247). Most observed significant increases in rCNV-associated risk for ADHD, autism or schizophrenia were moderate (HR:1.42-5.00), and risk estimates were highly correlated across these disorders, the most notable exception being high autism-associated risk with Prader-Willi/Angelman Syndrome duplications (HR=20.8). No rCNV was associated with significant increase in depression risk. Also, rCNV-associated risk was positively correlated with locus size and gene constraint. Comparison with published rCNV studies suggests that prevalence of some rCNVs is higher, and risk of psychiatric disorders lower, than previously estimated. In an era where genetics is increasingly being clinically applied, our results highlight the importance of population-based risk estimates for genetics-based predictions.
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Affiliation(s)
- Morteza Vaez
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Simone Montalbano
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Xabier Calle Sánchez
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Kajsa-Lotta Georgii Hellberg
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Saeid Rasekhi Dehkordi
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Morten Dybdahl Krebs
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Joeri Meijsen
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - John Shorter
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark
| | - Jonas Byberg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Preben B Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- National Centre for Register-based Research, Aarhus University, DK-8210 Aarhus, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Department of Biomedicine-Human Genetics and the iSEQ Center, Aarhus University, DK-8000 Aarhus, Denmark
- Center for Genomics and Personalized Medicine, DK-8000 Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, DK-2400 Copenhagen, Denmark
| | - Daniel H Geschwind
- Department of Neurology, University of California, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Center for Human Development, University of California, San Diego, CA, USA
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, DK-1350 Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Dorte Helenius
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Wesley K Thompson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Laureate Institute for Brain Research, Tulsa, OK, USA
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, DK-1350 Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Andrés Ingason
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, DK-4000 Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, DK-1350 Copenhagen, Denmark
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7
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Als TD, Kurki MI, Grove J, Voloudakis G, Therrien K, Tasanko E, Nielsen TT, Naamanka J, Veerapen K, Levey DF, Bendl J, Bybjerg-Grauholm J, Zeng B, Demontis D, Rosengren A, Athanasiadis G, Bækved-Hansen M, Qvist P, Bragi Walters G, Thorgeirsson T, Stefánsson H, Musliner KL, Rajagopal VM, Farajzadeh L, Thirstrup J, Vilhjálmsson BJ, McGrath JJ, Mattheisen M, Meier S, Agerbo E, Stefánsson K, Nordentoft M, Werge T, Hougaard DM, Mortensen PB, Stein MB, Gelernter J, Hovatta I, Roussos P, Daly MJ, Mors O, Palotie A, Børglum AD. Depression pathophysiology, risk prediction of recurrence and comorbid psychiatric disorders using genome-wide analyses. Nat Med 2023; 29:1832-1844. [PMID: 37464041 PMCID: PMC10839245 DOI: 10.1038/s41591-023-02352-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 04/17/2023] [Indexed: 07/20/2023]
Abstract
Depression is a common psychiatric disorder and a leading cause of disability worldwide. Here we conducted a genome-wide association study meta-analysis of six datasets, including >1.3 million individuals (371,184 with depression) and identified 243 risk loci. Overall, 64 loci were new, including genes encoding glutamate and GABA receptors, which are targets for antidepressant drugs. Intersection with functional genomics data prioritized likely causal genes and revealed new enrichment of prenatal GABAergic neurons, astrocytes and oligodendrocyte lineages. We found depression to be highly polygenic, with ~11,700 variants explaining 90% of the single-nucleotide polymorphism heritability, estimating that >95% of risk variants for other psychiatric disorders (anxiety, schizophrenia, bipolar disorder and attention deficit hyperactivity disorder) were influencing depression risk when both concordant and discordant variants were considered, and nearly all depression risk variants influenced educational attainment. Additionally, depression genetic risk was associated with impaired complex cognition domains. We dissected the genetic and clinical heterogeneity, revealing distinct polygenic architectures across subgroups of depression and demonstrating significantly increased absolute risks for recurrence and psychiatric comorbidity among cases of depression with the highest polygenic burden, with considerable sex differences. The risks were up to 5- and 32-fold higher than cases with the lowest polygenic burden and the background population, respectively. These results deepen the understanding of the biology underlying depression, its disease progression and inform precision medicine approaches to treatment.
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Affiliation(s)
- Thomas D Als
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Center for Genomics and Personalized Medicine, Aarhus, Denmark.
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Georgios Voloudakis
- Center for Disease Neurogenomics, 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 Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, 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
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J Peters VA Medical Center, Bronx, NY, USA
| | - Karen Therrien
- Center for Disease Neurogenomics, 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 Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, 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
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J Peters VA Medical Center, Bronx, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elisa Tasanko
- Department of Psychology and Logopedics, SleepWell Research Program, University of Helsinki, Helsinki, Finland
| | - Trine Tollerup Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Joonas Naamanka
- Department of Psychology and Logopedics, SleepWell Research Program, University of Helsinki, Helsinki, Finland
| | - Kumar Veerapen
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Daniel F Levey
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, 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 Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, 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
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Biao Zeng
- Center for Disease Neurogenomics, 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 Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, 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
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Anders Rosengren
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - Georgios Athanasiadis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Marie Bækved-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Per Qvist
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | | | | | | | - Katherine L Musliner
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research (NCRR), Business and Social Sciences, Aarhus University, Aarhus, Denmark
- Department of Affective Disorders, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
- The Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Veera M Rajagopal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Leila Farajzadeh
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Janne Thirstrup
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Bjarni J Vilhjálmsson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - John J McGrath
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Manuel Mattheisen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Community Health and Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sandra Meier
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department of Community Health and Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research (NCRR), Business and Social Sciences, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | | | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Clinical Sciences and GLOBE Institute, LF Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research (NCRR), Business and Social Sciences, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - Murray B Stein
- Psychiatry Service, VA San Diego Healthcare System, San Diego, CA, USA
- Departments of Psychiatry and Herbert Wertheim School of Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
| | - Iiris Hovatta
- Department of Psychology and Logopedics, SleepWell Research Program, University of Helsinki, Helsinki, Finland
| | - Panos Roussos
- Center for Disease Neurogenomics, 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 Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, 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
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J Peters VA Medical Center, Bronx, NY, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Center for Genomics and Personalized Medicine, Aarhus, Denmark.
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8
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Effect of storage temperature and duration on direct PCR amplification of various feather types and DBS matrices. Gene 2023; 854:147116. [PMID: 36526120 DOI: 10.1016/j.gene.2022.147116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
The use of direct PCR has been pioneered over the last decade for DNA analysis of biological specimens of distinct origins. The information on how longer these specimens can be stored and amplified by direct PCR is however scanty. Such a piece of information could expedite research and diagnostic studies without compromising the reliability of results. The current study was therefore designed to analyze the effect of storage temperature and duration on direct PCR amplification of biological specimens having either low quantity or high quantity of DNA. Whole blood, dried blood spots (DBS), and feathers from chicken were stored for five years at three different temperatures, viz. room temperature (∼25 °C), 4 °C, and -20 °C. These samples were subjected to crude DNA extraction by diluting them in PBS buffer and heating at 98 °C after 1 day, 7 days, 15 days, 1 month, 3 months, 6 months, 1 year, 3 years and 5 years of storage. The crude DNA was PCR-amplified with the use of DNA sexing primers as well as DNA barcoding primers. Incubation at 98 °C for 10 min of any type of sample in PBS buffer was sufficient for crude DNA extraction. There was irrelevant impact of feather type, DBS matrix nature and storage temperature on amplification success over the period of analysis. It was possible to successfully accomplish the amplification of 96 samples with the use of routine PCR reagents within 3.5-6.0 hrs. In short, economical and fast genetic analysis of commonly used avian samples is feasible after their storage for longer time at room temperature.
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9
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Ding Y, Owen M, Le J, Batalov S, Chau K, Kwon YH, Van Der Kraan L, Bezares-Orin Z, Zhu Z, Veeraraghavan N, Nahas S, Bainbridge M, Gleeson J, Baer RJ, Bandoli G, Chambers C, Kingsmore SF. Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots. NPJ Genom Med 2023; 8:5. [PMID: 36788231 PMCID: PMC9929090 DOI: 10.1038/s41525-023-00349-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 01/05/2023] [Indexed: 02/16/2023] Open
Abstract
Universal newborn screening (NBS) is a highly successful public health intervention. Archived dried bloodspots (DBS) collected for NBS represent a rich resource for population genomic studies. To fully harness this resource in such studies, DBS must yield high-quality genomic DNA (gDNA) for whole genome sequencing (WGS). In this pilot study, we hypothesized that gDNA of sufficient quality and quantity for WGS could be extracted from archived DBS up to 20 years old without PCR (Polymerase Chain Reaction) amplification. We describe simple methods for gDNA extraction and WGS library preparation from several types of DBS. We tested these methods in DBS from 25 individuals who had previously undergone diagnostic, clinical WGS and 29 randomly selected DBS cards collected for NBS from the California State Biobank. While gDNA from DBS had significantly less yield than from EDTA blood from the same individuals, it was of sufficient quality and quantity for WGS without PCR. All samples DBS yielded WGS that met quality control metrics for high-confidence variant calling. Twenty-eight variants of various types that had been reported clinically in 19 samples were recapitulated in WGS from DBS. There were no significant effects of age or paper type on WGS quality. Archived DBS appear to be a suitable sample type for WGS in population genomic studies.
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Affiliation(s)
- Yan Ding
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Mallory Owen
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, 92123, USA.
| | - Jennie Le
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Sergey Batalov
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Kevin Chau
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Yong Hyun Kwon
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Lucita Van Der Kraan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zaira Bezares-Orin
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Zhanyang Zhu
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Narayanan Veeraraghavan
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Shareef Nahas
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Matthew Bainbridge
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA
| | - Joe Gleeson
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Rebecca J. Baer
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA ,grid.266102.10000 0001 2297 6811California Preterm Birth Initiative, University of California San Francisco, San Francisco, CA USA
| | - Gretchen Bandoli
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Christina Chambers
- grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego, La Jolla, CA 92093 USA
| | - Stephen F. Kingsmore
- grid.286440.c0000 0004 0383 2910Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123 USA ,grid.419735.d0000 0004 0615 8415Keck Graduate Institute, Claremont, CA 91711 USA
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10
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Sanchez XC, Montalbano S, Vaez M, Krebs MD, Byberg-Grauholm J, Mortensen PB, Børglum AD, Hougaard DM, Nordentoft M, Geschwind DH, Buil A, Schork AJ, Thompson WK, Raznahan A, Helenius D, Werge T, Ingason A. Associations of psychiatric disorders with sex chromosome aneuploidies in the Danish iPSYCH2015 dataset: a case-cohort study. Lancet Psychiatry 2023; 10:129-138. [PMID: 36697121 PMCID: PMC9976199 DOI: 10.1016/s2215-0366(23)00004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/15/2022] [Accepted: 11/29/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Increased prevalence of mental illness has been reported in clinical studies of sex chromosome aneuploidies, but accurate population-based estimates of the prevalence and clinical detection rate of sex chromosome aneuploidies and the associated risks of psychiatric disorders are needed. In this study, we provide such estimates, valid for children and young adults of the contemporary Danish population. METHODS We used the iPSYCH2015 case-cohort dataset, which is based on a source population of single-born individuals born in Denmark between May 1, 1981, and Dec 31, 2008. The case sample comprises all individuals from the source population with a diagnosis of any index psychiatric disorder (schizophrenia spectrum disorder, bipolar disorder, major depressive disorder, autism spectrum disorder, or ADHD) by the end of follow-up (Dec 31, 2015), registered in the hospital-based Danish Psychiatric Central Research Register. The cohort consists of individuals randomly selected from the source population, and overlaps with the case sample. Biobanked blood samples for individuals in the case and cohort samples underwent genotyping and quality-control filtering, after which we analysed microarray data to detect sex chromosome aneuploidy karyotypes (45,X, 47,XXX, 47,XXY, and 47,XYY). We estimated the population-valid prevalence of these karyotypes from the cohort sample. Weighted Cox proportional hazards models were used to estimate the risks of each index psychiatric disorder associated with each sex chromosome aneuploidy karyotype, by use of date of first hospitalisation with the index disorder in the respective case group and the cohort as outcome. The clinical detection rate was determined by comparing records of clinical diagnoses of genetic conditions from the Danish National Patient Register with sex chromosome aneuploidy karyotype determined by our study. FINDINGS The assessed sample comprised 119 481 individuals (78 726 in the case sample and 43 326 in the cohort) who had genotyped and quality-control-filtered blood samples, including 64 533 (54%) people of gonadal male sex and 54 948 (46%) of gonadal female sex. Age during follow-up ranged from 0 to 34·7 years (mean 10·9 years [SD 3·5 years]). Information on ethnicity was not available. We identified 387 (0·3%) individuals as carriers of sex chromosome aneuploidies. The overall prevalence of sex chromosome aneuploidies was 1·5 per 1000 individuals. Each sex chromosome aneuploidy karyotype was associated with an increased risk of at least one index psychiatric disorder, with hazard ratios (HRs) of 2·20 (95% CI 1·42-3·39) for 47,XXY; 2·73 (1·25-6·00) for 47,XXX; 3·56 (1·01-12·53) for 45,X; and 4·30 (2·48-7·55) for 47,XYY. All karyotypes were associated with an increased risk of ADHD (HRs ranging from 1·99 [1·24-3·19] to 6·15 [1·63-23·19]), autism spectrum disorder (2·72 [1·72-4·32] to 8·45 [2·49-28·61]), and schizophrenia spectrum disorder (1·80 [1·15-2·80] to 4·60 [1·57-13·51]). Increased risk of major depressive disorder was found for individuals with 47,XXY (1·88 [1·07-3·33]) and 47,XYY (2·65 [1·12-5·90]), and of bipolar disorder for those with 47,XXX (4·32 [1·12-16·62]). The proportion of sex chromosome aneuploidy carriers who had been clinically diagnosed was 93% for 45,X, but lower for 47,XXY (22%), 47,XXX (15%), and 47,XYY (15%). Among carriers, the risk of diagnosis of at least one index psychiatric disorder did not significantly differ between those who had and had not been clinically diagnosed with sex chromosome aneuploidies (p=0·65). INTERPRETATION Increased risks of psychiatric disorders associated with sex chromosome aneuploidies, combined with low rates of clinical diagnosis of sex chromosome aneuploidies, compromise the adequate provision of necessary health care and counselling to affected individuals and their families, which might be helped by increased application of genetic testing in clinical settings. FUNDING Lundbeck Foundation and National Institutes of Health.
