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Wang S, Lenzini P, Thygarajan B, Lee JH, Vardarajan BN, Yashin A, Miljkovic I, Warwick Daw E, Lin SJ, Patti G, Brent M, Zmuda JM, Perls TT, Christensen K, Province MA, An P. A Novel Gene ARHGAP44 for Longitudinal Changes in Glycated Hemoglobin (HbA1c) in Subjects without Type 2 Diabetes: Evidence from the Long Life Family Study (LLFS) and the Framingham Offspring Study (FOS). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594575. [PMID: 38826208 PMCID: PMC11142083 DOI: 10.1101/2024.05.16.594575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Glycated hemoglobin (HbA1c) indicates average glucose levels over three months and is associated with insulin resistance and type 2 diabetes (T2D). Longitudinal changes in HbA1c (ΔHbA1c) are also associated with aging processes, cognitive performance, and mortality. We analyzed ΔHbA1c in 1,886 non-diabetic Europeans from the Long Life Family Study to uncover gene variants influencing ΔHbA1c. Using growth curve modeling adjusted for multiple covariates, we derived ΔHbA1c and conducted linkage-guided sequence analysis. Our genome-wide linkage scan identified a significant locus on 17p12. In-depth analysis of this locus revealed a variant rs56340929 (explaining 27% of the linkage peak) in the ARHGAP44 gene that was significantly associated with ΔHbA1c. RNA transcription of ARHGAP44 was associated with ΔHbA1c. The Framingham Offspring Study data further supported these findings on the gene level. Together, we found a novel gene ARHGAP44 for ΔHbA1c in family members without T2D. Follow-up studies using longitudinal omics data in large independent cohorts are warranted.
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Affiliation(s)
- Siyu Wang
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine. St. Louis, MO, USA
| | - Petra Lenzini
- Department of Radiology, Washington University School of Medicine. St. Louis, MO, USA
| | - Bharat Thygarajan
- Departments of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Joseph H. Lee
- Gertrude H. Sergievsky Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Departments of Neurology and Epidemiology, Columbia University, New York City, NY, USA
| | - Badri N. Vardarajan
- Gertrude H. Sergievsky Center and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Departments of Neurology and Epidemiology, Columbia University, New York City, NY, USA
| | - Anatoli Yashin
- Social Science Research Institute, Duke University, Durham, NC, USA
| | - Iva Miljkovic
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - E. Warwick Daw
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine. St. Louis, MO, USA
| | - Shiow J. Lin
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine. St. Louis, MO, USA
| | - Gary Patti
- Department of Chemistry, Washington University School of Art and Sciences, St. Louis, MO, USA
| | - Michael Brent
- Deptartment of Computer Science and Center for Genome Sciences, Washington University, St. Louis, MO, USA
| | - Joseph M. Zmuda
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thomas T. Perls
- Departments of Medicine and Geriatrics, Boston University School of Medicine, Boston, MA, USA
| | - Kaare Christensen
- Danish Aging Research Center, Epidemiology, University of Southern Denmark, Odense, Denmark
| | - Michael A. Province
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine. St. Louis, MO, USA
| | - Ping An
- Department of Genetics Division of Statistical Genomics, Washington University School of Medicine. St. Louis, MO, USA
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LeBlanc ES, Pittas AG, Nelson J, Chatterjee R, Rasouli N, Rhee MK, Pratley RE, Desouza CV, Neff LM, Peters AM, Dagogo-Jack S, Hsia DS. Racial differences in measures of glycemia in the Vitamin D and Type 2 Diabetes (D2d) Study: a secondary analysis of a randomized trial. BMJ Open Diabetes Res Care 2024; 12:e003613. [PMID: 38350671 PMCID: PMC10862329 DOI: 10.1136/bmjdrc-2023-003613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
INTRODUCTION Understanding how race may influence the association between A1c and glycemia can improve diabetes screening. We sought to determine whether, for a given A1c level, glucose levels during an oral glucose tolerance test (OGTT) differed by race. RESEARCH DESIGN AND METHODS From data collected at 22 US clinical sites, we conducted a cross-sectional study of concurrently measured A1c and OGTT and observational longitudinal follow-up of the subset with high-risk pre-diabetes. Numerical integration methods were used to calculate area under the glycemic curve (AUCglu) during OGTT and least squares regression model to estimate A1c for a given AUCglu by race, controlling for potential confounders. RESULTS 1016 black, 2658 white, and 193 Asian persons at risk of diabetes were included in cross-sectional analysis. Of these, 2154 with high-risk pre-diabetes were followed for 2.5 years. For a given A1c level, AUCglu was lower in black versus white participants. After adjustment for potential confounders, A1c levels for a given AUCglu quintile were 0.15-0.20 and 0.02-0.19 percentage points higher in black and Asian compared with white participants, respectively (p<0.05). In longitudinal analyses, black participants were more likely to be diagnosed with diabetes by A1c than white participants (28% vs 10%, respectively; p<0.01). Black and Asian participants were less likely to be diagnosed by fasting glucose than white participants (16% vs 15% vs 37%, respectively; p<0.05). Black participants with A1c levels in the lower-level quintiles had greater increase in A1c over time compared with white participants. CONCLUSIONS Use of additional testing beyond A1c to screen for diabetes may better stratify diabetes risk in the diverse US population.
