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Lu Y, Pike JR, Hoogeveen R, Walker K, Raffield L, Selvin E, Avery C, Engel S, Mielke MM, Garcia T, Heiss G, Palta P. Nonalcoholic Fatty Liver Disease and Longitudinal Change in Imaging and Plasma Biomarkers of Alzheimer Disease and Vascular Pathology. Neurology 2024; 102:e209203. [PMID: 38471046 PMCID: PMC11033987 DOI: 10.1212/wnl.0000000000209203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/23/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Prospective measures of plasma and cerebral MRI biomarkers of Alzheimer disease (AD) and vascular neuropathology provide an opportunity to investigate possible mechanisms linking liver disease and dementia. We aimed to quantify the association of midlife nonalcoholic fatty liver disease (NAFLD) with change in plasma and brain MRI biomarkers of AD and vascular neuropathology. METHODS We included participants from the Atherosclerosis Risk in Communities Study with brain MRI measurements of white matter hyperintensity (WMH) volume and temporal-parietal lobe cortical thickness meta region of interest (ROI) at up to 2 different visits, in 2011-13 and 2016-19, and plasma biomarkers of β-amyloid (Aβ)42:40, phosphorylated tau at threonine 181, and neurofilament light (NfL) were measured up to 3 times in 1993-95, 2011-13, and 2016-19. NAFLD was categorized using the fatty liver index in 1990-92. Multivariate linear regression was performed for associations between midlife NAFLD and change in plasma and brain MRI biomarkers of AD and vascular neuropathology. The primary models adjusted for demographics, Apolipoprotein E, alcohol use, and kidney function. RESULTS Among 1,706 participants (mean age 56 years, 62% female, 28% Black), midlife NAFLD vs no NAFLD was associated with greater late-life WMH volume (difference per SD 0.19, 95% CI 0.06-0.31) and faster late-life WMH increase over 6 years (difference in annual change, SD 0.28, 95% CI 0.05-0.51), suggesting accumulating vascular pathology. Midlife NAFLD vs no NAFLD was also associated with AD biomarkers in midlife (lower Aβ42:40 [SD -0.21, 95% CI -0.39 to -0.04] measured in 1993-95) and late life (lower Aβ42:40 [SD -0.13, 95% CI -0.23 to -0.03] and lower temporal-parietal lobe cortical thickness meta ROI [SD -0.16, 95% CI -0.28 to -0.05] measured in 2011-13). Although midlife NfL was lower in individuals with vs without midlife NAFLD, those with NAFLD exhibited a faster rate of NfL increase that accelerated over time. DISCUSSION Midlife NAFLD shows associations with AD and accumulating vascular pathology, revealing potential pathways linking liver function to dementia. Plasma biomarkers of neuropathology and neuronal injury may serve as easily measurable and dynamic indicators for monitoring the impacts of impaired liver function on brain health.
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Affiliation(s)
- Yifei Lu
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - James R Pike
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Ron Hoogeveen
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Keenan Walker
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Laura Raffield
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Elizabeth Selvin
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Christy Avery
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Stephanie Engel
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Michelle M Mielke
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Tanya Garcia
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Gerardo Heiss
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
| | - Priya Palta
- From the Departments of Epidemiology (Y.L., C.A., S.E., G.H.) and Biostatistics (T.G.), Gillings School of Global Public Health and Departments of Genetics (L.R.) and Neurology (P.P.), School of Medicine, University of North Carolina at Chapel Hill, NC; Department of Epidemiology (J.R.P., E.S.), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Medicine (R.H.), Baylor College of Medicine, Houston, TX; Laboratory of Behavioral Neuroscience (K.W.), National Institute on Aging, Bethesda, MD; and Department of Epidemiology and Prevention (M.M.M.), Wake Forest University School of Medicine, Winston-Salem, NC
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2
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Elgart M, Lyons G, Romero-Brufau S, Kurniansyah N, Brody JA, Guo X, Lin HJ, Raffield L, Gao Y, Chen H, de Vries P, Lloyd-Jones DM, Lange LA, Peloso GM, Fornage M, Rotter JI, Rich SS, Morrison AC, Psaty BM, Levy D, Redline S, Sofer T. Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations. Commun Biol 2022; 5:856. [PMID: 35995843 PMCID: PMC9395509 DOI: 10.1038/s42003-022-03812-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/05/2022] [Indexed: 01/03/2023] Open
Abstract
Polygenic risk scores (PRS) are commonly used to quantify the inherited susceptibility for a trait, yet they fail to account for non-linear and interaction effects between single nucleotide polymorphisms (SNPs). We address this via a machine learning approach, validated in nine complex phenotypes in a multi-ancestry population. We use an ensemble method of SNP selection followed by gradient boosted trees (XGBoost) to allow for non-linearities and interaction effects. We compare our results to the standard, linear PRS model developed using PRSice, LDpred2, and lassosum2. Combining a PRS as a feature in an XGBoost model results in a relative increase in the percentage variance explained compared to the standard linear PRS model by 22% for height, 27% for HDL cholesterol, 43% for body mass index, 50% for sleep duration, 58% for systolic blood pressure, 64% for total cholesterol, 66% for triglycerides, 77% for LDL cholesterol, and 100% for diastolic blood pressure. Multi-ancestry trained models perform similarly to specific racial/ethnic group trained models and are consistently superior to the standard linear PRS models. This work demonstrates an effective method to account for non-linearities and interaction effects in genetics-based prediction models. Combining a standard polygenic risk score (PRS) as a feature in a machine learning model increases the percentage variance explained for those traits, helping to account for non-linearities or interaction effects in genetics-based prediction models.
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Affiliation(s)
- Michael Elgart
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Genevieve Lyons
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Santiago Romero-Brufau
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Nuzulul Kurniansyah
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Henry J Lin
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Yan Gao
- The Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA
| | - Daniel Levy
- The Population Sciences Branch of the National Heart, Lung and Blood Institute, Bethesda, MD, USA.,The Framingham Heart Study, Framingham, MA, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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3
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Bhattacharya R, Zekavat SM, Haessler J, Fornage M, Raffield L, Uddin MM, Bick AG, Niroula A, Yu B, Gibson C, Griffin G, Morrison AC, Psaty BM, Longstreth WT, Bis JC, Rich SS, Rotter JI, Tracy RP, Correa A, Seshadri S, Johnson A, Collins MPH JM, Hayden KM, Madsen TE, Ballantyne CM, Jaiswal S, Ebert BL, Kooperberg C, Manson JE, Whitsel EA, Natarajan P, Reiner AP. Clonal Hematopoiesis Is Associated With Higher Risk of Stroke. Stroke 2022; 53:788-797. [PMID: 34743536 PMCID: PMC8885769 DOI: 10.1161/strokeaha.121.037388] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/25/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND AND PURPOSE Clonal hematopoiesis of indeterminate potential (CHIP) is a novel age-related risk factor for cardiovascular disease-related morbidity and mortality. The association of CHIP with risk of incident ischemic stroke was reported previously in an exploratory analysis including a small number of incident stroke cases without replication and lack of stroke subphenotyping. The purpose of this study was to discover whether CHIP is a risk factor for ischemic or hemorrhagic stroke. METHODS We utilized plasma genome sequence data of blood DNA to identify CHIP in 78 752 individuals from 8 prospective cohorts and biobanks. We then assessed the association of CHIP and commonly mutated individual CHIP driver genes (DNMT3A, TET2, and ASXL1) with any stroke, ischemic stroke, and hemorrhagic stroke. RESULTS CHIP was associated with an increased risk of total stroke (hazard ratio, 1.14 [95% CI, 1.03-1.27]; P=0.01) after adjustment for age, sex, and race. We observed associations with CHIP with risk of hemorrhagic stroke (hazard ratio, 1.24 [95% CI, 1.01-1.51]; P=0.04) and with small vessel ischemic stroke subtypes. In gene-specific association results, TET2 showed the strongest association with total stroke and ischemic stroke, whereas DMNT3A and TET2 were each associated with increased risk of hemorrhagic stroke. CONCLUSIONS CHIP is associated with an increased risk of stroke, particularly with hemorrhagic and small vessel ischemic stroke. Future studies clarifying the relationship between CHIP and subtypes of stroke are needed.
