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Paz V, Dashti HS, Burgess S, Garfield V. Selection of genetic instruments in Mendelian randomisation studies of sleep traits. Sleep Med 2023; 112:342-351. [PMID: 37956646 PMCID: PMC7615498 DOI: 10.1016/j.sleep.2023.10.036] [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: 05/17/2023] [Revised: 10/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]
Abstract
This review explores the criteria used for the selection of genetic instruments of sleep traits in the context of Mendelian randomisation studies. This work was motivated by the fact that instrument selection is the most important decision when designing a Mendelian randomisation study. As far as we are aware, no review has sought to address this to date, even though the number of these studies is growing rapidly. The review is divided into the following sections which are essential for genetic instrument selection: 1) Single-gene region vs polygenic analysis; 2) Polygenic analysis: biologically-vs statistically-driven approaches; 3) P-value; 4) Linkage disequilibrium clumping; 5) Sample overlap; 6) Type of exposure; 7) Total (R2) and average strength (F-statistic) metrics; 8) Number of single-nucleotide polymorphisms; 9) Minor allele frequency and palindromic variants; 10) Confounding. Our main aim is to discuss how instrumental choice impacts analysis and compare the strategies that Mendelian randomisation studies of sleep traits have used. We hope that our review will enable more researchers to take a more considered approach when selecting genetic instruments for sleep exposures.
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Affiliation(s)
- Valentina Paz
- Instituto de Psicología Clínica, Facultad de Psicología, Universidad de la República, Tristán Narvaja, 1674, Montevideo, 11200, Uruguay; MRC Unit for Lifelong Health & Ageing, Institute of Cardiovascular Science, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK.
| | - Hassan S Dashti
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA; Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA; Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Edwards 4-410C, Boston, MA, 02114, USA
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK; Department of Public Health and Primary Care, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - Victoria Garfield
- MRC Unit for Lifelong Health & Ageing, Institute of Cardiovascular Science, University College London, 1-19 Torrington Place, London, WC1E 7HB, UK
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2
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Scammell BH, Tchio C, Song Y, Nishiyama T, Louie TL, Dashti HS, Nakatochi M, Zee PC, Daghlas I, Momozawa Y, Cai J, Ollila HM, Redline S, Wakai K, Sofer T, Suzuki S, Lane JM, Saxena R. Multi-ancestry genome-wide analysis identifies shared genetic effects and common genetic variants for self-reported sleep duration. Hum Mol Genet 2023; 32:2797-2807. [PMID: 37384397 PMCID: PMC10656946 DOI: 10.1093/hmg/ddad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023] Open
Abstract
Both short (≤6 h per night) and long sleep duration (≥9 h per night) are associated with increased risk of chronic diseases. Despite evidence linking habitual sleep duration and risk of disease, the genetic determinants of sleep duration in the general population are poorly understood, especially outside of European (EUR) populations. Here, we report that a polygenic score of 78 European ancestry sleep duration single-nucleotide polymorphisms (SNPs) is associated with sleep duration in an African (n = 7288; P = 0.003), an East Asian (n = 13 618; P = 6 × 10-4) and a South Asian (n = 7485; P = 0.025) genetic ancestry cohort, but not in a Hispanic/Latino cohort (n = 8726; P = 0.71). Furthermore, in a pan-ancestry (N = 483 235) meta-analysis of genome-wide association studies (GWAS) for habitual sleep duration, 73 loci are associated with genome-wide statistical significance. Follow-up of five loci (near HACD2, COG5, PRR12, SH3RF1 and KCNQ5) identified expression-quantitative trait loci for PRR12 and COG5 in brain tissues and pleiotropic associations with cardiovascular and neuropsychiatric traits. Overall, our results suggest that the genetic basis of sleep duration is at least partially shared across diverse ancestry groups.
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Affiliation(s)
- B H Scammell
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
| | - C Tchio
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Y Song
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
| | - T Nishiyama
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya 467-8701, Japan
| | - T L Louie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - H S Dashti
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - M Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya 467-8701, Japan
| | - P C Zee
- Center for Circadian and Sleep Medicine, Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - I Daghlas
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
| | - Y Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - J Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - H M Ollila
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Institute for Molecular Medicine, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - S Redline
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - K Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya 467-8701, Japan
| | - T Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - S Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya 467-8701, Japan
| | - J M Lane
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - R Saxena
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02215, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
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3
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Kawada T. Habitual caffeine consumption, genetic polymorphisms of cytokines and sleep quality. Sleep Med 2023; 106:132. [PMID: 37005117 DOI: 10.1016/j.sleep.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
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Sauvet F, Drogou C, Leger D, Chennaoui M, Gomez-Merino D. Reply to a letter to the editor regarding the article “Relationship between genetic polymorphisms of cytokines and self-reported sleep complaints and habitual caffeine consumption”. Sleep Med 2023; 106:133-134. [PMID: 37059615 DOI: 10.1016/j.sleep.2023.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Affiliation(s)
- Fabien Sauvet
- Institut de recherche biomédicale des armées (IRBA), Brétigny sur Orge, France; URP 7330 VIFASOM, Université Paris-Cité, Paris, France.