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Affiliation(s)
- Erin S LeBlanc
- Kaiser Permanente Center for Health Research, Portland, Oregon, USA
| | - Anastassios G Pittas
- Division of Endocrinology, Diabetes and Metabolism, Tufts Medical Center, Boston, Massachusetts, USA
| | - Jason Nelson
- Tufts Medical Center, Boston, Massachusetts, USA
| | | | - Neda Rasouli
- Endocrinology, Metabolism and Diabetes, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
- Endocrinology, VA Eastern Colorado Health Care System, Denver, Colorado, USA
| | - Mary K Rhee
- Medicine/Endocrinology, Metabolism, and Lipids, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Richard E Pratley
- Translational Research Institute, AdventHealth Research Institute, Orlando, Florida, USA
| | | | - Lisa M Neff
- Northwestern Medicine, Chicago, Illinois, USA
| | - Anne M Peters
- Endocrinology, USC, Manhattan Beach, California, USA
| | - Samuel Dagogo-Jack
- Division of Endocrinology, Diabetes & Metabolism General Clinical Research Center, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Daniel S Hsia
- Pennington Biomedical Research Center, Baton Rouge, Louisiana, USA
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3
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Tobias DK, Manning AK, Wessel J, Raghavan S, Westerman KE, Bick AG, Dicorpo D, Whitsel EA, Collins J, Correa A, Cupples LA, Dupuis J, Goodarzi MO, Guo X, Howard B, Lange LA, Liu S, Raffield LM, Reiner AP, Rich SS, Taylor KD, Tinker L, Wilson JG, Wu P, Carson AP, Vasan RS, Fornage M, Psaty BM, Kooperberg C, Rotter JI, Meigs J, Manson JE. Clonal Hematopoiesis of Indeterminate Potential (CHIP) and Incident Type 2 Diabetes Risk. Diabetes Care 2023; 46:1978-1985. [PMID: 37756531 PMCID: PMC10620536 DOI: 10.2337/dc23-0805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/07/2023] [Indexed: 09/29/2023]
Abstract
OBJECTIVE Clonal hematopoiesis of indeterminate potential (CHIP) is an aging-related accumulation of somatic mutations in hematopoietic stem cells, leading to clonal expansion. CHIP presence has been implicated in atherosclerotic coronary heart disease (CHD) and all-cause mortality, but its association with incident type 2 diabetes (T2D) is unknown. We hypothesized that CHIP is associated with elevated risk of T2D. RESEARCH DESIGN AND METHODS CHIP was derived from whole-genome sequencing of blood DNA in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) prospective cohorts. We performed analysis for 17,637 participants from six cohorts, without prior T2D, cardiovascular disease, or cancer. We evaluated baseline CHIP versus no CHIP prevalence with incident T2D, including associations with DNMT3A, TET2, ASXL1, JAK2, and TP53 variants. We estimated multivariable-adjusted hazard ratios (HRs) and 95% CIs with adjustment for age, sex, BMI, smoking, alcohol, education, self-reported race/ethnicity, and combined cohorts' estimates via fixed-effects meta-analysis. RESULTS Mean (SD) age was 63.4 (11.5) years, 76% were female, and CHIP prevalence was 6.0% (n = 1,055) at baseline. T2D was diagnosed in n = 2,467 over mean follow-up of 9.8 years. Participants with CHIP had 23% (CI 1.04, 1.45) higher risk of T2D than those with no CHIP. Specifically, higher risk was for TET2 (HR 1.48; CI 1.05, 2.08) and ASXL1 (HR 1.76; CI 1.03, 2.99) mutations; DNMT3A was nonsignificant (HR 1.15; CI 0.93, 1.43). Statistical power was limited for JAK2 and TP53 analyses. CONCLUSIONS CHIP was associated with higher incidence of T2D. CHIP mutations located on genes implicated in CHD and mortality were also related to T2D, suggesting shared aging-related pathology.