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Affiliation(s)
- Romit Bhattacharya
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Seyedeh M. Zekavat
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Yale School of Medicine, New Haven, CT
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Md Mesbah Uddin
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Abhishek Niroula
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Christopher Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Gabriel Griffin
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
- Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington
| | - Adolfo Correa
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX 78229
- Boston University and the NHLBI’s Framingham Heart Study, Boston, MA, 02215, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Andrew Johnson
- Boston University and the NHLBI’s Framingham Heart Study, Boston, MA, 02215, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 01702
| | - Jason M. Collins MPH
- Department of Epidemiology, University of North Carolina, Gillings School of Global Public Health, Chapel Hill, NC
| | - Kathleen M. Hayden
- Department of Social Sciences and Health Policy, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tracy E. Madsen
- Departments of Emergency Medicine and Epidemiology, Brown University
| | | | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Eric A. Whitsel
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 01702
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC
| | | | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
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4
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Li G, Raffield L, Logue M, Miller MW, Santos HP, O’Shea TM, Fry RC, Li Y. CUE: CpG impUtation ensemble for DNA methylation levels across the human methylation450 (HM450) and EPIC (HM850) BeadChip platforms. Epigenetics 2021; 16:851-861. [PMID: 33016200 PMCID: PMC8330997 DOI: 10.1080/15592294.2020.1827716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/08/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022] Open
Abstract
DNA methylation at CpG dinucleotides is one of the most extensively studied epigenetic marks. With technological advancements, geneticists can profile DNA methylation with multiple reliable approaches. However, profiling platforms can differ substantially in the CpGs they assess, consequently hindering integrated analysis across platforms. Here, we present CpG impUtation Ensemble (CUE), which leverages multiple classical statistical and modern machine learning methods, to impute from the Illumina HumanMethylation450 (HM450) BeadChip to the Illumina HumanMethylationEPIC (HM850) BeadChip. Data were analysed from two population cohorts with methylation measured both by HM450 and HM850: the Extremely Low Gestational Age Newborns (ELGAN) study (n = 127, placenta) and the VA Boston Posttraumatic Stress Disorder (PTSD) genetics repository (n = 144, whole blood). Cross-validation results show that CUE achieves the lowest predicted root-mean-square error (RMSE) (0.026 in PTSD) and the highest accuracy (99.97% in PTSD) compared with five individual methods tested, including k-nearest-neighbours, logistic regression, penalized functional regression, random forest, and XGBoost. Finally, among all 339,033 HM850-only CpG sites shared between ELGAN and PTSD, CUE successfully imputed 289,604 (85.4%) sites, where success was defined as RMSE < 0.05 and accuracy >95% in PTSD. In summary, CUE is a valuable tool for imputing CpG methylation from the HM450 to HM850 platform.
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Affiliation(s)
- Gang Li
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Mark Logue
- National Center for PTSD: Behavioral Sciences Division at VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mark W. Miller
- National Center for PTSD: Behavioral Sciences Division at VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Hudson P. Santos
- School of Nursing, University of North Carolina, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
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Chen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Luan J, Willems SM, Wu Y, Zhang X, Horikoshi M, Boutin TS, Mägi R, Waage J, Li-Gao R, Chan KHK, Yao J, Anasanti MD, Chu AY, Claringbould A, Heikkinen J, Hong J, Hottenga JJ, Huo S, Kaakinen MA, Louie T, März W, Moreno-Macias H, Ndungu A, Nelson SC, Nolte IM, North KE, Raulerson CK, Ray D, Rohde R, Rybin D, Schurmann C, Sim X, Southam L, Stewart ID, Wang CA, Wang Y, Wu P, Zhang W, Ahluwalia TS, Appel EVR, Bielak LF, Brody JA, Burtt NP, Cabrera CP, Cade BE, Chai JF, Chai X, Chang LC, Chen CH, Chen BH, Chitrala KN, Chiu YF, de Haan HG, Delgado GE, Demirkan A, Duan Q, Engmann J, Fatumo SA, Gayán J, Giulianini F, Gong JH, Gustafsson S, Hai Y, Hartwig FP, He J, Heianza Y, Huang T, Huerta-Chagoya A, Hwang MY, Jensen RA, Kawaguchi T, Kentistou KA, Kim YJ, Kleber ME, Kooner IK, Lai S, Lange LA, Langefeld CD, Lauzon M, Li M, Ligthart S, Liu J, Loh M, Long J, Lyssenko V, Mangino M, Marzi C, Montasser ME, Nag A, Nakatochi M, Noce D, Noordam R, Pistis G, Preuss M, Raffield L, Rasmussen-Torvik LJ, Rich SS, Robertson NR, Rueedi R, Ryan K, Sanna S, Saxena R, Schraut KE, Sennblad B, Setoh K, Smith AV, Sparsø T, Strawbridge RJ, Takeuchi F, Tan J, Trompet S, van den Akker E, van der Most PJ, Verweij N, Vogel M, Wang H, Wang C, Wang N, Warren HR, Wen W, Wilsgaard T, Wong A, Wood AR, Xie T, Zafarmand MH, Zhao JH, Zhao W, Amin N, Arzumanyan Z, Astrup A, Bakker SJL, Baldassarre D, Beekman M, Bergman RN, Bertoni A, Blüher M, Bonnycastle LL, Bornstein SR, Bowden DW, Cai Q, Campbell A, Campbell H, Chang YC, de Geus EJC, Dehghan A, Du S, Eiriksdottir G, Farmaki AE, Frånberg M, Fuchsberger C, Gao Y, Gjesing AP, Goel A, Han S, Hartman CA, Herder C, Hicks AA, Hsieh CH, Hsueh WA, Ichihara S, Igase M, Ikram MA, Johnson WC, Jørgensen ME, Joshi PK, Kalyani RR, Kandeel FR, Katsuya T, Khor CC, Kiess W, Kolcic I, Kuulasmaa T, Kuusisto J, Läll K, Lam K, Lawlor DA, Lee NR, Lemaitre RN, Li H, Lin SY, Lindström J, Linneberg A, Liu J, Lorenzo C, Matsubara T, Matsuda F, Mingrone G, Mooijaart S, Moon S, Nabika T, Nadkarni GN, Nadler JL, Nelis M, Neville MJ, Norris JM, Ohyagi Y, Peters A, Peyser PA, Polasek O, Qi Q, Raven D, Reilly DF, Reiner A, Rivideneira F, Roll K, Rudan I, Sabanayagam C, Sandow K, Sattar N, Schürmann A, Shi J, Stringham HM, Taylor KD, Teslovich TM, Thuesen B, Timmers PRHJ, Tremoli E, Tsai MY, Uitterlinden A, van Dam RM, van Heemst D, van Hylckama Vlieg A, van Vliet-Ostaptchouk JV, Vangipurapu J, Vestergaard H, Wang T, Willems van Dijk K, Zemunik T, Abecasis GR, Adair LS, Aguilar-Salinas CA, Alarcón-Riquelme ME, An P, Aviles-Santa L, Becker DM, Beilin LJ, Bergmann S, Bisgaard H, Black C, Boehnke M, Boerwinkle E, Böhm BO, Bønnelykke K, Boomsma DI, Bottinger EP, Buchanan TA, Canouil M, Caulfield MJ, Chambers JC, Chasman DI, Chen YDI, Cheng CY, Collins FS, Correa A, Cucca F, de Silva HJ, Dedoussis G, Elmståhl S, Evans MK, Ferrannini E, Ferrucci L, Florez JC, Franks PW, Frayling TM, Froguel P, Gigante B, Goodarzi MO, Gordon-Larsen P, Grallert H, Grarup N, Grimsgaard S, Groop L, Gudnason V, Guo X, Hamsten A, Hansen T, Hayward C, Heckbert SR, Horta BL, Huang W, Ingelsson E, James PS, Jarvelin MR, Jonas JB, Jukema JW, Kaleebu P, Kaplan R, Kardia SLR, Kato N, Keinanen-Kiukaanniemi SM, Kim BJ, Kivimaki M, Koistinen HA, Kooner JS, Körner A, Kovacs P, Kuh D, Kumari M, Kutalik Z, Laakso M, Lakka TA, Launer LJ, Leander K, Li H, Lin X, Lind L, Lindgren C, Liu S, Loos RJF, Magnusson PKE, Mahajan A, Metspalu A, Mook-Kanamori DO, Mori TA, Munroe PB, Njølstad I, O'Connell JR, Oldehinkel AJ, Ong KK, Padmanabhan S, Palmer CNA, Palmer ND, Pedersen O, Pennell CE, Porteous DJ, Pramstaller PP, Province MA, Psaty BM, Qi L, Raffel LJ, Rauramaa R, Redline S, Ridker PM, Rosendaal FR, Saaristo TE, Sandhu M, Saramies J, Schneiderman N, Schwarz P, Scott LJ, Selvin E, Sever P, Shu XO, Slagboom PE, Small KS, Smith BH, Snieder H, Sofer T, Sørensen TIA, Spector TD, Stanton A, Steves CJ, Stumvoll M, Sun L, Tabara Y, Tai ES, Timpson NJ, Tönjes A, Tuomilehto J, Tusie T, Uusitupa M, van der Harst P, van Duijn C, Vitart V, Vollenweider P, Vrijkotte TGM, Wagenknecht LE, Walker M, Wang YX, Wareham NJ, Watanabe RM, Watkins H, Wei WB, Wickremasinghe AR, Willemsen G, Wilson JF, Wong TY, Wu JY, Xiang AH, Yanek LR, Yengo L, Yokota M, Zeggini E, Zheng W, Zonderman AB, Rotter JI, Gloyn AL, McCarthy MI, Dupuis J, Meigs JB, Scott RA, Prokopenko I, Leong A, Liu CT, Parker SCJ, Mohlke KL, Langenberg C, Wheeler E, Morris AP, Barroso I. The trans-ancestral genomic architecture of glycemic traits. Nat Genet 2021; 53:840-860. [PMID: 34059833 PMCID: PMC7610958 DOI: 10.1038/s41588-021-00852-9] [Citation(s) in RCA: 269] [Impact Index Per Article: 89.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10-8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.