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Affiliation(s)
- Xabier Calle Sanchez
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Simone Montalbano
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Morteza Vaez
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Morten Dybdahl Krebs
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Jonas Byberg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B. Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Anders D. Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Department of Biomedicine – Human Genetics and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - David M. Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Daniel H Geschwind
- Department of Neurology, University of California, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Center for Human Development, University of California, San Diego, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine at UCLA, University of California Los Angeles, CA, USA
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J. Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Wesley K. Thompson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Laureate Institute for Brain Research, Tulsa, OK USA
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA
| | - Dorte Helenius
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen and Aarhus, Denmark
- Lundbeck Foundation Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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11
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Musliner KL, Andersen KK, Agerbo E, Albiñana C, Vilhjalmsson BJ, Rajagopal VM, Bybjerg-Grauholm J, Bækved-Hansen M, Pedersen CB, Pedersen MG, Munk-Olsen T, Benros ME, Als TD, Grove J, Werge T, Børglum AD, Hougaard DM, Mors O, Nordentoft M, Mortensen PB, Suppli NP. Polygenic liability, stressful life events and risk for secondary-treated depression in early life: a nationwide register-based case-cohort study. Psychol Med 2023; 53:217-226. [PMID: 33949298 DOI: 10.1017/s0033291721001410] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND In this study, we examined the relationship between polygenic liability for depression and number of stressful life events (SLEs) as risk factors for early-onset depression treated in inpatient, outpatient or emergency room settings at psychiatric hospitals in Denmark. METHODS Data were drawn from the iPSYCH2012 case-cohort sample, a population-based sample of individuals born in Denmark between 1981 and 2005. The sample included 18 532 individuals who were diagnosed with depression by a psychiatrist by age 31 years, and a comparison group of 20 184 individuals. Information on SLEs was obtained from nationwide registers and operationalized as a time-varying count variable. Hazard ratios and cumulative incidence rates were estimated using Cox regressions. RESULTS Risk for depression increased by 35% with each standard deviation increase in polygenic liability (p < 0.0001), and 36% (p < 0.0001) with each additional SLE. There was a small interaction between polygenic liability and SLEs (β = -0.04, p = 0.0009). The probability of being diagnosed with depression in a hospital-based setting between ages 15 and 31 years ranged from 1.5% among males in the lowest quartile of polygenic liability with 0 events by age 15, to 18.8% among females in the highest quartile of polygenic liability with 4+ events by age 15. CONCLUSIONS These findings suggest that although there is minimal interaction between polygenic liability and SLEs as risk factors for hospital-treated depression, combining information on these two important risk factors could potentially be useful for identifying high-risk individuals.
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Affiliation(s)
- Katherine L Musliner
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
| | - Klaus K Andersen
- Unit for Statistics and Pharmacoepidemiology (SPE), Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Clara Albiñana
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
| | - Bjarni J Vilhjalmsson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Veera M Rajagopal
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Center for Genome Analysis and Personalized Medicine, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Marie Bækved-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Carsten B Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Marianne G Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Trine Munk-Olsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
| | - Michael E Benros
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas D Als
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Genome Analysis and Personalized Medicine, Aarhus, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Preben B Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- National Center for Register-based Research, Department of Economics, Aarhus University, Aarhus, Denmark
- The Center for Integrated Register-based Research at Aarhus University (CIRRAU), Aarhus, Denmark
| | - Nis P Suppli
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
- Mental Health Center Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
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12
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Tluczek A, Ersig AL, Lee S. Psychosocial Issues Related to Newborn Screening: A Systematic Review and Synthesis. Int J Neonatal Screen 2022; 8:ijns8040053. [PMID: 36278623 PMCID: PMC9589938 DOI: 10.3390/ijns8040053] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 11/20/2022] Open
Abstract
Genomic advances have contributed to a proliferation of newborn screening (NBS) programs. Psychosocial consequences of NBS have been identified as risks to these public health initiatives. Following PRISMA guidelines, this systematic review synthesizes findings from 92 evidence-based, peer-reviewed research reports published from 2000 through 2020 regarding psychosocial issues associated with NBS. Results describe parents' knowledge of and attitudes towards NBS, reactions to and understanding of positive NBS results, experiences of communication with health providers, decisions about carrier testing, and future pregnancies. Findings also explain the impact of positive NBS results on parent-child relationships, child development, informing children about carrier status, family burden, quality of life, and disparities. In conclusion, psychosocial consequences of receiving unexpected neonatal screening results and unsolicited genetic information remain significant risks to expansion of NBS. Findings suggest that risks may be mitigated by improved parent NBS education, effective communication, individualized genetic counseling, and anticipatory developmental guidance. Clinicians need to take extra measures to ensure equitable service delivery to marginalized subpopulations. Future investigations should be more inclusive of culturally and socioeconomically diverse families and conducted in low-resource countries. Providing these countries with adequate resources to develop NBS programs is an essential step towards achieving international health equity.
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Affiliation(s)
- Audrey Tluczek
- School of Nursing, University of Wisconsin-Madison, 701 Highland Ave, Madison, WI 53705, USA
- Correspondence:
| | - Anne L. Ersig
- School of Nursing, University of Wisconsin-Madison, 701 Highland Ave, Madison, WI 53705, USA
| | - Shinhyo Lee
- School of Nursing, Columbia University, 560 W 168th St, New York, NY 10032, USA
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13
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Eliasen AU, Pedersen CET, Rasmussen MA, Wang N, Soverini M, Fritz A, Stokholm J, Chawes BL, Morin A, Bork-Jensen J, Grarup N, Pedersen O, Hansen T, Linneberg A, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J, Bækvad-Hansen M, Mors O, Nordentoft M, Børglum AD, Werge T, Agerbo E, Söderhall C, Altman MC, Thysen AH, McKennan CG, Brix S, Gern JE, Ober C, Ahluwalia TS, Bisgaard H, Pedersen AG, Bønnelykke K. Genome-wide study of early and severe childhood asthma identifies interaction between CDHR3 and GSDMB. J Allergy Clin Immunol 2022; 150:622-630. [PMID: 35381269 DOI: 10.1016/j.jaci.2022.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Asthma with severe exacerbation is one of the most common causes of hospitalization among young children. Exacerbations are typically triggered by respiratory infections, but the host factors causing recurrent infections and exacerbations in some children are poorly understood. As a result, current treatment options and preventive measures are inadequate. OBJECTIVE We sought to identify genetic interaction associated with the development of childhood asthma. METHODS We performed an exhaustive search for pairwise interaction between genetic single nucleotide polymorphisms using 1204 cases of a specific phenotype of early childhood asthma with severe exacerbations in patients aged 2 to 6 years combined with 5328 nonasthmatic controls. Replication was attempted in 3 independent populations, and potential underlying immune mechanisms were investigated in the COPSAC2010 and COPSAC2000 birth cohorts. RESULTS We found evidence of interaction, including replication in independent populations, between the known childhood asthma loci CDHR3 and GSDMB. The effect of CDHR3 was dependent on the GSDMB genotype, and this interaction was more pronounced for severe and early onset of disease. Blood immune analyses suggested a mechanism related to increased IL-17A production after viral stimulation. CONCLUSIONS We found evidence of interaction between CDHR3 and GSDMB in development of early childhood asthma, possibly related to increased IL-17A response to viral infections. This study demonstrates the importance of focusing on specific disease subtypes for understanding the genetic mechanisms of asthma.
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Affiliation(s)
- Anders U Eliasen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Casper Emil T Pedersen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Ni Wang
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Soverini
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Fritz
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bo L Chawes
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Andréanne Morin
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preben B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; National Center for Register-Based Research (NCRR), Business and Social Sciences, Aarhus University, Aarhus, Denmark; Center for Integrated Register-Based Research (CIRRAU), Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; Department for Congenital Disorders, Statens Serum Institut (SSI), Copenhagen, Denmark; Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; Department for Congenital Disorders, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Risskov, Denmark
| | - Merete Nordentoft
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anders D Børglum
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; Center for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Institute of Clinical Medicine and GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Aarhus, Denmark; National Center for Register-Based Research (NCRR), Business and Social Sciences, Aarhus University, Aarhus, Denmark; Center for Integrated Register-Based Research (CIRRAU), Aarhus University, Aarhus, Denmark
| | - Cilla Söderhall
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Wash
| | - Matthew C Altman
- Department of Medicine, University of Washington, Seattle, Sweden
| | - Anna H Thysen
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Chris G McKennan
- Department of Statistics, University of Pittsburgh, Pittsburgh, Pa
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wis
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark; Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Anders G Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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14
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Rajagopal VM, Duan J, Vilar-Ribó L, Grove J, Zayats T, Ramos-Quiroga JA, Satterstrom FK, Artigas MS, Bybjerg-Grauholm J, Bækvad-Hansen M, Als TD, Rosengren A, Daly MJ, Neale BM, Nordentoft M, Werge T, Mors O, Hougaard DM, Mortensen PB, Ribasés M, Børglum AD, Demontis D. Differences in the genetic architecture of common and rare variants in childhood, persistent and late-diagnosed attention-deficit hyperactivity disorder. Nat Genet 2022; 54:1117-1124. [PMID: 35927488 PMCID: PMC10028590 DOI: 10.1038/s41588-022-01143-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 06/22/2022] [Indexed: 02/02/2023]
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with onset in childhood (childhood ADHD); two-thirds of affected individuals continue to have ADHD in adulthood (persistent ADHD), and sometimes ADHD is diagnosed in adulthood (late-diagnosed ADHD). We evaluated genetic differences among childhood (n = 14,878), persistent (n = 1,473) and late-diagnosed (n = 6,961) ADHD cases alongside 38,303 controls, and rare variant differences in 7,650 ADHD cases and 8,649 controls. We identified four genome-wide significant loci for childhood ADHD and one for late-diagnosed ADHD. We found increased polygenic scores for ADHD in persistent ADHD compared with the other two groups. Childhood ADHD had higher genetic overlap with hyperactivity and autism compared with late-diagnosed ADHD and the highest burden of rare protein-truncating variants in evolutionarily constrained genes. Late-diagnosed ADHD had a larger genetic overlap with depression than childhood ADHD and no increased burden in rare protein-truncating variants. Overall, these results suggest a genetic influence on age at first ADHD diagnosis, persistence of ADHD and the different comorbidity patterns among the groups.
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Affiliation(s)
- Veera M Rajagopal
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jinjie Duan
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Jakob Grove
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- BiRC, Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Tetyana Zayats
- 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
- PROMENTA, Department of Psychology, University of Oslo, Oslo, Norway
| | - J Antoni Ramos-Quiroga
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - F Kyle Satterstrom
- 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
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas D Als
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Anders Rosengren
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mark J Daly
- 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
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Benjamin M Neale
- 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
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - Marta Ribasés
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Anders D Børglum
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Ditte Demontis
- Department of Biomedicine (Human Genetics), Aarhus University, Aarhus, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Center for Genomics and Personalized Medicine, Aarhus, Denmark.