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Affiliation(s)
- Deirdre K. Tobias
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Nutrition Department, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Alisa K. Manning
- Broad Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
| | - Jennifer Wessel
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Department of Medicine, School of Medicine, and Diabetes Translational Research Center, Indiana University, Indianapolis, IN
| | - Sridharan Raghavan
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, and Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Kenneth E. Westerman
- Broad Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Daniel Dicorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Eric A. Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Collins
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | | | - Leslie A. Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, and Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Simin Liu
- Center for Global Cardiometabolic Health, Brown University, Providence, RI
| | - Laura M. Raffield
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Kent D. Taylor
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Lesley Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - James G. Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Ramachandran S. Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
- University of Texas School of Public Health, San Antonio, TX
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - James Meigs
- Department of Medicine, Harvard Medical School, and Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - JoAnn E. Manson
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Epidemiology Department, Harvard T.H. Chan School of Public Health, Boston, MA
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4
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Commodore-Mensah Y, Wang D, Jeon Y, Foti K, McEvoy JW, Coresh J, Tang O, Echouffo-Tcheugui JB, Christenson R, Ndumele CE, Selvin E. Racial and ethnic differences in circulating N-terminal pro-brain-type natriuretic peptide (NT-proBNP) in US adults. Am J Prev Cardiol 2023; 15:100526. [PMID: 37560479 PMCID: PMC10406957 DOI: 10.1016/j.ajpc.2023.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND The presence and interpretation of racial and ethnic differences in circulating N-terminal pro-brain-type natriuretic peptide (NT-proBNP), a diagnostic biomarker for heart failure, are controversial. OBJECTIVE To examine racial and ethnic differences in NT-proBNP levels among the general US adult population. METHODS We performed a cross-sectional analysis of data from the 1999-2004 National Health and Nutrition Examination Survey (NHANES). We included 4717 non-Hispanic White, 1675 non-Hispanic Black, and 2148 Mexican American adults aged 20 years or older without a history of cardiovascular disease. We examined the associations of race and ethnicity with NT-proBNP using linear and logistic regression models in the overall population and in a younger, 'healthy' subsample. RESULTS The mean age was 45 years. Median NT-proBNP levels were significantly lower among Black (29.3 pg/mL) and Mexican American adults (28.3.4 pg/mL) compared to White adults (49.1pg/mL, P-values<0.001). After adjusting for sociodemographic factors and cardiovascular risk factors, NT-proBNP was 34.4% lower (95%CI -39.2 to -29.3%) in Black adults and 22.8% lower (95%CI -29.4 to -15.5) in Mexican American adults compared to White adults. Our findings were consistent in a young, healthy subsample, suggesting non-cardiometabolic determinants of these differences. CONCLUSIONS NT-proBNP levels are significantly lower among Black and Mexican American adults compared with White adults, independent of cardiometabolic risk. Although race/ethnicity is a poor proxy for genetic differences, our findings may have clinical implications for the management of HF. However, studies in diverse populations are needed to characterize the biological basis of NT-proBNP variation.