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Affiliation(s)
- Ji Chen
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA
| | - Gaëlle Marenne
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- Inserm, Univ Brest, EFS, UMR 1078, GGB, Brest, France
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Laura J Corbin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sara M Willems
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Xiaoshuai Zhang
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Momoko Horikoshi
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Laboratory for Genomics of Diabetes and Metabolism, RIKEN Centre for Integrative Medical Sciences, Yokohama, Japan
| | - Thibaud S Boutin
- Medical Research Council Human Genetics Unit, Institute for Genetics and Molecular Medicine, Edinburgh, UK
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kei Hang Katie Chan
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong SAR, China
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mila D Anasanti
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Audrey Y Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jani Heikkinen
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jaeyoung Hong
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Shaofeng Huo
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Marika A Kaakinen
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Section of Statistical Multi-omics, Department of Clinical and Experimental Research, University of Surrey, Guildford, UK
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Winfried März
- SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University Graz, Graz, Austria
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, Heidelberg University, Mannheim, Baden-Württemberg, Germany
| | | | - Anne Ndungu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kari E North
- CVD Genetic Epidemiology Computational Laboratory, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | | | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Rebecca Rohde
- CVD Genetic Epidemiology Computational Laboratory, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Denis Rybin
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- HPI Digital Health Center, Digital Health and Personalized Medicine, Hasso Plattner Institute, Potsdam, Germany
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Lorraine Southam
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Carol A Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Yujie Wang
- CVD Genetic Epidemiology Computational Laboratory, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
| | - 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
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Emil V R Appel
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Brody
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Noël P Burtt
- Metabolism Program, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Claudia P Cabrera
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Brian E Cade
- Department of Medicine, Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
| | - Xiaoran Chai
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Brian H Chen
- Department of Epidemiology, The Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yen-Feng Chiu
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Hugoline G de Haan
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Graciela E Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, Heidelberg University, Mannheim, Baden-Württemberg, Germany
| | - Ayse Demirkan
- Section of Statistical Multi-omics, Department of Clinical and Experimental Research, University of Surrey, Guildford, UK
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jorgen Engmann
- Institute of Cardiovascular Science, University College London, London, UK
| | - Segun A Fatumo
- Uganda Medical Informatics Centre (UMIC), MRC/UVRI and London School of Hygiene & Tropical Medicine (Uganda Research Unit), Entebbe, Uganda
- London School of Hygiene & Tropical Medicine, London, UK
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | | | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jung Ho Gong
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
| | - Stefan Gustafsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Yang Hai
- Department of Statistics, The University of Auckland, Science Center, Auckland, New Zealand
| | - Fernando P Hartwig
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Jing He
- Department of Medicine, Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yoriko Heianza
- Department of Epidemiology, Tulane University Obesity Research Center, Tulane University, New Orleans, LA, USA
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Alicia Huerta-Chagoya
- Molecular Biology and Genomic Medicine Unit, National Council for Science and Technology, Mexico City, Mexico
- Molecular Biology and Genomic Medicine Unit, National Institute of Medical Sciences and Nutrition, Mexico City, Mexico
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Richard A Jensen
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, Heidelberg University, Mannheim, Baden-Württemberg, Germany
| | - Ishminder K Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
| | - Shuiqing Lai
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
| | - Leslie A Lange
- Department of Medicine, Divison of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Marie Lauzon
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Man Li
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | - Symen Ligthart
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jun Liu
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Valeriya Lyssenko
- Department of Clinical Science, Center for Diabetes Research, University of Bergen, Bergen, Norway
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmo, Sweden
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carola Marzi
- Institute of Epidemiology, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - May E Montasser
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Abhishek Nag
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Damia Noce
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Neil R Robertson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Richa Saxena
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Bengt Sennblad
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kazuya Setoh
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
| | - Thomas Sparsø
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rona J Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Department of Medicine Solna, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik van den Akker
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, the Netherlands
- Department of Biomedical Data Sciences, Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Genomics PLC, Oxford, UK
| | - Mandy Vogel
- Center of Pediatric Research, University Children's Hospital Leipzig, University of Leipzig Medical Center, Leipzig, Germany
| | - Heming Wang
- Department of Medicine, Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Nan Wang
- Department of Preventive Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- University of Southern California Diabetes and Obesity Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Helen R Warren
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tom Wilsgaard
- Department of Community Medicine, Faculty of Health Sciences, UIT the Arctic University of Norway, Tromsø, Norway
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Andrew R Wood
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Tian Xie
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mohammad Hadi Zafarmand
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Jing-Hua Zhao
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Zorayr Arzumanyan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Arne Astrup
- Department of Nutrition, Exercise, and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Stephan J L Bakker
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Damiano Baldassarre
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
- Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Marian Beekman
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Richard N Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alain Bertoni
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Matthias Blüher
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Lori L Bonnycastle
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institues of Health, Bethesda, MD, USA
| | - Stefan R Bornstein
- Department for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Qiuyin Cai
- Department of Medicine, Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Yi Cheng Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | - Eco J C de Geus
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Shufa Du
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | | | - Aliki Eleni Farmaki
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Mattias Frånberg
- Department of Medicine Solna, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Yutang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Anette P Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anuj Goel
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sohee Han
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Catharina A Hartman
- Department of Psychiatry, Interdisciplinary Center Psychopathy and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Düsseldorf, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Chang-Hsun Hsieh
- Internal Medicine, Endocrine and Metabolism, Tri-Service General Hospital, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Willa A Hsueh
- Internal Medicine, Endocrinology, Diabetes and Metabolism, Diabetes and Metabolism Research Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Michiya Igase
- Department of Anti-aging Medicine, Ehime University Graduate School of Medicine, Toon, Japan
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- National Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Rita R Kalyani
- Department of Medicine, Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fouad R Kandeel
- Clinical Diabetes, Endocrinology and Metabolism, Translational Research and Cellular Therapeutics, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Wieland Kiess
- Center of Pediatric Research, University Children's Hospital Leipzig, University of Leipzig Medical Center, Leipzig, Germany
| | - Ivana Kolcic
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Teemu Kuulasmaa
- Institute of Biomedicine, Bioinformatics Center, Univeristy of Eastern Finland, Kuopio, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kristi Läll
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kelvin Lam
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nanette R Lee
- USC-Office of Population Studies Foundation, University of San Carlos, Cebu City, the Philippines
- Department of Anthropology, Sociology and History, University of San Carlos, Cebu City, the Philippines
| | - Rozenn N Lemaitre
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Honglan Li
- State Key Laboratory of Oncogene and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shih-Yi Lin
- Center for Geriatrics and Gerontology, Taichung Veterans General Hospital, Taichung, Taiwan
- National Defense Medical Center, National Yang-Ming University, Taipei, Taiwan
| | - Jaana Lindström
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Carlos Lorenzo
- Department of Medicine, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Tatsuaki Matsubara
- Department of Internal Medicine, Aichi Gakuin University School of Dentistry, Nagoya, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Geltrude Mingrone
- Department of Diabetes, Diabetes, and Nutritional Sciences, James Black Centre, King's College London, London, UK
| | - Simon Mooijaart
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sanghoon Moon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerry L Nadler