| | - Catherine Drogou
- Institut de recherche biomédicale des armées (IRBA), Brétigny sur Orge, France; URP 7330 VIFASOM, Université Paris-Cité, Paris, France
| | - Damien Leger
- URP 7330 VIFASOM, Université Paris-Cité, Paris, France; Centre du sommeil et de la vigilance, Hôtel Dieu, APHP, Paris, France
| | - Mounir Chennaoui
- Institut de recherche biomédicale des armées (IRBA), Brétigny sur Orge, France; URP 7330 VIFASOM, Université Paris-Cité, Paris, France
| | - Danielle Gomez-Merino
- Institut de recherche biomédicale des armées (IRBA), Brétigny sur Orge, France; URP 7330 VIFASOM, Université Paris-Cité, Paris, France
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Wang J, Zhang Y, Liu Y, Zhang S, Yuan L, Zhong Y, Wu X, Yang J, Xu Z. Multi-Metabolomics Coupled with Quantitative Descriptive Analysis Revealed Key Alterations in Phytochemical Composition and Sensory Qualities of Decaffeinated Green and Black Tea from the Same Fresh Leaves. Foods 2022. [PMCID: PMC9602332 DOI: 10.3390/foods11203269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The supercritical CO2-based decaffeination (SCD) method can be used to prepare decaffeinated tea, but its overall effect on the phytochemicals, volatiles, and sensory qualities of green and black teas is still unclear, and its suitability to prepare decaffeinated green and black teas still needs to be compared. This study revealed the effect of SCD on phytochemicals, volatiles, and sensory qualities in black and green tea prepared from the same tea leaves, and compared the suitability of preparing decaffeinated green and black teas using SCD. The results showed that the SCD could remove 98.2 and 97.1% of the caffeine in green and black tea, respectively. However, it can cause further losses of phytochemicals in green and black teas, specifically the loss of epigallocatechin gallate, epigallocatechin, epicatechin gallate, and gallocatechin gallate in green tea and the loss of theanine and arginine in green and black teas. After the decaffeination, both green and black teas lost some volatiles but also generated new volatiles. Especially, the fruit/flower-like aroma, ocimene, linalyl acetate, geranyl acetate, and D-limonene, were generated in the decaffeinated black tea, while herbal/green-like aroma, β-cyclocitral, 2-ethylhexanol, and safranal, were generated in the decaffeinated green tea. The overall acceptance of decaffeinated green tea decreased due to the substantial reduction in bitterness and astringency, while the overall acceptance of decaffeinated black tea significantly increased. Therefore, SCD is more suitable for the preparation of decaffeinated black tea.
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Affiliation(s)
- Jie Wang
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Ying Zhang
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Yan Liu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Shaorong Zhang
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Linying Yuan
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Yingfu Zhong
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Xiuhong Wu
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Juan Yang
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Ze Xu
- Tea Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
- Correspondence:
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6
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Diagnosis of Insomnia Disorder. Respir Med 2022. [DOI: 10.1007/978-3-030-93739-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Williams JA, Russ D, Bravo-Merodio L, Cardoso VR, Pendleton SC, Aziz F, Acharjee A, Gkoutos GV. A Causal Web between Chronotype and Metabolic Health Traits. Genes (Basel) 2021; 12:genes12071029. [PMID: 34356044 PMCID: PMC8303793 DOI: 10.3390/genes12071029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 01/05/2023] Open
Abstract
Observational and experimental evidence has linked chronotype to both psychological and cardiometabolic traits. Recent Mendelian randomization (MR) studies have investigated direct links between chronotype and several of these traits, often in isolation of outside potential mediating or moderating traits. We mined the EpiGraphDB MR database for calculated chronotype–trait associations (p-value < 5 × 10−8). We then re-analyzed those relevant to metabolic or mental health and investigated for statistical evidence of horizontal pleiotropy. Analyses passing multiple testing correction were then investigated for confounders, colliders, intermediates, and reverse intermediates using the EpiGraphDB database, creating multiple chronotype–trait interactions among each of the the traits studied. We revealed 10 significant chronotype–exposure associations (false discovery rate < 0.05) exposed to 111 potential previously known confounders, 52 intermediates, 18 reverse intermediates, and 31 colliders. Chronotype–lipid causal associations collided with treatment and diabetes effects; chronotype–bipolar associations were mediated by breast cancer; and chronotype–alcohol intake associations were impacted by confounders and intermediate variables including known zeitgebers and molecular traits. We have reported the influence of chronotype on several cardiometabolic and behavioural traits, and identified potential confounding variables not reported on in studies while discovering new associations to drugs and disease.