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Affiliation(s)
- Yvonne Commodore-Mensah
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins School of Nursing, Baltimore, MD, USA
| | - Dan Wang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Yein Jeon
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn Foti
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - John William McEvoy
- Division of Cardiology & National Institute for Prevention & Cardiovascular Health, National University of Ireland, Galway, Ireland
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Olive Tang
- Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Justin B. Echouffo-Tcheugui
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Robert Christenson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Chiadi E. Ndumele
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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5
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Ray D, Loomis SJ, Venkataraghavan S, Tin A, Yu B, Chatterjee N, Selvin E, Duggal P. Characterizing common and rare variations in non-traditional glycemic biomarkers using multivariate approaches on multi-ancestry ARIC study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.13.23289200. [PMID: 37398180 PMCID: PMC10312851 DOI: 10.1101/2023.06.13.23289200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Glycated hemoglobin, fasting glucose, glycated albumin, and fructosamine are biomarkers that reflect different aspects of the glycemic process. Genetic studies of these glycemic biomarkers can shed light on unknown aspects of type 2 diabetes genetics and biology. While there exists several GWAS of glycated hemoglobin and fasting glucose, very few GWAS have focused on glycated albumin or fructosamine. We performed a multi-phenotype GWAS of glycated albumin and fructosamine from 7,395 White and 2,016 Black participants in the Atherosclerosis Risk in Communities (ARIC) study on the common variants from genotyped/imputed data. We found 2 genome-wide significant loci, one mapping to known type 2 diabetes gene (ARAP1/STARD10, p = 2.8 × 10-8) and another mapping to a novel gene (UGT1A, p = 1.4 × 10-8) using multi-omics gene mapping strategies in diabetes-relevant tissues. We identified additional loci that were ancestry-specific (e.g., PRKCA from African ancestry individuals, p = 1.7 × 10-8) and sex-specific (TEX29 locus in males only, p = 3.0 × 10-8). Further, we implemented multi-phenotype gene-burden tests on whole-exome sequence data from 6,590 White and 2,309 Black ARIC participants. Eleven genes across different rare variant aggregation strategies were exome-wide significant only in multi-ancestry analysis. Four out of 11 genes had notable enrichment of rare predicted loss of function variants in African ancestry participants despite smaller sample size. Overall, 8 out of 15 loci/genes were implicated to influence these biomarkers via glycemic pathways. This study illustrates improved locus discovery and potential effector gene discovery by leveraging joint patterns of related biomarkers across entire allele frequency spectrum in multi-ancestry analyses. Most of the loci/genes we identified have not been previously implicated in studies of type 2 diabetes, and future investigation of the loci/genes potentially acting through glycemic pathways may help us better understand risk of developing type 2 diabetes.
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Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | | | - Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Adrienne Tin
- School of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Bing Yu
- Department of Epidemiology, UTHealth School of Public Health, Houston, TX
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Elizabeth Selvin
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
- Welch Center for Prevention, Epidemiology, & Clinical Research, Johns Hopkins University, Baltimore, MD
| | - Priya Duggal
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
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6
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Costanzo MC, von Grotthuss M, Massung J, Jang D, Caulkins L, Koesterer R, Gilbert C, Welch RP, Kudtarkar P, Hoang Q, Boughton AP, Singh P, Sun Y, Duby M, Moriondo A, Nguyen T, Smadbeck P, Alexander BR, Brandes M, Carmichael M, Dornbos P, Green T, Huellas-Bruskiewicz KC, Ji Y, Kluge A, McMahon AC, Mercader JM, Ruebenacker O, Sengupta S, Spalding D, Taliun D, Smith P, Thomas MK, Akolkar B, Brosnan MJ, Cherkas A, Chu AY, Fauman EB, Fox CS, Kamphaus TN, Miller MR, Nguyen L, Parsa A, Reilly DF, Ruetten H, Wholley D, Zaghloul NA, Abecasis GR, Altshuler D, Keane TM, McCarthy MI, Gaulton KJ, Florez JC, Boehnke M, Burtt NP, Flannick J. The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits. Cell Metab 2023; 35:695-710.e6. [PMID: 36963395 PMCID: PMC10231654 DOI: 10.1016/j.cmet.2023.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 10/23/2022] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results.
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Affiliation(s)
- Maria C Costanzo
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Marcin von Grotthuss
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Jeffrey Massung
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Dongkeun Jang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Lizz Caulkins
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ryan Koesterer
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Clint Gilbert
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ryan P Welch
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Quy Hoang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Andrew P Boughton
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Preeti Singh
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ying Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Marc Duby
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Annie Moriondo
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Trang Nguyen
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Patrick Smadbeck
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Benjamin R Alexander
- Simulation and Modeling Sciences, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - MacKenzie Brandes
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Mary Carmichael
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Peter Dornbos
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Todd Green
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Kenneth C Huellas-Bruskiewicz
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Yue Ji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alexandria Kluge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Josep M Mercader
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oliver Ruebenacker
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Sebanti Sengupta
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Taliun
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Philip Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Melissa K Thomas
- Tailored Therapeutics-Diabetes, Eli Lilly and Company, Lilly Corporate Center DC 0545, Indianapolis, IN 46285, USA
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - M Julia Brosnan
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Andriy Cherkas
- Team Early Projects Type 1 Diabetes, Therapeutic Area Diabetes and Cardiovascular Medicine, Research & Development, Sanofi, Industriepark Höchst-H831, Frankfurt am Main 65926, Germany
| | - Audrey Y Chu
- Merck Research Laboratories, Boston, MA 02115, USA
| | - Eric B Fauman
- Integrative Biology, Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | | | | | - Melissa R Miller
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Lynette Nguyen
- Foundation for the National Institutes of Health, North Bethesda, MD 20852, USA
| | - Afshin Parsa
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Hartmut Ruetten
- CardioMetabolism & Respiratory Medicine, Boehringer Ingelheim International GmbH, 55216 Ingelheim/Rhein, Germany
| | - David Wholley
- Foundation for the National Institutes of Health, North Bethesda, MD 20852, USA
| | - Norann A Zaghloul
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - David Altshuler
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 9DU, UK; Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, Oxford OX3 7BN, UK
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Boehnke
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noël P Burtt
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA.