- Department of Medicine and Pharmacology, New York Medical College School of Medicine, Valhalla, NY, USA
| | - Mari Nelis
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jill M Norris
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yasumasa Ohyagi
- Department of Geriatric Medicine and Neurology, Ehime University Graduate School of Medicine, Toon, Japan
| | - Annette Peters
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians University Munich, Munich, Germany
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ozren Polasek
- Department of Public Health, University of Split School of Medicine, Split, Croatia
- Gen-Info, Zagreb, Croatia
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Dennis Raven
- Department of Psychiatry, Interdisciplinary Center Psychopathy and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dermot F Reilly
- Genetics and Pharmacogenomics, Merck Sharp & Dohme, Kenilworth, NJ, USA
| | - Alex Reiner
- Department of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Fernando Rivideneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kathryn Roll
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Igor Rudan
- Centre for Global Health, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Charumathi Sabanayagam
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Kevin Sandow
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Annette Schürmann
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jinxiu Shi
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Academy of Science & Technology (SAST), Shanghai, China
| | - Heather M Stringham
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Betina Thuesen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Michael Y Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Jana V van Vliet-Ostaptchouk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
| | - Ko Willems van Dijk
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
- Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Tatijana Zemunik
- Department of Human Biology, University of Split School of Medicine, Split, Croatia
| | - Gonçalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Linda S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Carlos Alberto Aguilar-Salinas
- Department of Endocrinology and Metabolism, Instituto Nacional de Ciencias Medicas y Nutricion, Mexico City, Mexico
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición and Tec Salud, Mexico City, Mexico
- Instituto Tecnológico y de Estudios Superiores de Monterrey Tec Salud, Monterrey, Mexico
| | - Marta E Alarcón-Riquelme
- Department of Medical Genomics, Pfizer/University of Granada/Andalusian Government Center for Genomics and Oncological Research (GENYO), Granada, Spain
- Institute for Environmental Medicine, Chronic Inflammatory Diseases, Karolinska Institutet, Solna, Sweden
| | - Ping An
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
| | - Larissa Aviles-Santa
- Clinical and Health Services Research, National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Diane M Becker
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence J Beilin
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Perth, Western Australia, Australia
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Corri Black
- Aberdeen Centre for Health Data Science, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Michael Boehnke
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Bernhard O Böhm
- Division of Endocrinology and Diabetes, Graduate School of Molecular Endocrinology and Diabetes, University of Ulm, Ulm, Germany
- LKC School of Medicine, Nanyang Technological University, Singapore and Imperial College London, UK, Singapore, Singapore
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - D I Boomsma
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Digital Health Center, Hasso Plattner Institut, University Potsdam, Potsdam, Germany
| | - Thomas A Buchanan
- University of Southern California Diabetes and Obesity Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Mickaël Canouil
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Université de Lille, Lille, France
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, France
| | - Mark J Caulfield
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ching-Yu Cheng
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Francis S Collins
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institues of Health, Bethesda, MD, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Kallithea, Greece
| | - Sölve Elmståhl
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - Luigi Ferrucci
- Intramural Research Program, National Institute of Aging, Baltimore, MD, USA
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul W Franks
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmo, Sweden
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Timothy M Frayling
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Philippe Froguel
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Université de Lille, Lille, France
- INSERM UMR 1283/CNRS UMR 8199, European Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, France
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Bruna Gigante
- Department of Medicine, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mark O Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Harald Grallert
- Institute of Epidemiology, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sameline Grimsgaard
- Department of Community Medicine, Faculty of Health Sciences, UIT the Arctic University of Norway, Tromsø, Norway
| | - Leif Groop
- Diabetes Centre, Lund University, Lund, Sweden
- Finnish Institute of Molecular Medicine, Helsinki University, Helsinki, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Anders Hamsten
- Department of Medicine Solna, Cardiovascular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan R Heckbert
- Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Bernardo L Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Wei Huang
- Department of Genetics, Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai (CHGC) and Shanghai Academy of Science & Technology (SAST), Shanghai, China
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Pankow S James
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Marjo-Ritta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu Univerisity Hospital, OYS, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Institute of Molecular and Clinical Ophthalmology Basel IOB, Basel, Switzerland
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, New York, NY, USA
- Department of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Sirkka M Keinanen-Kiukaanniemi
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, Oulu, Finland
- Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju, South Korea
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Heikki A Koistinen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Antje Körner
- Center of Pediatric Research, University Children's Hospital Leipzig, University of Leipzig Medical Center, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Zoltan Kutalik
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Institute of Primary Care and Public Health, Division of Biostatistics, University of Lausanne, Lausanne, Switzerland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Karin Leander
- Institute of Environmental Medicine, Cardiovascular and Nutritional Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - Huaixing Li
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xu Lin
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lars Lind
- Department of Medical Sciences, University of Uppsala, Uppsala, Sweden
| | - Cecilia Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | - Simin Liu
- Department of Epidemiology, Brown University School of Public Health, Brown University, Providence, RI, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics and the Swedish Twin Registry, Karolinska Institutet, Stockholm, Sweden
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Trevor A Mori
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Perth, Western Australia, Australia
| | - Patricia B Munroe
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Inger Njølstad
- Department of Community Medicine, Faculty of Health Sciences, UIT the Arctic University of Norway, Tromsø, Norway
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Albertine J Oldehinkel
- Department of Psychiatry, Interdisciplinary Center Psychopathy and Emotion Regulation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | | | - Michael A Province
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
| | - Bruce M Psaty
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Lu Qi
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, Irvine, CA, USA
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Susan Redline
- Department of Medicine, Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Havard Medical School, Boston, MA, USA
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Timo E Saaristo
- Tampere, Finnish Diabetes Association, Tampere, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | | | | | | | - Peter Schwarz
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Department for Prevention and Care of Diabetes, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich, University Hospital and Faculty of Medicine, Dresden, Germany
| | - Laura J Scott
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - P Eline Slagboom
- Department of Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Alice Stanton
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
- Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael Stumvoll
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Liang Sun
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National Univeristy of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Cardiovascular and Metabolic Disease Signature Research Program, Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Anke Tönjes
- Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Saudi Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Teresa Tusie
- Molecular Biology and Genomic Medicine Unit, National Institute of Medical Sciences and Nutrition, Mexico City, Mexico
- Department of Genomic Medicine and Environmental Toxicology, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| | - Matti Uusitupa
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Pim van der Harst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Tanja G M Vrijkotte
- Department of Public Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Lynne E Wagenknecht
- Department of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Mark Walker
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ya X Wang
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Nick J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Richard M Watanabe
- Department of Preventive Medicine, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- University of Southern California Diabetes and Obesity Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Hugh Watkins
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Wen B Wei
- Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | | | - Gonneke Willemsen
- Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Tien-Yin Wong
- Ocular Epidemiology, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Anny H Xiang
- Department of Research and Evaluation, Kaiser Permanente of Southern California, Pasadena, CA, USA
| | - Lisa R Yanek
- Department of Medicine, General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Loïc Yengo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Inga Prokopenko
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Section of Statistical Multi-omics, Department of Clinical and Experimental Research, University of Surrey, Guildford, UK
| | - Aaron Leong
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Diabetes Unit and Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Eleanor Wheeler
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Inês Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK.