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15
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Zhuang YJ, Mangwiro Y, Wake M, Saffery R, Greaves RF. Multi-omics analysis from archival neonatal dried blood spots: limitations and opportunities. Clin Chem Lab Med 2022; 60:1318-1341. [PMID: 35670573 DOI: 10.1515/cclm-2022-0311] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/25/2022] [Indexed: 02/07/2023]
Abstract
Newborn screening (NBS) programs operate in many countries, processing millions of dried bloodspot (DBS) samples annually. In addition to early identification of various adverse health outcomes, these samples have considerable potential as a resource for population-based research that could address key questions related to child health. The feasibility of archival DBS samples for emerging targeted and untargeted multi-omics analysis has not been previously explored in the literature. This review aims to critically evaluate the latest advances to identify opportunities and challenges of applying omics analyses to NBS cards in a research setting. Medline, Embase and PubMed databases were searched to identify studies utilizing DBS for genomic, proteomic and metabolomic assays. A total of 800 records were identified after removing duplicates, of which 23 records were included in this review. These papers consisted of one combined genomic/metabolomic, four genomic, three epigenomic, four proteomic and 11 metabolomic studies. Together they demonstrate that the increasing sensitivity of multi-omic analytical techniques makes the broad use of NBS samples achievable for large cohort studies. Maintaining the pre-analytical integrity of the DBS sample through storage at temperatures below -20 °C will enable this important resource to be fully realized in a research capacity.
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Affiliation(s)
- Yuan-Jessica Zhuang
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Yeukai Mangwiro
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Melissa Wake
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Richard Saffery
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Ronda F Greaves
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
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16
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Urtiaga GO, Domingues WB, Komninou ER, Martins AWS, Blödorn EB, Dellagostin EN, Woloski RDS, Pinto LS, Brum CB, Tovo-Rodrigues L, Campos VF. DNA microarray for forensic intelligence purposes: High-density SNP profiles obtained directly from casework-like samples with and without a DNA purification step. Forensic Sci Int 2022; 332:111181. [PMID: 35042181 DOI: 10.1016/j.forsciint.2022.111181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/16/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
SNP analyses from a forensic intelligence perspective have proven to be an important tool to restrict the number of suspected offenders and find missing persons. DNA microarray assays have been demonstrated as a potential feature in forensic analysis, like such as forensic genetic genealogy. The objective of this study was to describe the results from DNA microarray assay from saliva samples deposited on a glass surface collected from by a double swab technique, commonly applied in crime scenes. Eighteen samples from the same person were subjected to Infinium® Global Screening Array-24 v1.0 (~642.824 SNP markers) in two different protocols - with or without the DNA purification procedure. The measured genotype was compared with a Consensus Genotype, obtained from standard control samples, and the parameters such as Call Rate and GenCall Scores were evaluated. Results showed that the Call Rate parameter is enough to estimate the probability of obtaining a correct genotype in the SNP assay. Reliable genotypes with a confidence level of more than 90% (at least 90.15%) were observed in Call Rates above 69.41%, regardless of the experimental condition. Our data demonstrate that DNA Microarray from samples collected under conditions such as those found at crime scenes can generate high-density SNP genetic profiles with a confidence level greater than 90%. Enzymatic adjustments and protocol changes may enable DNA microarray assays for crime analysis and investigation purposes eliminating the purification step in the future. Our data suggest that DNA microarray can support criminal investigation teams from a forensic intelligence perspective.
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Affiliation(s)
- Gabriel O Urtiaga
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Núcleo de Identificação, Superintendência da Polícia Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eliza R Komninou
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Amanda W S Martins
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo B Blödorn
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo N Dellagostin
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rafael Dos S Woloski
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano S Pinto
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Clarice B Brum
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciana Tovo-Rodrigues
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius F Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
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17
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Krebs MD, Themudo GE, Benros ME, Mors O, Børglum AD, Hougaard D, Mortensen PB, Nordentoft M, Gandal MJ, Fan CC, Geschwind DH, Schork AJ, Werge T, Thompson WK. Associations between patterns in comorbid diagnostic trajectories of individuals with schizophrenia and etiological factors. Nat Commun 2021; 12:6617. [PMID: 34785645 PMCID: PMC8595374 DOI: 10.1038/s41467-021-26903-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
Schizophrenia is a heterogeneous disorder, exhibiting variability in presentation and outcomes that complicate treatment and recovery. To explore this heterogeneity, we leverage the comprehensive Danish health registries to conduct a prospective, longitudinal study from birth of 5432 individuals who would ultimately be diagnosed with schizophrenia, building individual trajectories that represent sequences of comorbid diagnoses, and describing patterns in the individual-level variability. We show that psychiatric comorbidity is prevalent among individuals with schizophrenia (82%) and multi-morbidity occur more frequently in specific, time-ordered pairs. Three latent factors capture 79% of variation in longitudinal comorbidity and broadly relate to the number of co-occurring diagnoses, the presence of child versus adult comorbidities and substance abuse. Clustering of the factor scores revealed five stable clusters of individuals, associated with specific risk factors and outcomes. The presentation and course of schizophrenia may be associated with heterogeneity in etiological factors including family history of mental disorders.
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Affiliation(s)
- Morten Dybdahl Krebs
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Gonçalo Espregueira Themudo
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Michael Eriksen Benros
- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Aarhus University Hospital, Risskov, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine and iSEQ-Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
| | - David Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus University, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Business and Social Sciences, Aarhus, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael J Gandal
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chun Chieh Fan
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Human Development, University of California, San Diego, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark.
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.
- Center for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Wesley K Thompson
- Institute of Biological Psychiatry, Mental Health Centre Sct Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Division of Biostatistics and Department of Radiology, Population Neuroscience and Genetics Lab, University of California, San Diego, CA, 92093, USA
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18
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Carpentieri D, Colvard A, Petersen J, Marsh W, David-Dirgo V, Huentelman M, Pirrotte P, Sivakumaran TA. Mind the Quality Gap When Banking on Dry Blood Spots. Biopreserv Biobank 2021; 19:136-142. [PMID: 33567235 DOI: 10.1089/bio.2020.0131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Dry blood spots (DBS) offer many advantages over other blood banking protocols due to the reduction of time and equipment needed for collection and the ease of processing, storage, and shipment. In addition, the sample size makes it a very attractive method when considering the banking of small pediatric samples. On that note, the Centers for Disease Control and Prevention (CDC) preanalytical standards for DBS are commonly used in the worldwide mass spectrometry-based inborn errors of metabolism screening programs. However, these guidelines may not apply for analytes and protocols not included in these programs. In fact, the availability of leftover samples and the ongoing interest in protocols outside this scenario are providing us with new DBS biobanking insights. Herein, we review the literature for indicators that should be considered in the design of prospective fit for purpose DBS biobanks, especially for those focused mostly on pediatric and OMIC platforms.
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Affiliation(s)
- David Carpentieri
- Department of Pathology and Laboratory Medicine, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Amber Colvard
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Jackie Petersen
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - William Marsh
- Department of Biorepository, Mayo Clinic, Phoenix, Arizona, USA
| | - Victoria David-Dirgo
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matt Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - T A Sivakumaran
- Department of Pathology, Clinical Genomics, Phoenix Children's Hospital, Phoenix, Arizona, USA
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19
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Demontis D, Walters RK, Rajagopal VM, Waldman ID, Grove J, Als TD, Dalsgaard S, Ribasés M, Bybjerg-Grauholm J, Bækvad-Hansen M, Werge T, Nordentoft M, Mors O, Mortensen PB, Cormand B, Hougaard DM, Neale BM, Franke B, Faraone SV, Børglum AD. Risk variants and polygenic architecture of disruptive behavior disorders in the context of attention-deficit/hyperactivity disorder. Nat Commun 2021; 12:576. [PMID: 33495439 PMCID: PMC7835232 DOI: 10.1038/s41467-020-20443-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 11/30/2020] [Indexed: 11/29/2022] Open
Abstract
Attention-Deficit/Hyperactivity Disorder (ADHD) is a childhood psychiatric disorder often comorbid with disruptive behavior disorders (DBDs). Here, we report a GWAS meta-analysis of ADHD comorbid with DBDs (ADHD + DBDs) including 3802 cases and 31,305 controls. We identify three genome-wide significant loci on chromosomes 1, 7, and 11. A meta-analysis including a Chinese cohort supports that the locus on chromosome 11 is a strong risk locus for ADHD + DBDs across European and Chinese ancestries (rs7118422, P = 3.15×10−10, OR = 1.17). We find a higher SNP heritability for ADHD + DBDs (h2SNP = 0.34) when compared to ADHD without DBDs (h2SNP = 0.20), high genetic correlations between ADHD + DBDs and aggressive (rg = 0.81) and anti-social behaviors (rg = 0.82), and an increased burden (polygenic score) of variants associated with ADHD and aggression in ADHD + DBDs compared to ADHD without DBDs. Our results suggest an increased load of common risk variants in ADHD + DBDs compared to ADHD without DBDs, which in part can be explained by variants associated with aggressive behavior. ADHD is often found to be comorbid with disruptive behavior disorders, but the genetic loci underlying this comorbidity are unknown. Here, the authors have performed a GWAS meta-analysis of ADHD with disruptive behavior disorders, finding three genome-wide significant loci in Europeans, and replicating one in a Chinese cohort.
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Affiliation(s)
- Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,Center for Genomics and Personalized Medicine, Aarhus, Denmark. .,Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark.
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Veera M Rajagopal
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark.,Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Irwin D Waldman
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark.,Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark.,Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
| | - Søren Dalsgaard
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Marta Ribasés
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain.,Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain.,Biomedical Network Research Center on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Maria Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,GLOBE Institute, Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Copenhagen University Hospital, Mental Health Centre Copenhagen Mental Health Services in the Capital Region of Denmark, Hellerup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Aarhus, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | | | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain.,Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Barcelona, Catalonia, Spain
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stephen V Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,Center for Genomics and Personalized Medicine, Aarhus, Denmark. .,Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark.
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20
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Ahluwalia TS, Eliasen AU, Sevelsted A, Pedersen CET, Stokholm J, Chawes B, Bork-Jensen J, Grarup N, Pedersen O, Hansen T, Linneberg A, Sharma A, Weiss ST, Evans MD, Jackson DJ, Morin A, Krogfelt KA, Schjørring S, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J, Bækvad-Hansen M, Mors O, Nordentoft M, Børglum AD, Werge T, Agerbo E, Gern JE, Lemanske RF, Ober C, Pedersen AG, Bisgaard H, Bønnelykke K. FUT2-ABO epistasis increases the risk of early childhood asthma and Streptococcus pneumoniae respiratory illnesses. Nat Commun 2020; 11:6398. [PMID: 33328473 PMCID: PMC7744576 DOI: 10.1038/s41467-020-19814-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
Asthma with severe exacerbation is the most common cause of hospitalization among young children. We aim to increase the understanding of this clinically important disease entity through a genome-wide association study. The discovery analysis comprises 2866 children experiencing severe asthma exacerbation between ages 2 and 6 years, and 65,415 non-asthmatic controls, and we replicate findings in 918 children from the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC) birth cohorts. We identify rs281379 near FUT2/MAMSTR on chromosome 19 as a novel risk locus (OR = 1.18 (95% CI = 1.11-1.25), Pdiscovery = 2.6 × 10-9) as well as a biologically plausible interaction between functional variants in FUT2 and ABO. We further discover and replicate a potential causal mechanism behind this interaction related to S. pneumoniae respiratory illnesses. These results suggest a novel mechanism of early childhood asthma and demonstrates the importance of phenotype-specificity for discovery of asthma genes and epistasis.
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Affiliation(s)
- Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Biology, The Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | - Anders U Eliasen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Astrid Sevelsted
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Casper-Emil T Pedersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael D Evans
- Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | - Andreanne Morin
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department of Biomedicine and iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus C, Denmark
- Center for Genomics and Personalized Medicine, Central Region Denmark, Aarhus C, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | | | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Anders G Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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21
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Liu X, Munk-Olsen T, Albiñana C, Vilhjálmsson BJ, Pedersen EM, Schlünssen V, Bækvad-Hansen M, Bybjerg-Grauholm J, Nordentoft M, Børglum AD, Werge T, Hougaard DM, Mortensen PB, Agerbo E. Genetic liability to major depression and risk of childhood asthma. Brain Behav Immun 2020; 89:433-439. [PMID: 32735934 PMCID: PMC8817239 DOI: 10.1016/j.bbi.2020.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Major depression and asthma frequently co-occur, suggesting shared genetic vulnerability between these two disorders. We aimed to determine whether a higher genetic liability to major depression was associated with increased childhood asthma risk, and if so, whether such an association differed by sex of the child. METHODS We conducted a population-based cohort study comprising 16,687 singletons born between 1991 and 2005 in Denmark. We calculated the polygenic risk score (PRS) for major depression as a measure of genetic liability based on the summary statistics from the Major Depressive Disorder Psychiatric Genomics Consortium collaboration. The outcome was incident asthma from age 5 to 15 years, identified from the Danish National Patient Registry and the Danish National Prescription Registry. Stratified Cox regression was used to analyze the data. RESULTS Greater genetic liability to major depression was associated with an increased asthma risk with a hazard ratio (HR) of 1.06 (95% CI: 1.01-1.10) per standard deviation increase in PRS. Children in the highest major depression PRS quartile had a HR for asthma of 1.20 (95% CI: 1.06-1.36), compared with children in the lowest quartile. However, major depression PRS explained only 0.03% of asthma variance (Pseudo-R2). The HRs of asthma by major depression PRS did not differ between boys and girls. CONCLUSION Our results suggest a shared genetic contribution to major depression and childhood asthma, and there is no evidence of a sex-specific difference in the association.