| | - Jason Flannick
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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7
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Nguyen A, Khafagy R, Hashemy H, Kuo KHM, Roshandel D, Paterson AD, Dash S. Investigating the association between fasting insulin, erythrocytosis and HbA1c through Mendelian randomization and observational analyses. Front Endocrinol (Lausanne) 2023; 14:1146099. [PMID: 37008938 PMCID: PMC10064082 DOI: 10.3389/fendo.2023.1146099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Insulin resistance (IR) with associated compensatory hyperinsulinemia (HI) are early abnormalities in the etiology of prediabetes (preT2D) and type 2 diabetes (T2D). IR and HI also associate with increased erythrocytosis. Hemoglobin A1c (HbA1c) is commonly used to diagnose and monitor preT2D and T2D, but can be influenced by erythrocytosis independent of glycemia. METHODS We undertook bidirectional Mendelian randomization (MR) in individuals of European ancestry to investigate potential causal associations between increased fasting insulin adjusted for BMI (FI), erythrocytosis and its non-glycemic impact on HbA1c. We investigated the association between the triglyceride-glucose index (TGI), a surrogate measure of IR and HI, and glycation gap (difference between measured HbA1c and predicted HbA1c derived from linear regression of fasting glucose) in people with normoglycemia and preT2D. RESULTS Inverse variance weighted MR (IVWMR) suggested that increased FI increases hemoglobin (Hb, b=0.54 ± 0.09, p=2.7 x 10-10), red cell count (RCC, b=0.54 ± 0.12, p=5.38x10-6) and reticulocyte (RETIC, b=0.70 ± 0.15, p=2.18x10-6). Multivariable MR indicated that increased FI did not impact HbA1c (b=0.23 ± 0.16, p=0.162) but reduced HbA1c after adjustment for T2D (b=0.31 ± 0.13, p=0.016). Increased Hb (b=0.03 ± 0.01, p=0.02), RCC (b=0.02 ± 0.01, p=0.04) and RETIC (b=0.03 ± 0.01, p=0.002) might modestly increase FI. In the observational cohort, increased TGI associated with decreased glycation gap, (i.e., measured HbA1c was lower than expected based on fasting glucose, (b=-0.09 ± 0.009, p<0.0001)) in people with preT2D but not in those with normoglycemia (b=0.02 ± 0.007, p<0.0001). CONCLUSIONS MR suggests increased FI increases erythrocytosis and might potentially decrease HbA1c by non-glycemic effects. Increased TGI, a surrogate measure of increased FI, associates with lower-than-expected HbA1c in people with preT2D. These findings merit confirmatory studies to evaluate their clinical significance.