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Affiliation(s)
- John A. Williams
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
- Correspondence:
| | - Dominic Russ
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Laura Bravo-Merodio
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Victor Roth Cardoso
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Samantha C. Pendleton
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Furqan Aziz
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Animesh Acharjee
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham B15 2WB, UK
| | - Georgios V. Gkoutos
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (D.R.); (L.B.-M.); (V.R.C.); (S.C.P.); (F.A.); (A.A.); (G.V.G.)
- Institute of Translational Medicine, University of Birmingham, Birmingham B15 2TT, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham B15 2WB, UK
- MRC Health Data Research UK (HDR), Midlands Site, Birmingham B15 2TT, UK
- NIHR Experimental Cancer Medicine Centre, Birmingham B15 2TT, UK
- NIHR Biomedical Research Centre, University Hospital Birmingham, Birmingham B15 2WB, UK
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Treur JL, Munafò MR, Logtenberg E, Wiers RW, Verweij KJH. Using Mendelian randomization analysis to better understand the relationship between mental health and substance use: a systematic review. Psychol Med 2021; 51:1593-1624. [PMID: 34030749 PMCID: PMC8327626 DOI: 10.1017/s003329172100180x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/17/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Poor mental health has consistently been associated with substance use (smoking, alcohol drinking, cannabis use, and consumption of caffeinated drinks). To properly inform public health policy it is crucial to understand the mechanisms underlying these associations, and most importantly, whether or not they are causal. METHODS In this pre-registered systematic review, we assessed the evidence for causal relationships between mental health and substance use from Mendelian randomization (MR) studies, following PRISMA. We rated the quality of included studies using a scoring system that incorporates important indices of quality, such as the quality of phenotype measurement, instrument strength, and use of sensitivity methods. RESULTS Sixty-three studies were included for qualitative synthesis. The final quality rating was '-' for 16 studies, '- +' for 37 studies, and '+'for 10 studies. There was robust evidence that higher educational attainment decreases smoking and that there is a bi-directional, increasing relationship between smoking and (symptoms of) mental disorders. Another robust finding was that higher educational attainment increases alcohol use frequency, but decreases binge-drinking and alcohol use problems, and that mental disorders causally lead to more alcohol drinking without evidence for the reverse. CONCLUSIONS The current MR literature increases our understanding of the relationship between mental health and substance use. Bi-directional causal relationships are indicated, especially for smoking, providing further incentive to strengthen public health efforts to decrease substance use. Future MR studies should make use of large(r) samples in combination with detailed phenotypes, a wide range of sensitivity methods, and triangulate with other research methods.