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Affiliation(s)
- Xiaoqin Liu
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark.
| | - Trine Munk-Olsen
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Clara Albiñana
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Bjarni J Vilhjálmsson
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; CIRRAU-Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Emil M Pedersen
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Vivi Schlünssen
- National Research Center for the Working Environment, Copenhagen, Denmark; Department of Public Health, Environment, Work and Health, Danish Ramazzini Centre, Aarhus University, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Merete Nordentoft
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Mental Health Centre Copenhagen, Copenhagen, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Anders D Børglum
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark; iSEQ, Center for Integrative Sequencing, and Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Capital Region of Denmark, Copenhagen, Denmark
| | - David M Hougaard
- iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; CIRRAU-Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark; iSEQ, Center for Integrative Sequencing, and Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Esben Agerbo
- NCRR-The National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH-Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; CIRRAU-Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
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22
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Dahlin AM, Wibom C, Andersson U, Bybjerg-Grauholm J, Deltour I, Hougaard DM, Scheurer ME, Lau CC, McKean-Cowdin R, Kennedy RJ, Hung LT, Yee J, Margol AS, Barrington-Trimis J, Gauderman WJ, Feychting M, Schüz J, Röösli M, Kjaerheim K, Januszkiewicz-Lewandowska D, Fichna M, Nowak J, Searles Nielsen S, Asgharzadeh S, Mirabello L, Hjalmars U, Melin B. A genome-wide association study on medulloblastoma. J Neurooncol 2020; 147:309-315. [PMID: 32056145 PMCID: PMC7136185 DOI: 10.1007/s11060-020-03424-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/03/2020] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Medulloblastoma is a malignant embryonal tumor of the cerebellum that occurs predominantly in children. To find germline genetic variants associated with medulloblastoma risk, we conducted a genome-wide association study (GWAS) including 244 medulloblastoma cases and 247 control subjects from Sweden and Denmark. METHODS Genotyping was performed using Illumina BeadChips, and untyped variants were imputed using IMPUTE2. RESULTS Fifty-nine variants in 11 loci were associated with increased medulloblastoma risk (p < 1 × 10-5), but none were statistically significant after adjusting for multiple testing (p < 5 × 10-8). Thirteen of these variants were genotyped, whereas 46 were imputed. Genotyped variants were further investigated in a validation study comprising 249 medulloblastoma cases and 629 control subjects. In the validation study, rs78021424 (18p11.23, PTPRM) was associated with medulloblastoma risk with OR in the same direction as in the discovery cohort (ORT = 1.59, pvalidation = 0.02). We also selected seven medulloblastoma predisposition genes for investigation using a candidate gene approach: APC, BRCA2, PALB2, PTCH1, SUFU, TP53, and GPR161. The strongest evidence for association was found for rs201458864 (PALB2, ORT = 3.76, p = 3.2 × 10-4) and rs79036813 (PTCH1, ORA = 0.42, p = 2.6 × 10-3). CONCLUSION The results of this study, including a novel potential medulloblastoma risk loci at 18p11.23, are suggestive but need further validation in independent cohorts.
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Affiliation(s)
- Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Jonas Bybjerg-Grauholm
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Isabelle Deltour
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
- Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - David M Hougaard
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Ching C Lau
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Roberta McKean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rebekah J Kennedy
- Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Long T Hung
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Janis Yee
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Ashley S Margol
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jessica Barrington-Trimis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maria Feychting
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joachim Schüz
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Martin Röösli
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Danuta Januszkiewicz-Lewandowska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Pediatric Oncology, Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Fichna
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Jerzy Nowak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Susan Searles Nielsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Shahab Asgharzadeh
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Saban Research Institute at Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
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23
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Sok P, Lupo PJ, Richard MA, Rabin KR, Ehli EA, Kallsen NA, Davies GE, Scheurer ME, Brown AL. Utilization of archived neonatal dried blood spots for genome-wide genotyping. PLoS One 2020; 15:e0229352. [PMID: 32084225 PMCID: PMC7034898 DOI: 10.1371/journal.pone.0229352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/04/2020] [Indexed: 01/14/2023] Open
Abstract
Introduction Heel pricks are performed on newborns for diagnostic screenings of various pre-symptomatic metabolic and genetic diseases. Excess blood is spotted on Guthrie cards and archived by many states in biobanks for follow-up diagnoses and public health research. However, storage environment may vary across biobanks and across time within biobanks. With increased applications of DNA extracted from spots for genetic studies, identifying factors associated with genotyping success is critical to maximize DNA quality for future studies. Method We evaluated 399 blood spots, which were part of a genome-wide association study of childhood leukemia risk in children with Down syndrome, archived at the Michigan Neonatal Biobank between 1992 and 2008. High quality DNA was defined as having post-quality control call rate ≥ 99.0% based on the Illumina GenomeStudio 2.0 GenCall algorithm after processing the samples on the Illumina Infinium Global Screening Array. Bivariate analyses and multivariable logistic regression models were applied to evaluate effects of storage environment and storage duration on DNA genotyping quality. Results Both storage environment and duration were associated with sample genotyping call rates (p-values < 0.001). Sample call rates were associated with storage duration independent of storage environment (p-trend = 0.006 for DBS archived in an uncontrolled environment and p-trend = 0.002 in a controlled environment). However, 95% of the total sample had high genotyping quality with a call rate ≥ 95.0%, a standard threshold for acceptable sample quality in many genetic studies. Conclusion Blood spot DNA quality was lower in samples archived in uncontrolled storage environments and for samples archived for longer durations. Still, regardless of storage environment or duration, neonatal biobanks including the Michigan Neonatal Biobanks can provide access to large collections of spots with DNA quality acceptable for most genotyping studies.
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Affiliation(s)
- Pagna Sok
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Philip J. Lupo
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Melissa A. Richard
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Karen R. Rabin
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Noah A. Kallsen
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Gareth E. Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Michael E. Scheurer
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
| | - Austin L. Brown
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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24
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Satterstrom FK, Walters RK, Singh T, Wigdor EM, Lescai F, Demontis D, Kosmicki JA, Grove J, Stevens C, Bybjerg-Grauholm J, Bækvad-Hansen M, Palmer DS, Maller JB, Nordentoft M, Mors O, Robinson EB, Hougaard DM, Werge TM, Bo Mortensen P, Neale BM, Børglum AD, Daly MJ. Autism spectrum disorder and attention deficit hyperactivity disorder have a similar burden of rare protein-truncating variants. Nat Neurosci 2019; 22:1961-1965. [PMID: 31768057 PMCID: PMC6884695 DOI: 10.1038/s41593-019-0527-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
We analyze the exome sequences of approximately 8,000 children with autism spectrum disorder (ASD) and/or attention-deficit/hyperactivity disorder (ADHD) and 5,000 controls, and we find that ASD and ADHD have a similar burden of rare protein-truncating variants in evolutionarily constrained genes, both significantly higher than controls. This motivates a combined analysis across ASD and ADHD, which identifies microtubule-associated protein 1A (MAP1A) as a novel exome-wide significant gene conferring risk for childhood psychiatric disorders.
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Affiliation(s)
- F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Raymond K Walters
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Emilie M Wigdor
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Francesco Lescai
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jack A Kosmicki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Christine Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Duncan S Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Julian B Maller
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Mental Health Services in the Capital Region of Denmark, Mental Health Centre Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Elise B Robinson
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas M Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Benjamin M Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. .,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland.
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25
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Gasse C, Wimberley T, Wang Y, Mors O, Børglum A, Als TD, Werge T, Nordentoft M, Hougaard DM, Horsdal HT. Schizophrenia polygenic risk scores, urbanicity and treatment-resistant schizophrenia. Schizophr Res 2019; 212:79-85. [PMID: 31447354 DOI: 10.1016/j.schres.2019.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/10/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
INTRODUCTION To investigate the impact of a polygenic risk score for schizophrenia (PRS-SZ) and urbanicity on the risk of treatment-resistant schizophrenia (TRS) in people diagnosed with schizophrenia and to evaluate the association between PRS-SZ and TRS across levels of urbanicity. METHODS Cohort study of people born after 1981 with a first registered diagnosis of schizophrenia between 1996 and 2012 using Danish population registry data. Through linkage to genome-wide data, we calculated PRS-SZ based on a Psychiatric Genomics Consortium meta-analysis. We assessed urbanicity at birth (capital, provincial and rural areas). TRS was defined using prescription and hospital data. Performing Cox regression analysis, we calculated hazard rate ratios (HRs) and 95% confidence intervals (CI). RESULTS Among 4475 people with schizophrenia, we identified 593 (13.3%) with TRS during 17,558 person years of follow-up. The adjusted HR for TRS associated with one standard deviation (SD) increase in the PRS-SZ was 1.11 (95% CI: 1.00-1.24). The adjusted HRs for TRS across levels of urbanicity were 1.20 (95% CI: 0.98-1.47) for provincial areas and 1.19 (95% CI 0.96-1.47) for rural areas compared with the capital area. Within strata of urbanicity, the adjusted HR for TRS was 1.39 (95% CI: 1.14-1.70) in the capital area with 1 SD increase in the PRS-SZ, 0.99 (95% CI 0.84-1.17) in provincial areas, and 1.03 (95% CI: 0.86-1.25) in rural areas. CONCLUSION The effect of genetic liability (i.e. PRS) on risk of TRS varied across urbanicity levels and was highest for people with schizophrenia born in the capital areas.
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Affiliation(s)
- Christiane Gasse
- NCRR - National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; CIRRAU - Centre for Integrated Register-Based Research at Aarhus University, Aarhus, Denmark; Department for Depression and Anxiety, Aarhus University Hospital - Psychiatry, Aarhus, Denmark.
| | - Theresa Wimberley
- NCRR - National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Yungpeng Wang
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States of America; Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, United States of America
| | - Ole Mors
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Psychosis Research Unit, Aarhus University Hospital - Psychiatry, Aarhus, Denmark
| | - Anders Børglum
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Central Region Denmark and Aarhus University, Aarhus, Denmark
| | - Thomas Damm Als
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine and Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark; Center for Genomics and Personalized Medicine, Central Region Denmark and Aarhus University, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Merete Nordentoft
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Copenhagen University Hospital, Mental Health Center Copenhagen, Mental Health Services in the Capital Region of Denmark, Denmark
| | - David M Hougaard
- iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institute, Denmark
| | - Henriette Thisted Horsdal
- NCRR - National Centre for Register-based Research, Aarhus University, Aarhus, Denmark; iPSYCH - The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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26
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Dahlin AM, Wibom C, Andersson U, Hougaard DM, Bybjerg-Grauholm J, Deltour I, Hultman CM, Kähler AK, Karlsson R, Hjalmars U, Melin B. Genetic Variants in the 9p21.3 Locus Associated with Glioma Risk in Children, Adolescents, and Young Adults: A Case-Control Study. Cancer Epidemiol Biomarkers Prev 2019; 28:1252-1258. [PMID: 31040135 DOI: 10.1158/1055-9965.epi-18-1026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/07/2019] [Accepted: 04/26/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified germline genetic variants in 25 genetic loci that increase the risk of developing glioma in adulthood. It is not known if these variants increase the risk of developing glioma in children and adolescents and young adults (AYA). To date, no studies have performed genome-wide analyses to find novel genetic variants associated with glioma risk in children and AYA. METHODS We investigated the association between 8,831,628 genetic variants and risk of glioma in 854 patients diagnosed up to the age of 29 years and 3,689 controls from Sweden and Denmark. Recruitment of patients and controls was population based. Genotyping was performed using Illumina BeadChips, and untyped variants were imputed with IMPUTE2. We selected 41 established adult glioma risk variants for detailed investigation. RESULTS Three adult glioma risk variants, rs634537, rs2157719, and rs145929329, all mapping to the 9p21.3 (CDKN2B-AS1) locus, were associated with glioma risk in children and AYA. The strongest association was seen for rs634537 (odds ratioG = 1.21; 95% confidence interval = 1.09-1.35; P = 5.8 × 10-4). In genome-wide analysis, an association with risk was suggested for 129 genetic variants (P <1 × 10-5). CONCLUSIONS Carriers of risk alleles in the 9p21.3 locus have an increased risk of glioma throughout life. The results from genome-wide association analyses require validation in independent cohorts. IMPACT Our findings line up with existing evidence that some, although not all, established adult glioma risk variants are associated with risk of glioma in children and AYA. Validation of results from genome-wide analyses may reveal novel susceptibility loci for glioma in children and AYA.