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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6
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Breeze CE, Batorsky A, Lee MK, Szeto MD, Xu X, McCartney DL, Jiang R, Patki A, Kramer HJ, Eales JM, Raffield L, Lange L, Lange E, Durda P, Liu Y, Tracy RP, Van Den Berg D, Evans KL, Kraus WE, Shah S, Tiwari HK, Hou L, Whitsel EA, Jiang X, Charchar FJ, Baccarelli AA, Rich SS, Morris AP, Irvin MR, Arnett DK, Hauser ER, Rotter JI, Correa A, Hayward C, Horvath S, Marioni RE, Tomaszewski M, Beck S, Berndt SI, London SJ, Mychaleckyj JC, Franceschini N. Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci. Genome Med 2021; 13:74. [PMID: 33931109 PMCID: PMC8088054 DOI: 10.1186/s13073-021-00877-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/24/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach. METHODS The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear mixed models adjusting for age, sex, smoking, and study-specific and technical variables. Summary results were meta-analyzed within and across ethnicities. Findings were assessed using integrative epigenomics methods and pathway analyses. RESULTS We identified 93 DMPs associated with eGFR at an FDR of 0.05 and replicated 13 and 1 DMPs across independent samples in trans-ethnic and African American meta-analyses, respectively. The study also validated 6 previously published DMPs. Identified DMPs showed significant overlap enrichment with DNase I hypersensitive sites in kidney tissue, sites associated with the expression of proximal genes, and transcription factor motifs and pathways associated with kidney tissue and kidney development. CONCLUSIONS We uncovered trans-ethnic and ethnic-specific DMPs associated with eGFR, including DMPs enriched in regulatory elements in kidney tissue and pathways related to kidney development. These findings shed light on epigenetic mechanisms associated with kidney function, bridging the gap between population-specific eGFR-associated DNAm and tissue-specific regulatory context.
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Affiliation(s)
- Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA.
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
- Altius Institute for Biomedical Sciences, Seattle, WA, 98121, USA.
| | - Anna Batorsky
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27516, USA
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Mindy D Szeto
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Rong Jiang
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, 27701, USA
| | - Amit Patki
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Holly J Kramer
- Department of Public Health Sciences and Medicine, Loyola University Chicago, Maywood, IL, USA
- Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, IL, USA
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ethan Lange
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Yongmei Liu
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Russ P Tracy
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - David Van Den Berg
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Svati Shah
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Hermant K Tiwari
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Global Oncology, Institute of Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Eric A Whitsel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Fadi J Charchar
- School of Health and Life Sciences, Federation University Australia, Ballarat, VIC, Australia
- Department of Physiology, University of Melbourne, Parkville, VIC, Australia
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Andrea A Baccarelli
- Laboratory of Environmental Epigenetics, Departments of Environmental Health Sciences and Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Elizabeth R Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Durham VA Health System, Durham, NC, 27705, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Heart Centre and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.
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7
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Polfus LM, Darst BF, Highland H, Sheng X, Ng MCY, Below JE, Petty L, Bien S, Sim X, Wang W, Fontanillas P, Patel Y, Preuss M, Schurmann C, Du Z, Lu Y, Rhie SK, Mercader JM, Tusie-Luna T, González-Villalpando C, Orozco L, Spracklen CN, Cade BE, Jensen RA, Sun M, Joo YY, An P, Yanek LR, Bielak LF, Tajuddin S, Nicolas A, Chen G, Raffield L, Guo X, Chen WM, Nadkarni GN, Graff M, Tao R, Pankow JS, Daviglus M, Qi Q, Boerwinkle EA, Liu S, Phillips LS, Peters U, Carlson C, Wikens LR, Marchand LL, North KE, Buyske S, Kooperberg C, Loos RJF, Stram DO, Haiman CA. Genetic discovery and risk characterization in type 2 diabetes across diverse populations. HGG Adv 2021; 2. [PMID: 34604815 PMCID: PMC8486151 DOI: 10.1016/j.xhgg.2021.100029] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genomic discovery and characterization of risk loci for type 2 diabetes (T2D) have been conducted primarily in individuals of European ancestry. We conducted a multiethnic genome-wide association study of T2D among 53,102 cases and 193,679 control subjects from African, Hispanic, Asian, Native Hawaiian, and European population groups in the Population Architecture Genomics and Epidemiology (PAGE) and Diabetes Genetics Replication and Meta-analysis (DIAGRAM) Consortia. In individuals of African ancestry, we discovered a risk variant in the TGFB1 gene (rs11466334, risk allele frequency (RAF) = 6.8%, odds ratio [OR] = 1.27, p = 2.06 × 10−8), which replicated in independent studies of African ancestry (p = 6.26 × 10−23). We identified a multiethnic risk variant in the BACE2 gene (rs13052926, RAF = 14.1%, OR = 1.08, p = 5.75 × 10−9), which also replicated in independent studies (p = 3.45 × 10−4). We also observed a significant difference in the performance of a multiethnic genetic risk score (GRS) across population groups (pheterogeneity = 3.85 × 10−20). Comparing individuals in the top GRS risk category (40%–60%), the OR was highest in Asians (OR = 3.08) and European (OR = 2.94) ancestry populations, followed by Hispanic (OR = 2.39), Native Hawaiian (OR = 2.02), and African ancestry (OR = 1.57) populations. These findings underscore the importance of genetic discovery and risk characterization in diverse populations and the urgent need to further increase representation of non-European ancestry individuals in genetics research to improve genetic-based risk prediction across populations.
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Affiliation(s)
- Linda M Polfus
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA.,These authors contributed equally
| | - Burcu F Darst
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA.,These authors contributed equally
| | - Heather Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xin Sheng
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Maggie C Y Ng
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer E Below
- The Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren Petty
- The Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | | | | | - Yesha Patel
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | | | | | | | - Michael Preuss
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Claudia Schurmann
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Zhaohui Du
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Yingchang Lu
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Cassandra N Spracklen
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Richard A Jensen
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Meng Sun
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK, USA
| | - Yoonjung Yoonie Joo
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ping An
- Division of Statistical Genomics, School of Medicine, Washington University, St. Louis, MO, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Salman Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wei-Min Chen
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Girish N Nadkarni
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois Chicago, Chicago, IL, USA
| | - Qibin Qi
- Center for Population Cohorts, Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eric A Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Simin Liu
- School of Public Health, Brown University, Providence, RI, USA
| | - Lawrence S Phillips
- Atlanta VA Medical Center, Decatur, GA, USA.,Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, University of Washington, Department of Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lynne R Wikens
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Loic Le Marchand
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ruth J F Loos
- Icahn School of Medicine at Mount Sinai, The Mindich Child Health and Development Institute, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
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8
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Irvin MR, Sitlani CM, Floyd JS, Psaty BM, Bis JC, Wiggins KL, Whitsel EA, Sturmer T, Stewart J, Raffield L, Sun F, Liu CT, Xu H, Cupples AL, Tanner RM, Rossing P, Smith A, Zilhão NR, Launer LJ, Noordam R, Rotter JI, Yao J, Li X, Guo X, Limdi N, Sundaresan A, Lange L, Correa A, Stott DJ, Ford I, Jukema JW, Gudnason V, Mook-Kanamori DO, Trompet S, Palmas W, Warren HR, Hellwege JN, Giri A, O'donnell C, Hung AM, Edwards TL, Ahluwalia TS, Arnett DK, Avery CL. Genome-Wide Association Study of Apparent Treatment-Resistant Hypertension in the CHARGE Consortium: The CHARGE Pharmacogenetics Working Group. Am J Hypertens 2019; 32:1146-1153. [PMID: 31545351 DOI: 10.1093/ajh/hpz150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Only a handful of genetic discovery efforts in apparent treatment-resistant hypertension (aTRH) have been described. METHODS We conducted a case-control genome-wide association study of aTRH among persons treated for hypertension, using data from 10 cohorts of European ancestry (EA) and 5 cohorts of African ancestry (AA). Cases were treated with 3 different antihypertensive medication classes and had blood pressure (BP) above goal (systolic BP ≥ 140 mm Hg and/or diastolic BP ≥ 90 mm Hg) or 4 or more medication classes regardless of BP control (nEA = 931, nAA = 228). Both a normotensive control group and a treatment-responsive control group were considered in separate analyses. Normotensive controls were untreated (nEA = 14,210, nAA = 2,480) and had systolic BP/diastolic BP < 140/90 mm Hg. Treatment-responsive controls (nEA = 5,266, nAA = 1,817) had BP at goal (<140/90 mm Hg), while treated with one antihypertensive medication class. Individual cohorts used logistic regression with adjustment for age, sex, study site, and principal components for ancestry to examine the association of single-nucleotide polymorphisms with case-control status. Inverse variance-weighted fixed-effects meta-analyses were carried out using METAL. RESULTS The known hypertension locus, CASZ1, was a top finding among EAs (P = 1.1 × 10-8) and in the race-combined analysis (P = 1.5 × 10-9) using the normotensive control group (rs12046278, odds ratio = 0.71 (95% confidence interval: 0.6-0.8)). Single-nucleotide polymorphisms in this locus were robustly replicated in the Million Veterans Program (MVP) study in consideration of a treatment-responsive control group. There were no statistically significant findings for the discovery analyses including treatment-responsive controls. CONCLUSION This genomic discovery effort for aTRH identified CASZ1 as an aTRH risk locus.