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Affiliation(s)
- Anthony Nguyen
- Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Rana Khafagy
- Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Divisions of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Habiba Hashemy
- Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Kevin H. M. Kuo
- Division of Medical Oncology and Haematology, Department of Medicine, University Health Network, Toronto, ON, Canada
- Division of Haematology, Department of Medicine, University of Toronto, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Divisions of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Satya Dash
- Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
- *Correspondence: Satya Dash,
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8
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McDonald MLN, Lakshman Kumar P, Srinivasasainagendra V, Nair A, Rocco AP, Wilson AC, Chiles JW, Richman JS, Pinson SA, Dennis RA, Jagadale V, Brown CJ, Pyarajan S, Tiwari HK, Bamman MM, Singh JA. Novel genetic loci associated with osteoarthritis in multi-ancestry analyses in the Million Veteran Program and UK Biobank. Nat Genet 2022; 54:1816-1826. [PMID: 36411363 DOI: 10.1038/s41588-022-01221-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/05/2022] [Indexed: 11/22/2022]
Abstract
Osteoarthritis is a common progressive joint disease. As no effective medical interventions are available, osteoarthritis often progresses to the end stage, in which only surgical options such as total joint replacement are available. A more thorough understanding of genetic influences of osteoarthritis is essential to develop targeted personalized approaches to treatment, ideally long before the end stage is reached. To date, there have been no large multiancestry genetic studies of osteoarthritis. Here, we leveraged the unique resources of 484,374 participants in the Million Veteran Program and UK Biobank to address this gap. Analyses included participants of European, African, Asian and Hispanic descent. We discovered osteoarthritis-associated genetic variation at 10 loci and replicated findings from previous osteoarthritis studies. We also present evidence that some osteoarthritis-associated regions are robust to population ancestry. Drug repurposing analyses revealed enrichment of targets of several medication classes and provide potential insight into the etiology of beneficial effects of antiepileptics on osteoarthritis pain.
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Affiliation(s)
- Merry-Lynn N McDonald
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA.
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Preeti Lakshman Kumar
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Vinodh Srinivasasainagendra
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ashwathy Nair
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Alison P Rocco
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Ava C Wilson
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joe W Chiles
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Joshua S Richman
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA
- Department of Surgery, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sarah A Pinson
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Richard A Dennis
- Central Arkansas Veterans Healthcare System (CAVHS), Little Rock, AR, USA
| | - Vivek Jagadale
- Central Arkansas Veterans Healthcare System (CAVHS), Little Rock, AR, USA
| | - Cynthia J Brown
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA
- Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), Veterans Affairs Boston Healthcare System (VABHS), Boston, MA, USA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marcas M Bamman
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA
- Department of Cell, Developmental, and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Florida Institute for Human & Machine Cognition, Pensacola, FL, USA
| | - Jasvinder A Singh
- Birmingham Veterans Affairs Health Care System (BVAHCS), Birmingham, AL, USA
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine at the School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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9
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The contribution of common and rare genetic variants to variation in metabolic traits in 288,137 East Asians. Nat Commun 2022; 13:6642. [PMID: 36333282 PMCID: PMC9636136 DOI: 10.1038/s41467-022-34163-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Metabolic traits are heritable phenotypes widely-used in assessing the risk of various diseases. We conduct a genome-wide association analysis (GWAS) of nine metabolic traits (including glycemic, lipid, liver enzyme levels) in 125,872 Korean subjects genotyped with the Korea Biobank Array. Following meta-analysis with GWAS from Biobank Japan identify 144 novel signals (MAF ≥ 1%), of which 57.0% are replicated in UK Biobank. Additionally, we discover 66 rare (MAF < 1%) variants, 94.4% of them co-incident to common loci, adding to allelic series. Although rare variants have limited contribution to overall trait variance, these lead, in carriers, substantial loss of predictive accuracy from polygenic predictions of disease risk from common variant alone. We capture groups with up to 16-fold variation in type 2 diabetes (T2D) prevalence by integration of genetic risk scores of fasting plasma glucose and T2D and the I349F rare protective variant. This study highlights the need to consider the joint contribution of both common and rare variants on inherited risk of metabolic traits and related diseases.
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10
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Dornbos P, Koesterer R, Ruttenburg A, Nguyen T, Cole JB, Leong A, Meigs JB, Florez JC, Rotter JI, Udler MS, Flannick J. A combined polygenic score of 21,293 rare and 22 common variants improves diabetes diagnosis based on hemoglobin A1C levels. Nat Genet 2022; 54:1609-1614. [PMID: 36280733 PMCID: PMC9995082 DOI: 10.1038/s41588-022-01200-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 09/07/2022] [Indexed: 11/08/2022]
Abstract
Polygenic scores (PGSs) combine the effects of common genetic variants1,2 to predict risk or treatment strategies for complex diseases3-7. Adding rare variation to PGSs has largely unknown benefits and is methodically challenging. Here, we developed a method for constructing rare variant PGSs and applied it to calculate genetically modified hemoglobin A1C thresholds for type 2 diabetes (T2D) diagnosis7-10. The resultant rare variant PGS is highly polygenic (21,293 variants across 154 genes), depends on ultra-rare variants (72.7% observed in fewer than three people) and identifies significantly more undiagnosed T2D cases than expected by chance (odds ratio = 2.71; P = 1.51 × 10-6). A PGS combining common and rare variants is expected to identify 4.9 million misdiagnosed T2D cases in the United States-nearly 1.5-fold more than the common variant PGS alone. These results provide a method for constructing complex trait PGSs from rare variants and suggest that rare variants will augment common variants in precision medicine approaches for common disease.