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Affiliation(s)
- Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - David M Hougaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Isabelle Deltour
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
- Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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27
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Comparison between different methods of DNA isolation from dried blood spots for determination of malaria to determine specificity and cost effectiveness. J Parasit Dis 2019; 43:337-342. [PMID: 31406397 DOI: 10.1007/s12639-019-01136-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/18/2019] [Indexed: 01/17/2023] Open
Abstract
DNA extraction from filter paper by using different methods was compiled through a thorough review of many research articles published in various journals. When performing malaria epidemiological surveys in remote area, it is difficult to collect blood samples and transport it. In field particularly in remote area where facilities for storing and processing of samples does not exist, there surveillance and diagnosis of malaria is very difficult. In this review we are focused upon four simple methods of DNA isolation from the field collected blood and mosquito abdomen blood meal spotted on Whatman No. 1 or No. 3 filter paper. The main DNA isolation methods are Chelex-100, Tris-EDTA (TE) buffer; Methanol based DNA extraction and Phosphate buffer saline (PBS) using Lysis buffer and Phenol-Chloroform method. Efforts have been taken to identify the methods which are cost-effective and take less time to extract DNA from dried blood spots (DBS) and whole mosquitoes. The purpose of this paper is to update the knowledge and find a method to extract DNA from DBS which will be specific, rapid, cost-effective, less time consuming and feasible for epidemiological survey in remote area.
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28
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Demontis D, Rajagopal VM, Thorgeirsson TE, Als TD, Grove J, Leppälä K, Gudbjartsson DF, Pallesen J, Hjorthøj C, Reginsson GW, Tyrfingsson T, Runarsdottir V, Qvist P, Christensen JH, Bybjerg-Grauholm J, Bækvad-Hansen M, Huckins LM, Stahl EA, Timmermann A, Agerbo E, Hougaard DM, Werge T, Mors O, Mortensen PB, Nordentoft M, Daly MJ, Stefansson H, Stefansson K, Nyegaard M, Børglum AD. Genome-wide association study implicates CHRNA2 in cannabis use disorder. Nat Neurosci 2019; 22:1066-1074. [PMID: 31209380 DOI: 10.1038/s41593-019-0416-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/25/2019] [Indexed: 12/22/2022]
Abstract
Cannabis is the most frequently used illicit psychoactive substance worldwide; around one in ten users become dependent. The risk for cannabis use disorder (CUD) has a strong genetic component, with twin heritability estimates ranging from 51 to 70%. Here we performed a genome-wide association study of CUD in 2,387 cases and 48,985 controls, followed by replication in 5,501 cases and 301,041 controls. We report a genome-wide significant risk locus for CUD (P = 9.31 × 10-12) that replicates in an independent population (Preplication = 3.27 × 10-3, Pmeta-analysis = 9.09 × 10-12). The index variant (rs56372821) is a strong expression quantitative trait locus for cholinergic receptor nicotinic α2 subunit (CHRNA2); analyses of the genetically regulated gene expression identified a significant association of CHRNA2 expression with CUD in brain tissue. At the polygenic level, analyses revealed a significant decrease in the risk of CUD with increased load of variants associated with cognitive performance. The results provide biological insights and inform on the genetic architecture of CUD.
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Affiliation(s)
- Ditte Demontis
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark. .,Center for Genomics and Personalized Medicine, Aarhus, Denmark.
| | - Veera Manikandan Rajagopal
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | | | - Thomas D Als
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jakob Grove
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Kalle Leppälä
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | | | - Jonatan Pallesen
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Carsten Hjorthøj
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Copenhagen University Hospital, Mental Health Centre Copenhagen, Mental Health Services in the Capital Region of Denmark, Hellerup, Denmark
| | | | | | | | - Per Qvist
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jane Hvarregaard Christensen
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Laura M Huckins
- Division of Psychiatric Genomic, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Division of Psychiatric Genomic, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allan Timmermann
- National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- 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
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,National Centre for Register-based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Copenhagen University Hospital, Mental Health Centre Copenhagen, Mental Health Services in the Capital Region of Denmark, Hellerup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Mette Nyegaard
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Anders D Børglum
- Department of Biomedicine-Human Genetics and Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark. .,Center for Genomics and Personalized Medicine, Aarhus, Denmark.
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29
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Wang Y, Karstoft KI, Nievergelt CM, Maihofer AX, Stein MB, Ursano RJ, Bybjerg-Grauholm J, Bækvad-Hansen M, Hougaard DM, Andreassen OA, Werge T, Thompson WK, Andersen SB. Post-traumatic stress following military deployment: Genetic associations and cross-disorder genetic correlations. J Affect Disord 2019; 252:350-357. [PMID: 30999091 DOI: 10.1016/j.jad.2019.04.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/22/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Post-traumatic stress disorder (PTSD) is a complex psychiatric disorder that occurs with relatively high frequency after deployment to warzones (∼10%). While twin studies have estimated the heritability to be up to 40%, thus indicating a considerable genetic component in the etiology, the biological mechanisms underlying risk and development of PTSD remain unknown. METHODS Here, we conduct a genome-wide association study (GWAS; N = 2,481) to identify genome regions that associate with PTSD in a highly homogenous, trauma-exposed sample of Danish soldiers deployed to war and conflict zones. We perform integrated analyses of our results with gene-expression and chromatin-contact datasets to prioritized genes. We also leverage on other large GWAS (N>300,000) to investigate genetic correlations between PTSD and other psychiatric disorders and traits. RESULTS We discover, but do not replicate, one region, 4q31, close to the IL15 gene, which is genome-wide significantly associated with PTSD. We demonstrate that gene-set enrichment, polygenic risk score and genetic correlation analyses show consistent and significant genetic correlations between PTSD and depression, insomnia and schizophrenia. LIMITATIONS The limited sample size, the lack of replication, and the PTSD case definition by questionnaire are limitations to the study. CONCLUSIONS Our results suggest that genetic perturbations of inflammatory response may contribute to the risk of PTSD. In addition, shared genetic components contribute to observed correlations between PTSD and depression, insomnia and schizophrenia.
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Affiliation(s)
- Yunpeng Wang
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Boserupvej 2, DK-4000 Roskilde, Denmark; Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway; Department of Psychology, University of Oslo, Harald Schelderups Hus Forskningsveien 3A 0373 Oslo
| | - Karen-Inge Karstoft
- Research and Knowledge Center, The Danish Veteran Center, Garnisonen 1, 4100 Ringsted, Denmark; Department of Psychology, University of Copenhagen, Øster Farimagsgade 2A, 1353 Copenhagen, Denmark.
| | - Caroline M Nievergelt
- VA Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla Village Drive 3350, 92161 La Jolla, CA, USA; Department of Psychiatry, School of Medicine, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
| | - Adam X Maihofer
- VA Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla Village Drive 3350, 92161 La Jolla, CA, USA; Department of Psychiatry, School of Medicine, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
| | - Murray B Stein
- Department of Psychiatry, School of Medicine, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA; Department of Family Medicine and Public Health, University of California San Diego, Gilman Drive 9500, 92093 La Jolla, CA, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University of the Health Sciences, Jones Bridge Road 4301, 20814 Bethesda, MD, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Boserupvej 2, DK-4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Wesley K Thompson
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Institute of Biological Psychiatry, Mental Health Center St. Hans, Mental Health Services Copenhagen, Boserupvej 2, DK-4000 Roskilde, Denmark; Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway; Division of Biostatistics, Department of Family Medicine and Public Health, University of California, San Diego
| | - Søren B Andersen
- Research and Knowledge Center, The Danish Veteran Center, Garnisonen 1, 4100 Ringsted, Denmark
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30
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Zhao J, Xu Z, You X, Zhao Y, He W, Zhao L, Chen A, Yang S. Genetic traceability practices in a large-size beef company in China. Food Chem 2019; 277:222-228. [PMID: 30502138 DOI: 10.1016/j.foodchem.2018.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
Abstract
An effective and trustworthy traceability system is important for food safety and quality; however, traditional traceability systems that only rely on the recording method do not completely prevent food fraud. DNA-based traceability techniques facilitate seamless connectivity within the entire food supply chain. A convenient and low-cost ear tag device was invented for collecting animal blood samples as an identity control, and a panel including 12 single nucleotide polymorphic (SNP) loci was selected to distinguish individuals with a matching probability of 1.70 × 10-5. The exact animal individual was identified by comparing the SNP genotype barcodes between the meat and blood samples derived from the recording system to further validate authenticity of the recording system. These results illustrate that a combination of the genetic traceability method and a traditional recording system can provide trustworthy traceability for consumers.
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Affiliation(s)
- Jie Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, PR China
| | - Zhenzhen Xu
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xinyong You
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, PR China
| | - Yan Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wenjing He
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Luyao Zhao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ailiang Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
| | - Shuming Yang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agrifood Safety and Quality, Ministry of Agriculture of China, Beijing 100081, PR China; Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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31
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Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, Pallesen J, Agerbo E, Andreassen OA, Anney R, Awashti S, Belliveau R, Bettella F, Buxbaum JD, Bybjerg-Grauholm J, Bækvad-Hansen M, Cerrato F, Chambert K, Christensen JH, Churchhouse C, Dellenvall K, Demontis D, De Rubeis S, Devlin B, Djurovic S, Dumont AL, Goldstein JI, Hansen CS, Hauberg ME, Hollegaard MV, Hope S, Howrigan DP, Huang H, Hultman CM, Klei L, Maller J, Martin J, Martin AR, Moran JL, Nyegaard M, Nærland T, Palmer DS, Palotie A, Pedersen CB, Pedersen MG, dPoterba T, Poulsen JB, Pourcain BS, Qvist P, Rehnström K, Reichenberg A, Reichert J, Robinson EB, Roeder K, Roussos P, Saemundsen E, Sandin S, Satterstrom FK, Davey Smith G, Stefansson H, Steinberg S, Stevens CR, Sullivan PF, Turley P, Walters GB, Xu X, Stefansson K, Geschwind DH, Nordentoft M, Hougaard DM, Werge T, Mors O, Mortensen PB, Neale BM, Daly MJ, Børglum AD. Identification of common genetic risk variants for autism spectrum disorder. Nat Genet 2019; 51:431-444. [PMID: 30804558 DOI: 10.1038/s41588-019-0344-8] [Citation(s) in RCA: 1161] [Impact Index Per Article: 232.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/12/2018] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample-size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 individuals with ASD and 27,969 controls that identified five genome-wide-significant loci. Leveraging GWAS results from three phenotypes with significantly overlapping genetic architectures (schizophrenia, major depression, and educational attainment), we identified seven additional loci shared with other traits at equally strict significance levels. Dissecting the polygenic architecture, we found both quantitative and qualitative polygenic heterogeneity across ASD subtypes. These results highlight biological insights, particularly relating to neuronal function and corticogenesis, and establish that GWAS performed at scale will be much more productive in the near term in ASD.
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Affiliation(s)
- Jakob Grove
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Thomas D Als
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Manuel Mattheisen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany.,Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonatan Pallesen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Esben Agerbo
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Ole A Andreassen
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Richard Anney
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Swapnil Awashti
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Rich Belliveau
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Francesco Bettella
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, 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.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonas Bybjerg-Grauholm
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Felecia Cerrato
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jane H Christensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Claire Churchhouse
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Karin Dellenvall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, 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
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Srdjan Djurovic
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ashley L Dumont
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jacqueline I Goldstein
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Christine S Hansen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.,Institute of Biological Psychiatry, MHC SctHans, Mental Health Services, Copenhagen, Denmark
| | - Mads Engel Hauberg
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Mads V Hollegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Sigrun Hope
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway.,Department of Neurohabilitation, Oslo University Hospital, Oslo, Norway
| | - Daniel P Howrigan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Julian Maller
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Genomics plc, Oxford, UK.,Vertex Pharmaceuticals, Abingdon, UK
| | - Joanna Martin
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mette Nyegaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Terje Nærland
- NORMENT-KG Jebsen Centre for Psychosis Research, University of Oslo, Oslo, Norway.,NevSom, Department of Rare Disorders and Disabilities, , Oslo University Hospital, Oslo, Norway
| | - Duncan S Palmer
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Carsten Bøcker Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Marianne Giørtz Pedersen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Timothy dPoterba
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jesper Buchhave Poulsen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Beate St Pourcain
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Per Qvist
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | | | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, 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
| | - Jennifer Reichert
- Seaver Autism Center for Research and Treatment, 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
| | - Elise B Robinson
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kathryn Roeder
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.,Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Sven Sandin
- Seaver Autism Center for Research and Treatment, 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 Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | | | - Christine R Stevens
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick Turley
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - G Bragi Walters
- deCODE genetics/Amgen, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, 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
| | | | | | | | | | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavík, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Center for Autism Research and Treatment and Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - David M Hougaard
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Institute of Biological Psychiatry, MHC SctHans, Mental Health Services, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark.,Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark. .,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark. .,Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark.