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Affiliation(s)
- Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Health Services, University of Washington, Seattle, Washington, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Eric A Whitsel
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Til Sturmer
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - James Stewart
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Fangui Sun
- Department of Biostatistics, Boston University, Boston, Maryland, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University, Boston, Maryland, USA
| | - Hanfei Xu
- Department of Biostatistics, Boston University, Boston, Maryland, USA
| | | | - Rikki M Tanner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Albert Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | | | - Lenore J Launer
- Laboratory of Epidemiology and Population Science, Intramural Research Program, National Institute on Aging, Bethesda, Maryland, USA
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, LABioMed at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Nita Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Aishwarya Sundaresan
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Leslie Lange
- Department of Medicine, University of Colorado–Denver, Aurora, Colorado, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Vilmundur Gudnason
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Walter Palmas
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Helen R Warren
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- National Institute for Health Research Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, UK
| | - Jacklyn N Hellwege
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, Tennessee, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ayush Giri
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, Tennessee, USA
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher O'donnell
- VA Boston Health Care System, Boston, Massachusetts, USA
- Section of Cardiology and Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adriana M Hung
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, Tennessee, USA
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Todd L Edwards
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, Tennessee, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Donna K Arnett
- Deans Office, School of Public Health, University of Kentucky, Lexington, Kentucky, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
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9
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Sofer T, Zheng X, Gogarten SM, Laurie CA, Grinde K, Shaffer JR, Shungin D, O’Connell JR, Durazo-Arvizo RA, Raffield L, Lange L, Musani S, Vasan RS, Cupples LA, Reiner AP, Laurie CC, Rice KM. A fully adjusted two-stage procedure for rank-normalization in genetic association studies. Genet Epidemiol 2019; 43:263-275. [PMID: 30653739 PMCID: PMC6416071 DOI: 10.1002/gepi.22188] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/11/2018] [Indexed: 12/20/2022]
Abstract
When testing genotype-phenotype associations using linear regression, departure of the trait distribution from normality can impact both Type I error rate control and statistical power, with worse consequences for rarer variants. Because genotypes are expected to have small effects (if any) investigators now routinely use a two-stage method, in which they first regress the trait on covariates, obtain residuals, rank-normalize them, and then use the rank-normalized residuals in association analysis with the genotypes. Potential confounding signals are assumed to be removed at the first stage, so in practice, no further adjustment is done in the second stage. Here, we show that this widely used approach can lead to tests with undesirable statistical properties, due to both combination of a mis-specified mean-variance relationship and remaining covariate associations between the rank-normalized residuals and genotypes. We demonstrate these properties theoretically, and also in applications to genome-wide and whole-genome sequencing association studies. We further propose and evaluate an alternative fully adjusted two-stage approach that adjusts for covariates both when residuals are obtained and in the subsequent association test. This method can reduce excess Type I errors and improve statistical power.
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Affiliation(s)
- Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Dividsion of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Cecelia A. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kelsey Grinde
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - John R. Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dmitry Shungin
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Jeffrey R. O’Connell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ramon A. Durazo-Arvizo
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Solomon Musani
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Ramachandran S. Vasan
- Departments of Medicine, Biostatistics and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA, USA
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alexander P. Reiner
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | | | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
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10
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Duan Q, Xu Z, Raffield L, Chang S, Wu D, Lange EM, Reiner AP, Li Y. A robust and powerful two-step testing procedure for local ancestry adjusted allelic association analysis in admixed populations. Genet Epidemiol 2018; 42:288-302. [PMID: 29226381 PMCID: PMC5851818 DOI: 10.1002/gepi.22104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 09/07/2017] [Accepted: 10/20/2017] [Indexed: 12/23/2022]
Abstract
Genetic association studies in admixed populations allow us to gain deeper understanding of the genetic architecture of human diseases and traits. However, population stratification, complicated linkage disequilibrium (LD) patterns, and the complex interplay of allelic and ancestry effects on phenotypic traits pose challenges in such analyses. These issues may lead to detecting spurious associations and/or result in reduced statistical power. Fortunately, if handled appropriately, these same challenges provide unique opportunities for gene mapping. To address these challenges and to take these opportunities, we propose a robust and powerful two-step testing procedure Local Ancestry Adjusted Allelic (LAAA) association. In the first step, LAAA robustly captures associations due to allelic effect, ancestry effect, and interaction effect, allowing detection of effect heterogeneity across ancestral populations. In the second step, LAAA identifies the source of association, namely allelic, ancestry, or the combination. By jointly modeling allele, local ancestry, and ancestry-specific allelic effects, LAAA is highly powerful in capturing the presence of interaction between ancestry and allele effect. We evaluated the validity and statistical power of LAAA through simulations over a broad spectrum of scenarios. We further illustrated its usefulness by application to the Candidate Gene Association Resource (CARe) African American participants for association with hemoglobin levels. We were able to replicate independent groups' previously identified loci that would have been missed in CARe without joint testing. Moreover, the loci, for which LAAA detected potential effect heterogeneity, were replicated among African Americans from the Women's Health Initiative study. LAAA is freely available at https://yunliweb.its.unc.edu/LAAA.
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Affiliation(s)
- Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of North Carolina, Chapel Hill, NC, USA
| | - Zheng Xu
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE
- Initiative of Quantitative Life Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Suhua Chang
- Institute of Psychology, Chinese Academy of Science, Beijing, China
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Periodontology, University of North Carolina, Chapel Hill, NC, USA
| | - Ethan M. Lange
- Department of Medicine, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO, USA
- Department of Biostatistics and Informatics, University of Colorado at Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Alex P. Reiner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
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11
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Joshi PK, Pirastu N, Kentistou KA, Fischer K, Hofer E, Schraut KE, Clark DW, Nutile T, Barnes CLK, Timmers PRHJ, Shen X, Gandin I, McDaid AF, Hansen TF, Gordon SD, Giulianini F, Boutin TS, Abdellaoui A, Zhao W, Medina-Gomez C, Bartz TM, Trompet S, Lange LA, Raffield L, van der Spek A, Galesloot TE, Proitsi P, Yanek LR, Bielak LF, Payton A, Murgia F, Concas MP, Biino G, Tajuddin SM, Seppälä I, Amin N, Boerwinkle E, Børglum AD, Campbell A, Demerath EW, Demuth I, Faul JD, Ford I, Gialluisi A, Gögele M, Graff M, Hingorani A, Hottenga JJ, Hougaard DM, Hurme MA, Ikram MA, Jylhä M, Kuh D, Ligthart L, Lill CM, Lindenberger U, Lumley T, Mägi R, Marques-Vidal P, Medland SE, Milani L, Nagy R, Ollier WER, Peyser PA, Pramstaller PP, Ridker PM, Rivadeneira F, Ruggiero D, Saba Y, Schmidt R, Schmidt H, Slagboom PE, Smith BH, Smith JA, Sotoodehnia N, Steinhagen-Thiessen E, van Rooij FJA, Verbeek AL, Vermeulen SH, Vollenweider P, Wang Y, Werge T, Whitfield JB, Zonderman AB, Lehtimäki T, Evans MK, Pirastu M, Fuchsberger C, Bertram L, Pendleton N, Kardia SLR, Ciullo M, Becker DM, Wong A, Psaty BM, van Duijn CM, Wilson JG, Jukema JW, Kiemeney L, Uitterlinden AG, Franceschini N, North KE, Weir DR, Metspalu A, Boomsma DI, Hayward C, Chasman D, Martin NG, Sattar N, Campbell H, Esko T, Kutalik Z, Wilson JF. Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity. Nat Commun 2017; 8:910. [PMID: 29030599 PMCID: PMC5715013 DOI: 10.1038/s41467-017-00934-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/08/2017] [Indexed: 01/03/2023] Open
Abstract
Genomic analysis of longevity offers the potential to illuminate the biology of human aging. Here, using genome-wide association meta-analysis of 606,059 parents’ survival, we discover two regions associated with longevity (HLA-DQA1/DRB1 and LPA). We also validate previous suggestions that APOE, CHRNA3/5, CDKN2A/B, SH2B3 and FOXO3A influence longevity. Next we show that giving up smoking, educational attainment, openness to new experience and high-density lipoprotein (HDL) cholesterol levels are most positively genetically correlated with lifespan while susceptibility to coronary artery disease (CAD), cigarettes smoked per day, lung cancer, insulin resistance and body fat are most negatively correlated. We suggest that the effect of education on lifespan is principally mediated through smoking while the effect of obesity appears to act via CAD. Using instrumental variables, we suggest that an increase of one body mass index unit reduces lifespan by 7 months while 1 year of education adds 11 months to expected lifespan. Variability in human longevity is genetically influenced. Using genetic data of parental lifespan, the authors identify associations at HLA-DQA/DRB1 and LPA and find that genetic variants that increase educational attainment have a positive effect on lifespan whereas increasing BMI negatively affects lifespan.