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Affiliation(s)
- Jorien L. Treur
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Addiction Development and Psychopathology (ADAPT) Lab, Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands
| | - Marcus R. Munafò
- School of Psychological Science, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, the University of Bristol, Bristol, UK
| | - Emma Logtenberg
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Reinout W. Wiers
- Addiction Development and Psychopathology (ADAPT) Lab, Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands
- Center for Urban Mental Health, University of Amsterdam, Amsterdam, the Netherlands
| | - Karin J. H. Verweij
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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Daghlas I, Vgontzas A, Guo Y, Chasman DI, Saxena R. Habitual sleep disturbances and migraine: a Mendelian randomization study. Ann Clin Transl Neurol 2020; 7:2370-2380. [PMID: 33125193 PMCID: PMC7732254 DOI: 10.1002/acn3.51228] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/09/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Sleep disturbances are associated with increased risk of migraine, however the extent of shared underlying biology and the direction of causal relationships between these traits is unclear. Delineating causality between sleep patterns and migraine may offer new pathophysiologic insights and inform subsequent intervention studies. Here, we used genetic approaches to test for shared genetic influences between sleep patterns and migraine, and to test whether habitual sleep patterns may be causal risk factors for migraine and vice versa. METHODS To quantify genetic overlap, we performed genome-wide genetic correlation analyses using genome-wide association studies of nine sleep traits in the UK Biobank (n ≥ 237,627), and migraine from the International Headache Genetics Consortium (59,674 cases and 316,078 controls). We then tested for potential causal effects between sleep traits and migraine using bidirectional, two-sample Mendelian randomization. RESULTS Seven sleep traits demonstrated genetic overlap with migraine, including insomnia symptoms (rg = 0.29, P < 10-31 ) and difficulty awakening (rg = 0.11, P < 10-4 ). Mendelian randomization analyses provided evidence for potential causal effects of difficulty awakening on risk of migraine (OR [95% CI] = 1.37 [1.12-1.68], P = 0.002), and nominal evidence that liability to insomnia symptoms increased the risk of migraine (1.09 [1.02-1.16], P = 0.02). In contrast, there was minimal evidence for an effect of migraine liability on sleep patterns or disturbances. INTERPRETATION These data support a shared genetic basis between several sleep traits and migraine, and support potential causal effects of difficulty awakening and insomnia symptoms on migraine risk. Treatment of sleep disturbances may therefore be a promising clinical intervention in the management of migraine.
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Affiliation(s)
- Iyas Daghlas
- Broad Institute of MIT and Harvard415 Main StreetCambridgeMassachusetts02142USA
- Center for Genomic MedicineMassachusetts General Hospital185 Cambridge StreetBostonMassachusetts02114USA
- Division of Preventive MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMassachusetts02115USA
| | - Angeliki Vgontzas
- Department of NeurologyBrigham and Women’s HospitalHarvard Medical SchoolBostonMassachusetts02115USA
| | - Yanjun Guo
- Division of Preventive MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMassachusetts02115USA
| | - Daniel I. Chasman
- Division of Preventive MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMassachusetts02115USA
| | - Richa Saxena
- Broad Institute of MIT and Harvard415 Main StreetCambridgeMassachusetts02142USA
- Center for Genomic MedicineMassachusetts General Hospital185 Cambridge StreetBostonMassachusetts02114USA
- Anesthesia, Critical Care and Pain MedicineMassachusetts General HospitalHarvard Medical SchoolBostonMassachusetts02114USA
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Deng L, Zhang H, Song L, Yu K. Approximation of bias and mean-squared error in two-sample Mendelian randomization analyses. Biometrics 2019; 76:369-379. [PMID: 31651042 PMCID: PMC7182476 DOI: 10.1111/biom.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 08/08/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022]
Abstract
Mendelian randomization (MR) is a type of instrumental variable (IV) analysis that uses genetic variants as IVs for a risk factor to study its causal effect on an outcome. Extensive investigations on the performance of IV analysis procedures, such as the one based on the two-stage least squares (2SLS) procedure, have been conducted under the one-sample scenario, where measures on IVs, the risk factor, and the outcome are assumed to be available for each study participant. Recent MR analysis usually is performed with data from two independent or partially overlapping genetic association studies (two-sample setting), with one providing information on the association between the IVs and the outcome, and the other on the association between the IVs and the risk factor. We investigate the performance of 2SLS in the two-sample-based MR when the IVs are weakly associated with the risk factor. We derive closed form formulas for the bias and mean squared error of the 2SLS estimate and verify them with numeric simulations under realistic circumstances. Using these analytic formulas, we can study the pros and cons of conducting MR analysis under one-sample and two-sample settings and assess the impact of having overlapping samples. We also propose and validate a bias-corrected estimator for the causal effect.