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Gao L, Urman R, Millstein J, Siegmund KD, Dubeau L, Breton CV. Association between AXL promoter methylation and lung function growth during adolescence. Epigenetics 2018; 13:1027-1038. [PMID: 30277126 PMCID: PMC6342069 DOI: 10.1080/15592294.2018.1529517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/19/2018] [Accepted: 09/22/2018] [Indexed: 12/26/2022] Open
Abstract
AXL is one of the TAM (TYRO3, AXL and MERTK) receptor tyrosine kinases and may be involved in airway inflammation. Little is known about how epigenetic changes in AXL may affect lung development during adolescence. We investigated the association between AXL DNA methylation at birth and lung function growth from 10 to 18 years of age in 923 subjects from the Children's Health Study (CHS). DNA methylation from newborn bloodspots was measured at multiple CpG loci across the regulatory regions of AXL using Pyrosequencing. Linear spline mixed-effects models were fitted to assess the association between DNA methylation and 8-year lung function growth. Findings were evaluated for replication in a separate population of 237 CHS subjects using methylation data from the Illumina HumanMethylation450 (HM450) array when possible. A 5% higher average methylation level of the AXL promoter region at birth was associated with a 48.4 ml decrease in mean FEV1 growth from 10 to 18 years of age in the primary study population (95% CI: -100.2, 3.4), and a 53.9 ml decrease in mean FEV1 growth from 11 to 15 years of age in the replication population (95% CI: -104.3, -3.5). One CpG locus in the promoter region, cg10564498, was significantly associated with decreased growth in FEV1, FVC and MMEF from 10 to 18 years of age and the negative associations were observed in a similar age range in the replication population. These findings suggest a potential association between AXL promoter methylation at birth and lower lung function growth during adolescence.
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Affiliation(s)
- Lu Gao
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Robert Urman
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Joshua Millstein
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Louis Dubeau
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Carrie V. Breton
- Department of Preventive Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
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Bäumer C, Fisch E, Wedler H, Reinecke F, Korfhage C. Exploring DNA quality of single cells for genome analysis with simultaneous whole-genome amplification. Sci Rep 2018; 8:7476. [PMID: 29748573 PMCID: PMC5945709 DOI: 10.1038/s41598-018-25895-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Single cell genome analysis methods are powerful tools to define features of single cells and to identify differences between them. Since the DNA amount of a single cell is very limited, cellular DNA usually needs to be amplified by whole-genome amplification before being subjected to further analysis. A single nucleus only contains two haploid genomes. Thus, any DNA damage that prevents amplification results in loss of damaged DNA sites and induces an amplification bias. Therefore, the assessment of single cell DNA quality is urgently required. As of today, there is no simple method to determine the quality of a single cell DNA in a manner that will still retain the entire cellular DNA for amplification and downstream analysis. Here, we describe a method for whole-genome amplification with simultaneous quality control of single cell DNA by using a competitive spike-in DNA template.
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Affiliation(s)
- Christiane Bäumer
- QIAGEN GmbH, Department for Research & Foundation, QIAGEN-Strasse 1, 40724, Hilden, Germany
| | - Evelyn Fisch
- QIAGEN GmbH, Department for Research & Foundation, QIAGEN-Strasse 1, 40724, Hilden, Germany
| | - Holger Wedler
- QIAGEN GmbH, Department for NGS, PCR-Array and WGA-Service, QIAGEN-Strasse 1, 40724, Hilden, Germany
| | - Frank Reinecke
- QIAGEN GmbH, Department for Research & Foundation, QIAGEN-Strasse 1, 40724, Hilden, Germany
| | - Christian Korfhage
- QIAGEN GmbH, Department for Research & Foundation, QIAGEN-Strasse 1, 40724, Hilden, Germany.
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34
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Segundo GRS, Nguyen ATV, Thuc HT, Nguyen LNQ, Kobayashi RH, Le HT, Le HTM, Torgerson TR, Ochs HD. Dried Blood Spots, an Affordable Tool to Collect, Ship, and Sequence gDNA from Patients with an X-Linked Agammaglobulinemia Phenotype Residing in a Developing Country. Front Immunol 2018; 9:289. [PMID: 29503650 PMCID: PMC5820318 DOI: 10.3389/fimmu.2018.00289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/01/2018] [Indexed: 11/16/2022] Open
Abstract
Background New sequencing techniques have revolutionized the identification of the molecular basis of primary immunodeficiency disorders (PID) not only by establishing a gene-based diagnosis but also by facilitating defect-specific treatment strategies, improving quality of life and survival, and allowing factual genetic counseling. Because these techniques are generally not available for physicians and their patients residing in developing countries, collaboration with overseas laboratories has been explored as a possible, albeit cumbersome, strategy. To reduce the cost of time and temperature-sensitive shipping, we selected Guthrie cards, developed for newborn screening, to collect dried blood spots (DBS), as a source of DNA that can be shipped by regular mail at minimal cost. Method Blood was collected and blotted onto the filter paper of Guthrie cards by completely filling three circles. We enrolled 20 male patients with presumptive X-linked agammaglobulinemia (XLA) cared for at the Vietnam National Children’s Hospital, their mothers, and several sisters for carrier analysis. DBS were stored at room temperature until ready to be shipped together, using an appropriately sized envelope, to a CLIA-certified laboratory in the US for sequencing. The protocol for Sanger sequencing was modified to account for the reduced quantity of gDNA extracted from DBS. Result High-quality gDNA could be extracted from every specimen. Bruton tyrosine kinase (BTK) mutations were identified in 17 of 20 patients studied, confirming the diagnosis of XLA in 85% of the study cohort. Type and location of the mutations were similar to those reported in previous reviews. The mean age when XLA was suspected clinically was 4.6 years, similar to that reported by Western countries. Two of 15 mothers, each with an affected boy, had a normal BTK sequence, suggesting gonadal mosaicism. Conclusion DBS collected on Guthrie cards can be shipped inexpensively by airmail across continents, providing sufficient high-quality gDNA for Sanger sequencing overseas. By using this method of collecting gDNA, we were able to confirm the diagnosis of XLA in 17 of 20 Vietnamese patients with the clinical diagnosis of agammaglobulinemia.
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Affiliation(s)
- Gesmar R S Segundo
- University of Washington and Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, Universidade Federal de Uberlandia, Uberlandia, Brazil
| | | | | | | | | | - Hai T Le
- National Children's Hospital, Hanoi, Vietnam
| | | | - Troy R Torgerson
- University of Washington and Seattle Children's Research Institute, Seattle, WA, United States
| | - Hans D Ochs
- University of Washington and Seattle Children's Research Institute, Seattle, WA, United States
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35
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Pedersen CB, Bybjerg-Grauholm J, Pedersen MG, Grove J, Agerbo E, Bækvad-Hansen M, Poulsen JB, Hansen CS, McGrath JJ, Als TD, Goldstein JI, Neale BM, Daly MJ, Hougaard DM, Mors O, Nordentoft M, Børglum AD, Werge T, Mortensen PB. The iPSYCH2012 case-cohort sample: new directions for unravelling genetic and environmental architectures of severe mental disorders. Mol Psychiatry 2018; 23:6-14. [PMID: 28924187 PMCID: PMC5754466 DOI: 10.1038/mp.2017.196] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/06/2017] [Accepted: 07/13/2017] [Indexed: 12/16/2022]
Abstract
The Integrative Psychiatric Research (iPSYCH) consortium has established a large Danish population-based Case-Cohort sample (iPSYCH2012) aimed at unravelling the genetic and environmental architecture of severe mental disorders. The iPSYCH2012 sample is nested within the entire Danish population born between 1981 and 2005, including 1 472 762 persons. This paper introduces the iPSYCH2012 sample and outlines key future research directions. Cases were identified as persons with schizophrenia (N=3540), autism (N=16 146), attention-deficit/hyperactivity disorder (N=18 726) and affective disorder (N=26 380), of which 1928 had bipolar affective disorder. Controls were randomly sampled individuals (N=30 000). Within the sample of 86 189 individuals, a total of 57 377 individuals had at least one major mental disorder. DNA was extracted from the neonatal dried blood spot samples obtained from the Danish Neonatal Screening Biobank and genotyped using the Illumina PsychChip. Genotyping was successful for 90% of the sample. The assessments of exome sequencing, methylation profiling, metabolome profiling, vitamin-D, inflammatory and neurotrophic factors are in progress. For each individual, the iPSYCH2012 sample also includes longitudinal information on health, prescribed medicine, social and socioeconomic information, and analogous information among relatives. To the best of our knowledge, the iPSYCH2012 sample is the largest and most comprehensive data source for the combined study of genetic and environmental aetiologies of severe mental disorders.
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Affiliation(s)
- C B Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Fuglesangs Allé 4, Aarhus 8210, Denmark. E-mail:
| | - J Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - M G Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - J Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark,BiRC-Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - E Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark
| | - M Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - J B Poulsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - C S Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - J J McGrath
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia,Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Wacol, QLD, Australia
| | - T D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
| | - J I Goldstein
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - B M Neale
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - M J Daly
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - D M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - O Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - M Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Mental Health Centre Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - A D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
| | - T Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,Mental Health Centre Sct. Hans, Capital Region of Denmark, Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
| | - P B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark,National Centre for Register-Based Research, Business and Social Sciences, Aarhus University, Aarhus V, Denmark,Centre for Integrated Register-Based Research, CIRRAU, Aarhus University, Aarhus, Denmark,Centre for Integrative Sequencing, Department of Biomedicine and iSEQ, Aarhus University, Aarhus, Denmark
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36
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Bækvad-Hansen M, Bybjerg-Grauholm J, Poulsen JB, Hansen CS, Hougaard DM, Hollegaard MV. Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality. Mol Genet Metab Rep 2017; 11:36-45. [PMID: 28487825 PMCID: PMC5408502 DOI: 10.1016/j.ymgmr.2017.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/02/2017] [Accepted: 04/02/2017] [Indexed: 02/04/2023] Open
Abstract
Aim The overall aim of this study is to evaluate whole genome amplification of DNA extracted from dried blood spot samples. We wish to explore ways of optimizing the amplification process, while decreasing the amount of input material and inherently the cost. Our primary focus of optimization is on the amount of input material, the amplification reaction volume, the number of replicates and amplification time and temperature. Increasing the quality of the amplified DNA and the subsequent results of array genotyping is a secondary aim of this project. Methods This study is based on DNA extracted from dried blood spot samples. The extracted DNA was subsequently whole genome amplified using the REPLIg kit and genotyped on the PsychArray BeadChip (assessing > 570,000 SNPs genome wide). We used Genome Studio to evaluate the quality of the genotype data by call rates and log R ratios. Results The whole genome amplification process is robust and does not vary between replicates. Altering amplification time, temperature or number of replicates did not affect our results. We found that spot size i.e. amount of input material could be reduced without compromising the quality of the array genotyping data. We also showed that whole genome amplification reaction volumes can be reduced by a factor of 4, without compromising the DNA quality. Discussion Whole genome amplified DNA samples from dried blood spots is well suited for array genotyping and produces robust and reliable genotype data. However, the amplification process introduces additional noise to the data, making detection of structural variants such as copy number variants difficult. With this study, we explore ways of optimizing the amplification protocol in order to reduce noise and increase data quality. We found, that the amplification process was very robust, and that changes in amplification time or temperature did not alter the genotyping calls or quality of the array data. Adding additional replicates of each sample also lead to insignificant changes in the array data. Thus, the amount of noise introduced by the amplification process was consistent regardless of changes made to the amplification protocol. We also explored ways of decreasing material expenditure by reducing the spot size or the amplification reaction volume. The reduction did not affect the quality of the genotyping data.
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Affiliation(s)
- Marie Bækvad-Hansen
- Corresponding author at: Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark.Danish Center for Neonatal ScreeningDepartment of Congenital DiseasesStatens Serum InstitutArtillerivej 5Copenhagen SDK-2300Denmark
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37
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Bybjerg-Grauholm J, Hagen CM, Khoo SK, Johannesen ML, Hansen CS, Bækvad-Hansen M, Christiansen M, Hougaard DM, Hollegaard MV. RNA sequencing of archived neonatal dried blood spots. Mol Genet Metab Rep 2016; 10:33-37. [PMID: 28053876 PMCID: PMC5198792 DOI: 10.1016/j.ymgmr.2016.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 01/25/2023] Open
Abstract
Neonatal dried blood spots (DBS) are routinely collected on standard Guthrie cards for all-comprising national newborn screening programs for inborn errors of metabolism, hypothyroidism and other diseases. In Denmark, the Guthrie cards are stored at − 20 °C in the Danish Neonatal Screening Biobank and each sample is linked to elaborate social and medical registries. This provides a unique biospecimen repository to enable large population research at a perinatal level. Here, we demonstrate the feasibility to obtain gene expression data from DBS using next-generation RNA sequencing (RNA-seq). RNA-seq was performed on five males and five females. Sequencing results have an average of > 30 million reads per sample. 26,799 annotated features can be identified with 64% features detectable without fragments per kilobase of transcript per million mapped reads (FPKM) cutoff; number of detectable features dropped to 18% when FPKM ≥ 1. Sex can be discriminated using blood-based sex-specific gene set identified by the Genotype-Tissue Expression consortium. Here, we demonstrate the feasibility to acquire biologically-relevant gene expression from DBS using RNA-seq which provide a new avenue to investigate perinatal diseases in a high throughput manner.