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Affiliation(s)
- Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK.
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK.,Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, Scotland
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, University of Tartu, Tartu, 51010, Estonia
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, 8036, Austria.,Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, 8036, Austria
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK.,Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, Scotland
| | - David W Clark
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Teresa Nutile
- Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Naples, 80131, Italy
| | - Catriona L K Barnes
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Xia Shen
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Ilaria Gandin
- Department of Medical Sciences, University of Trieste, Trieste, 34100, Italy.,Institute for Maternal and Child Health, IRCCS "Burlo Garofolo", Trieste, 34137, Italy
| | - Aaron F McDaid
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, 1010, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Thomas Folkmann Hansen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, DK-4000, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, DK-8000, Denmark
| | - Scott D Gordon
- QIMR Berghofer Institute of Medical Research, Brisbane, QLD, 4006, Australia
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA
| | - Thibaud S Boutin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Abdel Abdellaoui
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, Amsterdam Public Health Institute (APH), Amsterdam, 1081BT, Netherlands
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, 2300RC, The Netherlands.,Department of Cardiology, Leiden University Medical Center, Leiden, 2300RC, The Netherlands
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ashley van der Spek
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, 6500 HB, The Netherlands
| | - Petroula Proitsi
- MRC Unit for Lifelong Health & Ageing at UCL, University College London, London, WC1B 5JU, UK
| | - Lisa R Yanek
- Department of Medicine, GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Antony Payton
- Centre for Epidemiology, Division of Population Health, Health Services Research & Primary Care, The University of Manchester, Manchester, Greater, Manchester, M13 9PL, UK
| | - Federico Murgia
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), (Affiliated Institute of the University of Lübeck, Lübeck, Germany), Bolzano, 39100, Italy
| | - Maria Pina Concas
- Institute of Genetic and Biomedical Research - Support Unity, National Research Council of Italy, Sassari, 07100, Italy
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, 27100, Italy
| | - Salman M Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore City, MD, 21224, USA
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - Eric Boerwinkle
- Health Science Center at Houston, UTHealth School of Public Health, University of Texas, Houston, TX, 77030, USA
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, DK-8000, Denmark.,Department of Biomedicine-Human Genetics, Aarhus University, DK-8000, Aarhus C, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ellen W Demerath
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Ilja Demuth
- Charité Research Group on Geriatrics, Charité, Universitätsmedizin Berlin, Berlin, 13347, Germany.,Lipid Clinic at the Interdisciplinary Metabolism Center, Charité, Universitätsmedizin Berlin, Berlin, 13353, Germany.,Institute for Medical and Human Genetics, Charité, Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48014, USA
| | - Ian Ford
- Robertson Center for biostatistics, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Martin Gögele
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), (Affiliated Institute of the University of Lübeck, Lübeck, Germany), Bolzano, 39100, Italy
| | - MariaElisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Aroon Hingorani
- Institute of Cardiovascular Science, University College London, London, WC1E 6BT, UK
| | - Jouke-Jan Hottenga
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, Amsterdam Public Health Institute (APH), Amsterdam, 1081BT, Netherlands
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, DK-8000, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, 2300, Denmark
| | - Mikko A Hurme
- Department of Microbiology and Immunology, Fimlab Laboratories and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - Marja Jylhä
- Gerontology Research Center, Tampere, Finland, Faculty of Social Sciences, University of Tampere, Tampere, 33104, Finland
| | - Diana Kuh
- MRC Unit for Lifelong Health & Ageing at UCL, University College London, London, WC1B 5JU, UK
| | - Lannie Ligthart
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, Amsterdam Public Health Institute (APH), Amsterdam, 1081BT, Netherlands
| | - Christina M Lill
- Genetic and Molecular Epidemiology Group, Institute of Neurogenetics, University of Lübeck, 23562, Lübeck, Germany
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, 14195, Germany.,Max Planck UCL Centre for Computational Psychiatry and Ageing Research, Berlin, 14195, Germany
| | - Thomas Lumley
- Department of Statistics, University of Auckland, Auckland, 1010, New Zealand
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, University of Tartu, Tartu, 51010, Estonia
| | - Pedro Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, 1011, Switzerland
| | - Sarah E Medland
- QIMR Berghofer Institute of Medical Research, Brisbane, QLD, 4006, Australia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, University of Tartu, Tartu, 51010, Estonia
| | - Reka Nagy
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - William E R Ollier
- Division of Population Health, Health Services Research & Primary Care, School of Health Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, Greater Manchester, M13 9PL, UK
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), (Affiliated Institute of the University of Lübeck, Lübeck, Germany), Bolzano, 39100, Italy
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA.,TH Chan School of Public Health, Harvard Medical School, Boston, MA, 02115, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Naples, 80131, Italy
| | - Yasaman Saba
- Austrian Stroke Prevention Study, Institute of Molecular Biology and Biochemistry, Centre for Molecular Medicine, Medical University of Graz, Graz, 8010, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, 8036, Austria
| | - Helena Schmidt
- Austrian Stroke Prevention Study, Institute of Molecular Biology and Biochemistry, Centre for Molecular Medicine, Medical University of Graz, Graz, 8010, Austria
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of medical statistics, Leiden University Medical Center, Leiden, 2300RC, The Netherlands
| | - Blair H Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.,Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48014, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, 98101, USA
| | | | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - André L Verbeek
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, 6500 HB, The Netherlands
| | - Sita H Vermeulen
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, 6500 HB, The Netherlands
| | - Peter Vollenweider
- Department of Medicine, Internal Medicine, Lausanne University Hospital, Lausanne, 1011, Switzerland
| | - Yunpeng Wang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, DK-8000, Denmark.,NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, 0450, Norway
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, DK-4000, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, DK-8000, Denmark
| | - John B Whitfield
- QIMR Berghofer Institute of Medical Research, Brisbane, QLD, 4006, Australia
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore City, MD, 21224, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore City, MD, 21224, USA
| | - Mario Pirastu
- Institute of Genetic and Biomedical Research - Support Unity, National Research Council of Italy, Sassari, 07100, Italy
| | - Christian Fuchsberger
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), (Affiliated Institute of the University of Lübeck, Lübeck, Germany), Bolzano, 39100, Italy
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics & Cardiogenetics, University of Lübeck, Lübeck, 23562, Germany.,Neuroepidemiology and Ageing Research Group, School of Public Health, Imperial College, London, W6 8RP, UK
| | - Neil Pendleton
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, Greater Manchester, M13 9PL, UK
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marina Ciullo
- Institute of Genetics and Biophysics "A. Buzzati-Traverso" - CNR, Naples, 80131, Italy.,IRCCS Neuromed, Pozzilli (IS), 86077, Italy
| | - Diane M Becker
- Department of Medicine, GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Andrew Wong
- MRC Unit for Lifelong Health & Ageing at UCL, University College London, London, WC1B 5JU, UK
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA.,Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, 2300RC, The Netherlands
| | - Lambertus Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, 6500 HB, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015 CN, Netherlands
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, 48014, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, University of Tartu, Tartu, 51010, Estonia
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit, Amsterdam, Amsterdam Public Health Institute (APH), Amsterdam, 1081BT, Netherlands
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Daniel Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, 02215, USA.,TH Chan School of Public Health, Harvard Medical School, Boston, MA, 02115, USA
| | - Nicholas G Martin
- QIMR Berghofer Institute of Medical Research, Brisbane, QLD, 4006, Australia