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Affiliation(s)
- Lu Deng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
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Nishiyama T, Nakatochi M, Goto A, Iwasaki M, Hachiya T, Sutoh Y, Shimizu A, Wang C, Tanaka H, Watanabe M, Hosono A, Tamai Y, Yamada T, Yamaji T, Sawada N, Fukumoto K, Otsuka K, Tanno K, Tomita H, Kojima K, Nagasaki M, Hozawa A, Hishida A, Sasakabe T, Nishida Y, Hara M, Ito H, Oze I, Nakamura Y, Mikami H, Ibusuki R, Takezaki T, Koyama T, Kuriyama N, Endoh K, Kuriki K, Turin TC, Naoyuki T, Katsuura-Kamano S, Uemura H, Okada R, Kawai S, Naito M, Momozawa Y, Kubo M, Sasaki M, Yamamoto M, Tsugane S, Wakai K, Suzuki S. Genome-wide association meta-analysis and Mendelian randomization analysis confirm the influence of ALDH2 on sleep durationin the Japanese population. Sleep 2019; 42:5362027. [DOI: 10.1093/sleep/zsz046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 02/20/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Takeshi Nishiyama
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya, Japan
- Department of Public Health, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Masahiro Nakatochi
- Data Science Division, Data Coordinating Center, Department of Advanced Medicine, Nagoya University Hospital, Japan
| | - Atsushi Goto
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Yoichi Sutoh
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Chaochen Wang
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya, Japan
- Department of Public Health, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Hideo Tanaka
- Osaka Prefectural Kishiwada Public Health Center, Osaka, Japan
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya, Japan
| | - Akihiro Hosono
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya, Japan
| | - Yuya Tamai
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya, Japan
| | | | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Kentaro Fukumoto
- Department of Neuropsychiatry, School of Medicine, Iwate Medical University, Iwate, Japan
| | - Kotaro Otsuka
- Department of Neuropsychiatry, School of Medicine, Iwate Medical University, Iwate, Japan
- Division of Clinical Research and Epidemiology, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Kozo Tanno
- Division of Clinical Research and Epidemiology, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
- Department of Hygiene and Preventive Medicine, School of Medicine, Iwate Medical University, Iwate, Japan
| | - Hiroaki Tomita
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tae Sasakabe
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichiro Nishida
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Isao Oze
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yohko Nakamura
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Rie Ibusuki
- Department of International Islands and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Toshiro Takezaki
- Department of International Islands and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Teruhide Koyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Nagato Kuriyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto, Japan
| | - Kaori Endoh
- Laboratory of Public Health, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Tanvir C Turin
- Department of Health Science, Shiga University of Medical Science, Shiga, Japan
| | - Takashima Naoyuki
- Department of Health Science, Shiga University of Medical Science, Shiga, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hirokazu Uemura
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sayo Kawai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Oral Epidemiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
- Division of Ultra-High Field MRI and Department of Radiology, Iwate Medical University, Iwate, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medicine, Nagoya, Japan
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12
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Landolt HP, Holst SC, Valomon A. Clinical and Experimental Human Sleep-Wake Pharmacogenetics. Handb Exp Pharmacol 2019; 253:207-241. [PMID: 30443785 DOI: 10.1007/164_2018_175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sleep and wakefulness are highly complex processes that are elegantly orchestrated by fine-tuned neurochemical changes among neuronal and non-neuronal ensembles, nuclei, and networks of the brain. Important neurotransmitters and neuromodulators regulating the circadian and homeostatic facets of sleep-wake physiology include melatonin, γ-aminobutyric acid, hypocretin, histamine, norepinephrine, serotonin, dopamine, and adenosine. Dysregulation of these neurochemical systems may cause sleep-wake disorders, which are commonly classified into insomnia disorder, parasomnias, circadian rhythm sleep-wake disorders, central disorders of hypersomnolence, sleep-related movement disorders, and sleep-related breathing disorders. Sleep-wake disorders can have far-reaching consequences on physical, mental, and social well-being and health and, thus, need be treated with effective and rational therapies. Apart from behavioral (e.g., cognitive behavioral therapy for insomnia), physiological (e.g., chronotherapy with bright light), and mechanical (e.g., continuous positive airway pressure treatment of obstructive sleep apnea) interventions, pharmacological treatments often are the first-line clinical option to improve disturbed sleep and wake states. Nevertheless, not all patients respond to pharmacotherapy in uniform and beneficial fashion, partly due to genetic differences. The improved understanding of the neurochemical mechanisms regulating sleep and wakefulness and the mode of action of sleep-wake therapeutics has provided a conceptual framework, to search for functional genetic variants modifying individual drug response phenotypes. This article will summarize the currently known genetic polymorphisms that modulate drug sensitivity and exposure, to partly determine individual responses to sleep-wake pharmacotherapy. In addition, a pharmacogenetic strategy will be outlined how based upon classical and opto-/chemogenetic strategies in animals, as well as human genetic associations, circuit mechanisms regulating sleep-wake functions in humans can be identified. As such, experimental human sleep-wake pharmacogenetics forms a bridge spanning basic research and clinical medicine and constitutes an essential step for the search and development of novel sleep-wake targets and therapeutics.
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Affiliation(s)
- Hans-Peter Landolt
- Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland.