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Affiliation(s)
- Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christian Munch Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA
| | - Maria Louise Johannesen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Christine Søholm Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Marie Bækvad-Hansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Biomedicine, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Mads V Hollegaard
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen DK-2300, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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38
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Robustness of comprehensive DNA- and RNA-based assays at diagnosis of acute myeloid leukemia using blood and bone marrow stored on filter cards. Leukemia 2016; 30:2123-2125. [DOI: 10.1038/leu.2016.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Lucena-Aguilar G, Sánchez-López AM, Barberán-Aceituno C, Carrillo-Ávila JA, López-Guerrero JA, Aguilar-Quesada R. DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis. Biopreserv Biobank 2016; 14:264-70. [PMID: 27158753 PMCID: PMC4991598 DOI: 10.1089/bio.2015.0064] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-quality human DNA samples and associated information of individuals are necessary for biomedical research. Biobanks act as a support infrastructure for the scientific community by providing a large number of high-quality biological samples for specific downstream applications. For this purpose, biobank methods for sample preparation must ensure the usefulness and long-term functionality of the products obtained. Quality indicators are the tool to measure these parameters, the purity and integrity determination being those specifically used for DNA. This study analyzes the quality indicators in DNA samples derived from 118 frozen human tissues in optimal cutting temperature (OCT) reactive, 68 formalin-fixed paraffin-embedded (FFPE) tissues, 119 frozen blood samples, and 26 saliva samples. The results obtained for DNA quality are discussed in association with the usefulness for downstream applications and availability of the DNA source in the target study. In brief, if any material is valid, blood is the most approachable option of prospective collection of samples providing high-quality DNA. However, if diseased tissue is a requisite or samples are available, the recommended source of DNA would be frozen tissue. These conclusions will determine the best source of DNA, according to the planned downstream application. Furthermore our results support the conclusion that a complete procedure of DNA quantification and qualification is necessary to guarantee the appropriate management of the samples, avoiding low confidence results, high costs, and a waste of samples.
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Affiliation(s)
- Gema Lucena-Aguilar
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - Ana María Sánchez-López
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | | | - José Antonio Carrillo-Ávila
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
| | - José Antonio López-Guerrero
- 3 Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología , Valencia, Spain .,4 Biobank, Fundación Instituto Valenciano de Oncología , Valencia, Spain
| | - Rocío Aguilar-Quesada
- 1 Andalusian Public Health System Biobank, Armilla, Spain .,2 Instituto de Investigación Biosanitaria de Granada , Armilla, Spain
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Robinson EB, St. Pourcain B, Anttila V, Kosmicki JA, Bulik-Sullivan B, Grove J, Maller J, Samocha KE, Sanders SJ, Ripke S, Martin J, Hollegaard MV, Werge T, Hougaard DM, Neale BM, Evans DM, Skuse D, Mortensen PB, Børglum AD, Ronald A, Smith GD, Daly MJ. Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population. Nat Genet 2016; 48:552-5. [PMID: 26998691 PMCID: PMC4986048 DOI: 10.1038/ng.3529] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/22/2016] [Indexed: 12/13/2022]
Abstract
Almost all genetic risk factors for autism spectrum disorders (ASDs) can be found in the general population, but the effects of this risk are unclear in people not ascertained for neuropsychiatric symptoms. Using several large ASD consortium and population-based resources (total n > 38,000), we find genome-wide genetic links between ASDs and typical variation in social behavior and adaptive functioning. This finding is evidenced through both LD score correlation and de novo variant analysis, indicating that multiple types of genetic risk for ASDs influence a continuum of behavioral and developmental traits, the severe tail of which can result in diagnosis with an ASD or other neuropsychiatric disorder. A continuum model should inform the design and interpretation of studies of neuropsychiatric disease biology.
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Affiliation(s)
- Elise B. Robinson
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Beate St. Pourcain
- The Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
- Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen The Netherlands
| | - Verneri Anttila
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Jack A. Kosmicki
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan Bulik-Sullivan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Jakob Grove
- Department of Biomedicine, University of Aarhus, Aarhus, DK
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Julian Maller
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Kaitlin E. Samocha
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Program in Genetics and Genomics, Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02114, USA
| | - Stephan J. Sanders
- Department of Psychiatry, University of California San Francisco, San Francisco, California 94143, USA
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Department of Psychiatry and Psychotherapy, Charité, Campus Mitte, 10117 Berlin, Germany
| | - Joanna Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Mads V. Hollegaard
- Statens Serum Institut, Department of Congenital Disorders, DK-2300 Copenhagen, Denmark
| | - Thomas Werge
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David M. Hougaard
- Statens Serum Institut, Department of Congenital Disorders, DK-2300 Copenhagen, Denmark
| | | | - Benjamin M. Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Department of Psychiatry, Harvard Medical School, Boston MA 02114, USA
| | - David M. Evans
- The Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
- Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Australia
| | - David Skuse
- Behavioural Sciences Unit, Institute of Child Health, University College London, Gower Street, London WC1E 6BT, UK
| | - Preben Bo Mortensen
- Department of Biomedicine, University of Aarhus, Aarhus, DK
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- National Centre for Register-based Research, University of Aarhus, Aarhus, DK
| | - Anders D. Børglum
- Department of Biomedicine, University of Aarhus, Aarhus, DK
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Angelica Ronald
- Department of Psychological Sciences, Centre for Brain and Cognitive Development, Birkbeck, University of London, London WC1E 7HX, UK
| | - George Davey Smith
- The Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
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Huang MC, Chuang TP, Chen CH, Wu JY, Chen YT, Li LH, Yang HC. An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays. BMC Genomics 2016; 17:266. [PMID: 27029637 PMCID: PMC4815280 DOI: 10.1186/s12864-016-2478-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/16/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Affymetrix Axiom single nucleotide polymorphism (SNP) arrays provide a cost-effective, high-density, and high-throughput genotyping solution for population-optimized analyses. However, no public software is available for the integrated genomic analysis of hybridization intensities and genotypes for this new-generation population-optimized genotyping platform. RESULTS A set of statistical methods was developed for an integrated analysis of allele frequency (AF), allelic imbalance (AI), loss of heterozygosity (LOH), long contiguous stretch of homozygosity (LCSH), and copy number variation or alteration (CNV/CNA) on the basis of SNP probe hybridization intensities and genotypes. This study analyzed 3,236 samples that were genotyped using different SNP platforms. The proposed AF adjustment method considerably increased the accuracy of AF estimation. The proposed quick circular binary segmentation algorithm for segmenting copy number reduced the computation time of the original segmentation method by 30-67 %. The proposed CNV/CNA detection, which integrates AI and LOH/LCSH detection, had a promising true positive rate and well-controlled false positive rate in simulation studies. Moreover, our real-time quantitative polymerase chain reaction experiments successfully validated the CNVs/CNAs that were identified in the Axiom data analyses using the proposed methods; some of the validated CNVs/CNAs were not detected in the Affymetrix Array 6.0 data analysis using the Affymetrix Genotyping Console. All the analysis functions are packaged into the ALICE (AF/LOH/LCSH/AI/CNV/CNA Enterprise) software. CONCLUSIONS ALICE and the used genomic reference databases, which can be downloaded from http://hcyang.stat.sinica.edu.tw/software/ALICE.html , are useful resources for analyzing genomic data from the Axiom and other SNP arrays.
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Affiliation(s)
- Mei-Chu Huang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 112, Taiwan
| | - Tzu-Po Chuang
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan
| | - Ling-Hui Li
- Institute of Biomedical Sciences, Academia Sinica, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan.
| | - Hsin-Chou Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Statistical Science, Academia Sinica, No 128, Academia Rd, Sec 2, Nankang, Taipei, 115, Taiwan. .,Institute of Public Health, National Yang Ming University, Taipei, 112, Taiwan. .,Department of Statistics, National Cheng Kung University, Tainan, 701, Taiwan. .,Institute of Statistics, National Tsing Hua University, Hsinchu, 300, Taiwan. .,School of Public Health, National Defense Medical Center, Taipei, 114, Taiwan.
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Nissen JB, Hansen CS, Starnawska A, Mattheisen M, Børglum AD, Buttenschøn HN, Hollegaard M. DNA Methylation at the Neonatal State and at the Time of Diagnosis: Preliminary Support for an Association with the Estrogen Receptor 1, Gamma-Aminobutyric Acid B Receptor 1, and Myelin Oligodendrocyte Glycoprotein in Female Adolescent Patients with OCD. Front Psychiatry 2016; 7:35. [PMID: 27047397 PMCID: PMC4796012 DOI: 10.3389/fpsyt.2016.00035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/26/2016] [Indexed: 12/26/2022] Open
Abstract
Obsessive-compulsive disorder (OCD) is a neuropsychiatric disorder. Non-genetic factors and their interaction with genes have attracted increasing attention. Epigenetics is regarded an important interface between environmental signals and activation/repression of genomic responses. Epigenetic mechanisms have not previously been examined in OCD in children and adolescents. The aim of the present study was to examine the DNA methylation profile of selected genes in blood spots from neonates later diagnosed with OCD and in the same children/adolescents at the time of diagnosis compared with age- and sex-matched controls. Furthermore, we wanted to characterize the association of the differential methylation profiles with the severity of OCD and treatment outcome. Dried and new blood spot samples were obtained from 21 female children/adolescents with verified OCD and 12 female controls. The differential methylation was analyzed using a linear model and the correlation with the severity of OCD and treatment outcome was analyzed using the Pearson correlation. We evaluated selected Illumina Infinium HumanMethylation450 BeadChip probes within and up to 100,000 bp up- and downstream of 14 genes previously associated with OCD (SLC1A1, SLC25A12, GABBR1, GAD1, DLGAP1, MOG, BDNF, OLIG2, NTRK2 and 3, ESR1, SL6A4, TPH2, and COMT). The study found no significantly differential methylation. However, preliminary support for a difference was found for the gamma-aminobutyric acid (GABA) B receptor 1 (cg10234998, cg17099072) in blood samples at birth and for the estrogen receptor 1 (ESR1) (cg10939667), the myelin oligodendrocyte glycoprotein (MOG) (cg16650906), and the brain-derived neurotrophic factor (BDNF) (cg14080521) in blood samples at the time of diagnosis. Preliminary support for an association was observed between the methylation profiles of GABBR1 and MOG and baseline severity, treatment effect, and responder status; and between the methylation profile of ESR1 and baseline severity. To our knowledge, this is the first study to examine the DNA methylation profiles in OCD. The study points towards possible differences in the methylation profiles and suggests a correlation with the severity of OCD. However, the results warrant further studies in larger sample sets.
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Affiliation(s)
- Judith Becker Nissen
- Center of Child and Adolescent Psychiatry (BUC), Aarhus University Hospital , Risskov , Denmark
| | - Christine Søholm Hansen
- Department of Congenital Diseases, Neonatal Genetics, Statens Serum Institut , Copenhagen , Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus, Denmark
| | - Manuel Mattheisen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus, Denmark
| | - Anders Dupont Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus, Denmark
| | | | - Mads Hollegaard
- Department of Congenital Diseases, Neonatal Genetics, Statens Serum Institut , Copenhagen , Denmark
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Genetic Variation in NFKBIE Is Associated With Increased Risk of Pneumococcal Meningitis in Children. EBioMedicine 2015; 3:93-99. [PMID: 26870821 PMCID: PMC4739413 DOI: 10.1016/j.ebiom.2015.11.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 11/29/2022] Open
Abstract
Background Streptococcus pneumoniae and Neisseria meningitidis are frequent pathogens in life-threatening infections. Genetic variation in the immune system may predispose to these infections. Nuclear factor-κB is a key component of the TLR-pathway, controlled by inhibitors, encoded by the genes NFKBIA, NFKBIE and NFKBIZ. We aimed to replicate previous findings of genetic variation associated with invasive pneumococcal disease (IPD), and to assess whether similar associations could be found in invasive meningococcal disease (IMD). Methods Cases with IPD and IMD and controls were identified by linking Danish national registries. DNA was obtained from the Danish Neonatal Screening Biobank. The association between SNPs and susceptibility to IPD and IMD, mortality and pneumococcal serotypes was investigated. Results 372 children with pneumococcal meningitis, 907 with pneumococcal bacteremia and 1273 controls were included. We included 406 cases with meningococcal meningitis, 272 with meningococcal bacteremia, and 672 controls. The NFKBIE SNP was associated with increased risk of pneumococcal meningitis (aOR 1.68; 95% CI: 1.20–2.36), but not bacteremia (aOR 1.08; 95% CI: 0.86–1.35). The remaining SNPs were not associated with susceptibility to invasive disease. None of the SNPs were associated with risk of IMD or mortality. Conclusions A NFKBIE polymorphism was associated with increased risk of pneumococcal meningitis. A polymorphism in the NFKBIE gene was associated with an increased risk of pneumococcal meningitis in children. This single nucleotide polymorphism (SNP) was not associated with bacteremia. None of the studied SNPs were associated with risk or severity of invasive meningococcal disease.