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, G12 8TD, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Tōnu Esko
- Estonian Genome Center, University of Tartu, University of Tartu, Tartu, 51010, Estonia.,Program in Medical and Population Genetics, Broad Institute, Broad Institute, Cambridge, MA, 02142, USA
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, 1010, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
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12
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Nielson CM, Liu CT, Smith AV, Ackert-Bicknell CL, Reppe S, Jakobsdottir J, Wassel C, Register TC, Oei L, Alonso N, Oei EH, Parimi N, Samelson EJ, Nalls MA, Zmuda J, Lang T, Bouxsein M, Latourelle J, Claussnitzer M, Siggeirsdottir K, Srikanth P, Lorentzen E, Vandenput L, Langefeld C, Raffield L, Terry G, Cox AJ, Allison MA, Criqui MH, Bowden D, Ikram MA, Mellström D, Karlsson MK, Carr J, Budoff M, Phillips C, Cupples LA, Chou WC, Myers RH, Ralston SH, Gautvik KM, Cawthon PM, Cummings S, Karasik D, Rivadeneira F, Gudnason V, Orwoll ES, Harris TB, Ohlsson C, Kiel DP, Hsu YH. Novel Genetic Variants Associated With Increased Vertebral Volumetric BMD, Reduced Vertebral Fracture Risk, and Increased Expression of SLC1A3 and EPHB2. J Bone Miner Res 2016; 31:2085-2097. [PMID: 27476799 PMCID: PMC5477772 DOI: 10.1002/jbmr.2913] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/22/2016] [Accepted: 07/08/2016] [Indexed: 12/26/2022]
Abstract
Genome-wide association studies (GWASs) have revealed numerous loci for areal bone mineral density (aBMD). We completed the first GWAS meta-analysis (n = 15,275) of lumbar spine volumetric BMD (vBMD) measured by quantitative computed tomography (QCT), allowing for examination of the trabecular bone compartment. SNPs that were significantly associated with vBMD were also examined in two GWAS meta-analyses to determine associations with morphometric vertebral fracture (n = 21,701) and clinical vertebral fracture (n = 5893). Expression quantitative trait locus (eQTL) analyses of iliac crest biopsies were performed in 84 postmenopausal women, and murine osteoblast expression of genes implicated by eQTL or by proximity to vBMD-associated SNPs was examined. We identified significant vBMD associations with five loci, including: 1p36.12, containing WNT4 and ZBTB40; 8q24, containing TNFRSF11B; and 13q14, containing AKAP11 and TNFSF11. Two loci (5p13 and 1p36.12) also contained associations with radiographic and clinical vertebral fracture, respectively. In 5p13, rs2468531 (minor allele frequency [MAF] = 3%) was associated with higher vBMD (β = 0.22, p = 1.9 × 10-8 ) and decreased risk of radiographic vertebral fracture (odds ratio [OR] = 0.75; false discovery rate [FDR] p = 0.01). In 1p36.12, rs12742784 (MAF = 21%) was associated with higher vBMD (β = 0.09, p = 1.2 × 10-10 ) and decreased risk of clinical vertebral fracture (OR = 0.82; FDR p = 7.4 × 10-4 ). Both SNPs are noncoding and were associated with increased mRNA expression levels in human bone biopsies: rs2468531 with SLC1A3 (β = 0.28, FDR p = 0.01, involved in glutamate signaling and osteogenic response to mechanical loading) and rs12742784 with EPHB2 (β = 0.12, FDR p = 1.7 × 10-3 , functions in bone-related ephrin signaling). Both genes are expressed in murine osteoblasts. This is the first study to link SLC1A3 and EPHB2 to clinically relevant vertebral osteoporosis phenotypes. These results may help elucidate vertebral bone biology and novel approaches to reducing vertebral fracture incidence. © 2016 American Society for Bone and Mineral Research.
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Affiliation(s)
- Carrie M Nielson
- School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Albert V Smith
- Icelandic Heart Association, Kópavogur, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | | | - Sjur Reppe
- Department of Medical Biochemistry, Oslo University Hospital, Ullevål, Oslo, Norway.,Lovisenberg Diakonale Hospital, Oslo, Norway.,Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Christina Wassel
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Thomas C Register
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ling Oei
- Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.,Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Nerea Alonso
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Edwin H Oei
- Radiology & Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Neeta Parimi
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Elizabeth J Samelson
- Institute for Aging Research, Hebrew SeniorLife, Harvard Medical School, Boston, MA, USA
| | - Mike A Nalls
- National Institute on Aging (NIA), National Institutes of Health, Bethesda, MD, USA
| | - Joseph Zmuda
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Thomas Lang
- Department of Radiology, University of California, San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Mary Bouxsein
- Center for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, Harvard University Medical School, Boston, MA, USA
| | | | - Melina Claussnitzer
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Technical University Munich, Munich, Germany
| | | | - Priya Srikanth
- School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Erik Lorentzen
- Department of Bioinformatics, Gothenburg University, Gothenburg, Sweden
| | - Liesbeth Vandenput
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Carl Langefeld
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Laura Raffield
- Center for Human Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Greg Terry
- Department of Radiology & Radiological Sciences, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, USA
| | - Amanda J Cox
- Center for Diabetes Research, Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Matthew A Allison
- Department of Family Medicine and Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Michael H Criqui
- Department of Family Medicine and Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Don Bowden
- Center for Diabetes Research, Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Internal Medicine/Endocrinology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus K Karlsson
- Department of Orthopaedics and Clinical Sciences, Malmö University Hospital, Lund University, Malmö, Sweden
| | - John Carr
- Department of Radiology & Radiological Sciences, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, USA
| | - Matthew Budoff
- Los Angeles Biomedical Research Institute, Torrance, CA, USA
| | - Caroline Phillips
- National Institute on Aging (NIA), National Institutes of Health, Bethesda, MD, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Wen-Chi Chou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Stuart H Ralston
- Rheumatic Diseases Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Kaare M Gautvik
- Lovisenberg Diakonale Hospital, Oslo, Norway.,Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Peggy M Cawthon
- California Pacific Medical Center Research Institute, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Steven Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Harvard Medical School, Boston, MA, USA.,Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kópavogur, Iceland.,Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Eric S Orwoll
- Division of Endocrinology, Oregon Health & Science University, Portland, OR, USA
| | - Tamara B Harris
- National Institute on Aging (NIA), National Institutes of Health, Bethesda, MD, USA
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Douglas P Kiel
- Institute for Aging Research, Hebrew SeniorLife, Harvard Medical School, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University Medical School, Boston, MA, USA
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, MA, USA
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13
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Haws BE, Wuertzer S, Raffield L, Lenchik L, Miller AN. Criteria for level 1 and level 2 trauma codes: Are pelvic ring injuries undertriaged? World J Orthop 2016; 7:481-486. [PMID: 27622148 PMCID: PMC4990769 DOI: 10.5312/wjo.v7.i8.481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/08/2016] [Accepted: 06/03/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To determine the association of unstable pelvic ring injuries with trauma code status.
METHODS: A retrospective review of all pelvic ring injuries at a single academic center from July 2010 to June 2013 was performed. The trauma registry was used to identify level 1 and level 2 trauma codes for each injury. The computed tomography scans in all patients were classified as stable or unstable using the Abbreviated Injury Scale. Pelvic injury classifications in level 1 and level 2 groups were compared. Patient disposition at discharge in level 1 and level 2 groups were also compared.
RESULTS: There were 108 level 1 and 130 level 2 blunt trauma admissions. In the level 1 group, 67% of pelvic injuries were classified as stable fracture patterns and 33% were classified as unstable. In the level 2 group, 62% of pelvic injuries were classified as stable fracture patterns and 38% were classified as unstable. level 1 trauma code was not associated with odds of having an unstable fracture pattern (OR = 0.83, 95%CI: 0.48-1.41, P = 0.485). In the level 1 group with unstable pelvic injuries, 33% were discharged to home, 36% to a rehabilitation facility, and 32% died. In the level 2 group with unstable pelvic injuries, 65% were discharged to home, 31% to a rehabilitation facility, and 4% died. For those with unstable pelvic fractures (n = 85), assignment of a level 2 trauma code was associated with reduced odds of death (OR = 0.07, 95%CI: 0.01-0.35, P = 0.001) as compared to being discharged to home.
CONCLUSION: Trauma code level assignment is not correlated with severity of pelvic injury. Because an unstable pelvis can lead to hemodynamic instability, these injuries may be undertriaged.
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