- Zürich Center for Interdisciplinary Sleep Research (ZiS), University of Zürich, Zürich, Switzerland.
| | - Sebastian C Holst
- Neurobiology Research Unit and Neuropharm, Department of Neurology, Rigshospitalet, Copenhagen, Denmark
| | - Amandine Valomon
- Wisconsin Institute for Sleep and Consciousness, University of Wisconsin Madison, Madison, WI, USA
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13
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Cornelis MC, Munafo MR. Mendelian Randomization Studies of Coffee and Caffeine Consumption. Nutrients 2018; 10:E1343. [PMID: 30241358 PMCID: PMC6213346 DOI: 10.3390/nu10101343] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/26/2022] Open
Abstract
Habitual coffee and caffeine consumption has been reported to be associated with numerous health outcomes. This perspective focuses on Mendelian Randomization (MR) approaches for determining whether such associations are causal. Genetic instruments for coffee and caffeine consumption are described, along with key concepts of MR and particular challenges when applying this approach to studies of coffee and caffeine. To date, at least fifteen MR studies have investigated the causal role of coffee or caffeine use on risk of type 2 diabetes, cardiovascular disease, Alzheimer's disease, Parkinson's disease, gout, osteoarthritis, cancers, sleep disturbances and other substance use. Most studies provide no consistent support for a causal role of coffee or caffeine on these health outcomes. Common study limitations include low statistical power, potential pleiotropy, and risk of collider bias. As a result, in many cases a causal role cannot confidently be ruled out. Conceptual challenges also arise from the different aspects of coffee and caffeine use captured by current genetic instruments. Nevertheless, with continued genome-wide searches for coffee and caffeine related loci along with advanced statistical methods and MR designs, MR promises to be a valuable approach to understanding the causal impact that coffee and caffeine have in human health.
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Affiliation(s)
- Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
| | - Marcus R Munafo
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, UK Centre for Tobacco and Alcohol Studies, School of Psychological Science, University of Bristol, Bristol BS8 1TU, UK.
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14
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Treur JL, Gibson M, Taylor AE, Rogers PJ, Munafò MR. Investigating genetic correlations and causal effects between caffeine consumption and sleep behaviours. J Sleep Res 2018; 27:e12695. [PMID: 29682839 PMCID: PMC6175249 DOI: 10.1111/jsr.12695] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 02/01/2023]
Abstract
Observationally, higher caffeine consumption is associated with poorer sleep and insomnia. We investigated whether these associations are a result of shared genetic risk factors and/or (possibly bidirectional) causal effects. Summary-level data were available from genome-wide association studies on caffeine intake (n = 91 462), plasma caffeine and caffeine metabolic rate (n = 9876), sleep duration and chronotype (being a "morning" versus an "evening" person) (n = 128 266), and insomnia complaints (n = 113 006). First, genetic correlations were calculated, reflecting the extent to which genetic variants influencing caffeine consumption and those influencing sleep overlap. Next, causal effects were estimated with bidirectional, two-sample Mendelian randomization. This approach utilizes the genetic variants most robustly associated with an exposure variable as an "instrument" to test causal effects. Estimates from individual variants were combined using inverse-variance weighted meta-analysis, weighted median regression and MR-Egger regression. We found no clear evidence for a genetic correlation between caffeine intake and sleep duration (rg = 0.000, p = .998), chronotype (rg = 0.086, p = .192) or insomnia complaints (rg = -0.034, p = .700). For plasma caffeine and caffeine metabolic rate, genetic correlations could not be calculated because of the small sample size. Mendelian randomization did not support causal effects of caffeine intake on sleep, or vice versa. There was weak evidence that higher plasma caffeine levels causally decrease the odds of being a morning person. Although caffeine may acutely affect sleep when taken shortly before bedtime, our findings suggest that a sustained pattern of high caffeine consumption is more likely to be associated with poorer sleep through shared environmental factors. Future research should identify such environments, which could aid the development of interventions to improve sleep.
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Affiliation(s)
- Jorien L Treur
- School of Experimental Psychology, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Mark Gibson
- School of Experimental Psychology, University of Bristol, Bristol, UK
| | - Amy E Taylor
- School of Experimental Psychology, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK.,UK Centre for Tobacco and Alcohol Studies, Bristol, UK
| | - Peter J Rogers
- School of Experimental Psychology, University of Bristol, Bristol, UK
| | - Marcus R Munafò
- School of Experimental Psychology, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK.,UK Centre for Tobacco and Alcohol Studies, Bristol, UK
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