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Key Words
- CI, confidence intervals
- CRS, Danish Civil Registration System
- CSF, cerebrospinal fluid
- DNPR, Danish National Patient Registry
- DNSB, Danish Neonatal Screening Biobank
- HWE, Hardy–Weinberg equilibrium
- IMD, invasive meningococcal disease
- IPD, Invasive pneumococcal disease
- IQR, interquartile range
- Invasive Meningococcal Disease
- Invasive Pneumococcal Disease
- LD, linkage disequilibrium
- NF, nuclear factor-κB
- Nuclear Factor-κB
- OR, odds ratio
- Pneumoccoccal Serotypes
- RSV, respiratory syncytial virus
- SNPs, single nucleotide polymorphisms
- SSI, Statens Serum Institut
- WGA, whole-genome-amplification
- aOR, adjusted odds ratio
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Grauholm J, Khoo SK, Nickolov RZ, Poulsen JB, Bækvad-Hansen M, Hansen CS, Hougaard DM, Hollegaard MV. Gene expression profiling of archived dried blood spot samples from the Danish Neonatal Screening Biobank. Mol Genet Metab 2015. [PMID: 26212339 DOI: 10.1016/j.ymgme.2015.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A large part of the human genome is transcribed into various forms of RNA, and the global gene expression profile (GEP) has been studied for several years using technology such as RNA-microarrays. In this study, we evaluate whether neonatal dried blood spot (DBS) samples stored in the Danish Neonatal Screening Biobank (DNSB) can be used for GEP. This paper is divided into sub-studies examining the effects of: 1) different whole transcriptome amplification kits (WTA); 2) years of storage and storage in room temperature (RT) versus freezers (-20°C) on DNSB DBS samples; 3) effects of RT storage vs freezer storage on DBS samples from the USA and DNSB, and 4) using smaller disc sizes, thereby decreasing DBS use. We present evidence that reliable and reproducible GEPs can be obtained using neonatal DBS samples. The main source of variation is the storage condition. When samples are stored at -20°C, the dynamic range is increased, and Pearson correlations are higher. Differential analysis reveals no statistically significant differences between samples collected a decade apart and stored at -20°C. However, samples stored at RT show differential expression for a third of the gene-specific probes. Our data also suggests that using alternate WTA kits significantly changes the GEP. Finally, the amount of input material, i.e., the size and number of DBS discs used, can be reduced to preserve this valuable and limited material. We conclude that DNSB DBS samples provide a reproducible resource for GEP. Results are improved if the cards are stored at -20°C. Furthermore, it is important to use a single type of kit for analysis because using alternate kits introduces differential expression.
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Affiliation(s)
- Jonas Grauholm
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Sok Kean Khoo
- Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA.
| | - Radoslav Z Nickolov
- Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA.
| | - Jesper B Poulsen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Marie Bækvad-Hansen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Christine S Hansen
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - David M Hougaard
- Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
| | - Mads V Hollegaard
- Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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45
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Dahlin AM, Hollegaard MV, Wibom C, Andersson U, Hougaard DM, Deltour I, Hjalmars U, Melin B. CCND2, CTNNB1, DDX3X, GLI2, SMARCA4, MYC, MYCN, PTCH1, TP53, and MLL2 gene variants and risk of childhood medulloblastoma. J Neurooncol 2015; 125:75-8. [PMID: 26290144 PMCID: PMC4592490 DOI: 10.1007/s11060-015-1891-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/08/2015] [Indexed: 12/30/2022]
Abstract
Recent studies have described a number of genes that are frequently altered in medulloblastoma tumors and that have putative key roles in the development of the disease. We hypothesized that common germline genetic variations in these genes may be associated with medulloblastoma development. Based on recent publications, we selected 10 genes that were frequently altered in medulloblastoma: CCND2, CTNNB1, DDX3X, GLI2, SMARCA4, MYC, MYCN, PTCH1, TP53, and MLL2 (now renamed as KMT2D). Common genetic variants (single nucleotide polymorphisms) annotating these genes (n = 221) were genotyped in germline DNA (neonatal dried blood spot samples) from 243 childhood medulloblastoma cases and 247 control subjects from Sweden and Denmark. Eight genetic variants annotating three genes in the sonic hedgehog signaling pathway; CCND2, PTCH1, and GLI2, were found to be associated with the risk of medulloblastoma (P(combined) < 0.05). The findings were however not statistically significant following correction for multiple testing by the very stringent Bonferroni method. The results do not support our hypothesis that common germline genetic variants in the ten studied genes are associated with the risk of developing medulloblastoma.
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Affiliation(s)
- Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
| | - Mads V Hollegaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - David M Hougaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Isabelle Deltour
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
- Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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Lundbo LF, Sørensen HT, Clausen LN, Hollegaard MV, Hougaard DM, Konradsen HB, Harboe ZB, Nørgaard M, Benfield T. Mannose-Binding Lectin Gene, MBL2, Polymorphisms Do Not Increase Susceptibility to Invasive Meningococcal Disease in a Population of Danish Children. Open Forum Infect Dis 2015; 2:ofv127. [PMID: 26464842 PMCID: PMC4602025 DOI: 10.1093/ofid/ofv127] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/27/2015] [Indexed: 01/17/2023] Open
Abstract
Background. Neisseria meningitidis is the cause of meningococcal bacteremia and meningitis, and nasopharyngeal colonization with this pathogen is common. The incidence of invasive disease is highest in infants, whereas adolescents more often are carriers. Altered regulation or dysfunction of the innate immune system may predispose to invasive meningococcal disease (IMD). In this study, we investigated the effect of genetic variation in the mannose-binding lectin gene, MBL2, and its promoter on susceptibility to IMD and IMD-associated mortality among children. Methods. Children (<5 years) diagnosed during 1982-2007 with IMD and controls were identified through Danish national registries. DNA was obtained from the Danish Neonatal Screening Biobank. The associations between MBL2 diplotypes and IMD susceptibility and 30- and 90-day mortality were investigated using logistic regression analysis. Results. We included 1351 children: 406 with meningitis, 272 with bacteremia, and 673 age- and sex-matched controls. Of the children studied, 1292 (96%) were successfully genotyped and assigned MBL2 diplotypes. The median age in IMD cases was 19.1 months (interquartile range [IQR], 8.8-32.2 months). Children with defective MBL2 diplotypes were not at higher risk for meningococcal meningitis than children with intermediate and normal diplotypes (odds ratio [OR] = 0.69; 95% confidence interval [CI], .47-1.02). Similar results were found for children with bacteremia and defective diplotypes (OR = 0.84; 95% CI, .53-1.32) as well as for all cases (OR = 0.75; 95% CI, .56-1.01). There was no association between MBL2 diplotypes and mortality. Conclusions. Defective MBL2 diplotypes did not predict either an increased IMD susceptibility or mortality in a Danish population of children.
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Affiliation(s)
- Lene F Lundbo
- Department of Infectious Diseases ; Clinical Research Centre , Hvidovre Hospital ; Faculty of Health Sciences , University of Copenhagen
| | | | | | - Mads V Hollegaard
- Danish Centre for Neonatal Screening, Department for Congenital Disorders
| | - David M Hougaard
- Danish Centre for Neonatal Screening, Department for Congenital Disorders
| | | | - Zitta Barrella Harboe
- Department of Microbiological Surveillance and Research , Statens Serum Institut , Copenhagen ; Department for Pulmonary and Infectious Diseases , North Zealand Hospital Hillerød , Denmark
| | - Mette Nørgaard
- Department of Clinical Epidemiology , Aarhus University Hospital
| | - Thomas Benfield
- Department of Infectious Diseases ; Clinical Research Centre , Hvidovre Hospital ; Faculty of Health Sciences , University of Copenhagen
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Ellervik C, Vaught J. Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking. Clin Chem 2015; 61:914-34. [DOI: 10.1373/clinchem.2014.228783] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/13/2015] [Indexed: 12/20/2022]
Abstract
Abstract
BACKGROUND
Most errors in a clinical chemistry laboratory are due to preanalytical errors. Preanalytical variability of biospecimens can have significant effects on downstream analyses, and controlling such variables is therefore fundamental for the future use of biospecimens in personalized medicine for diagnostic or prognostic purposes.
CONTENT
The focus of this review is to examine the preanalytical variables that affect human biospecimen integrity in biobanking, with a special focus on blood, saliva, and urine. Cost efficiency is discussed in relation to these issues.
SUMMARY
The quality of a study will depend on the integrity of the biospecimens. Preanalytical preparations should be planned with consideration of the effect on downstream analyses. Currently such preanalytical variables are not routinely documented in the biospecimen research literature. Future studies using biobanked biospecimens should describe in detail the preanalytical handling of biospecimens and analyze and interpret the results with regard to the effects of these variables.
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Affiliation(s)
- Christina Ellervik
- Department of Research, Nykoebing Falster Hospital, Nykoebing Falster, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA
| | - Jim Vaught
- International Society for Biological and Environmental Repositories, Vancouver, Canada
- Editor-in-Chief, Biopreservation and Biobanking, Vancouver, Canada
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48
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Nguyen-Dumont T, Mahmoodi M, Hammet F, Tran T, Tsimiklis H, Giles GG, Hopper JL, Southey MC, Park DJ. Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots. Anal Biochem 2015; 470:48-51. [PMID: 25447460 PMCID: PMC4275364 DOI: 10.1016/j.ab.2014.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 11/28/2022]
Abstract
Many genetic epidemiology resources have collected dried blood spots (predominantly as Guthrie Cards) as an economical and efficient means of archiving sources of DNA, conferring great value to genetic screening methods that are compatible with this medium. We applied Hi-Plex to screen the breast cancer predisposition gene PALB2 in 93 Guthrie Card-derived DNA specimens previously characterized for PALB2 genetic variants via DNA derived from lymphoblastoid cell lines, whole blood, and buffy coat. Of the 93 archival Guthrie Card-derived DNAs, 92 (99%) were processed successfully and sequenced using approximately half of a MiSeq run. From these 92 DNAs, all 59 known variants were detected and no false-positive variant calls were yielded. Fully 98.13% of amplicons (5417/5520) were represented within 15-fold of the median coverage (2786 reads), and 99.98% of amplicons (5519/5520) were represented at a depth of 10 read-pairs or greater. With Hi-Plex, we show for the first time that a High-Plex amplicon-based massively parallel sequencing (MPS) system can be applied effectively to DNA prepared from dried blood spot archival specimens and, as such, can dramatically increase the scopes of both method and resource.
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Affiliation(s)
- T Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - M Mahmoodi
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - F Hammet
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - T Tran
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - H Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - G G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
| | - J L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Parkville, Victoria 3010, Australia
| | - M C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - D J Park
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
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49
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Sørensen KM. Whole Genome Amplification from Blood Spot Samples. Methods Mol Biol 2015; 1347:163-178. [PMID: 26374317 DOI: 10.1007/978-1-4939-2990-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole genome amplification is an invaluable technique when working with DNA extracted from blood spots, as the DNA obtained from this source often is too limited for extensive genetic analysis. Two techniques that amplify the entire genome are common. Here, both are described with focus on the benefits and drawbacks of each system. However, in order to obtain the best possible WGA result the quality of input DNA extracted from the blood spot is essential, but also time consumption, flexibility in format and elution volume and price of the technology are factors influencing system choice. Here, three DNA extraction techniques are described and the above aspects are compared between the systems.
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Affiliation(s)
- Karina Meden Sørensen
- The Danish National Biobank, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Danmark.
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50
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Rapid DNA extraction from dried blood spots on filter paper: potential applications in biobanking. Osong Public Health Res Perspect 2014; 5:351-7. [PMID: 25562044 PMCID: PMC4281615 DOI: 10.1016/j.phrp.2014.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/14/2014] [Accepted: 09/29/2014] [Indexed: 01/19/2023] Open
Abstract
Objectives Dried blood spot (DBS) technology is a microsampling alternative to traditional plasma or serum sampling for pharmaco- or toxicokinetic evaluation. DBS technology has been applied to diagnostic screening in drug discovery, nonclinical, and clinical settings. We have developed an improved elution protocol involving boiling of blood spots dried on Whatman filter paper. Methods The purpose of this study was to compare the quality, purity, and quantity of DNA isolated from frozen blood samples and DBSs. We optimized a method for extraction and estimation of DNA from blood spots dried on filter paper (3-mm FTA card). A single DBS containing 40 μL blood was used. Results DNA was efficiently extracted in phosphate-buffered saline (PBS) or Tris-EDTA (TE) buffer by incubation at 37°C overnight. DNA was stable in DBSs that were stored at room temperature or frozen. The housekeeping genes GAPDH and beta-actin were used as positive standards for polymerase chain reaction (PCR) validation of general diagnostic screening. Conclusion Our simple and convenient DBS storage and extraction methods are suitable for diagnostic screening by using very small volumes of blood collected on filter paper, and can be used in biobanks for blood sample storage.
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