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Affiliation(s)
- Peter Dornbos
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ryan Koesterer
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
| | - Andrew Ruttenburg
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
| | - Trang Nguyen
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
| | - Joanne B Cole
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Aaron Leong
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James B Meigs
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 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
| | - Miriam S Udler
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jason Flannick
- Programs in Metabolism Program, Broad Institute, Cambridge, MA, USA.
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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11
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Alfonsi T, Bernasconi A, Canakoglu A, Masseroli M. Genomic data integration and user-defined sample-set extraction for population variant analysis. BMC Bioinformatics 2022; 23:401. [PMID: 36175857 PMCID: PMC9520931 DOI: 10.1186/s12859-022-04927-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Population variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000 Genomes Project established a valuable reference for human genetic variation; however, the integrative use of the corresponding data with other datasets within existing repositories and pipelines is not fully supported. Particularly, there is a pressing need for flexible and fast selection of population partitions based on their variant and metadata-related characteristics. RESULTS Here, we target general germline or somatic mutation data sources for their seamless inclusion within an interoperable-format repository, supporting integration among them and with other genomic data, as well as their integrated use within bioinformatic workflows. In addition, we provide VarSum, a data summarization service working on sub-populations of interest selected using filters on population metadata and/or variant characteristics. The service is developed as an optimized computational framework with an Application Programming Interface (API) that can be called from within any existing computing pipeline or programming script. Provided example use cases of biological interest show the relevance, power and ease of use of the API functionalities. CONCLUSIONS The proposed data integration pipeline and data set extraction and summarization API pave the way for solid computational infrastructures that quickly process cumbersome variation data, and allow biologists and bioinformaticians to easily perform scalable analysis on user-defined partitions of large cohorts from increasingly available genetic variation studies. With the current tendency to large (cross)nation-wide sequencing and variation initiatives, we expect an ever growing need for the kind of computational support hereby proposed.
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Affiliation(s)
- Tommaso Alfonsi
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy.
| | - Anna Bernasconi
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy
| | - Arif Canakoglu
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy.,Dipartimento di Anestesia, Rianimazione ed Emergenza-Urgenza, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Policlinico di Milano, Via Francesco Sforza, 35, 20122, Milan, Italy
| | - Marco Masseroli
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Via Ponzio 34/5, 20133, Milan, Italy
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12
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DiCorpo D, Gaynor SM, Russell EM, Westerman KE, Raffield LM, Majarian TD, Wu P, Sarnowski C, Highland HM, Jackson A, Hasbani NR, de Vries PS, Brody JA, Hidalgo B, Guo X, Perry JA, O'Connell JR, Lent S, Montasser ME, Cade BE, Jain D, Wang H, D'Oliveira Albanus R, Varshney A, Yanek LR, Lange L, Palmer ND, Almeida M, Peralta JM, Aslibekyan S, Baldridge AS, Bertoni AG, Bielak LF, Chen CS, Chen YDI, Choi WJ, Goodarzi MO, Floyd JS, Irvin MR, Kalyani RR, Kelly TN, Lee S, Liu CT, Loesch D, Manson JE, Minster RL, Naseri T, Pankow JS, Rasmussen-Torvik LJ, Reiner AP, Reupena MS, Selvin E, Smith JA, Weeks DE, Xu H, Yao J, Zhao W, Parker S, Alonso A, Arnett DK, Blangero J, Boerwinkle E, Correa A, Cupples LA, Curran JE, Duggirala R, He J, Heckbert SR, Kardia SLR, Kim RW, Kooperberg C, Liu S, Mathias RA, McGarvey ST, Mitchell BD, Morrison AC, Peyser PA, Psaty BM, Redline S, Shuldiner AR, Taylor KD, Vasan RS, Viaud-Martinez KA, Florez JC, Wilson JG, Sladek R, Rich SS, Rotter JI, Lin X, Dupuis J, Meigs JB, Wessel J, Manning AK. Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program. Commun Biol 2022; 5:756. [PMID: 35902682 PMCID: PMC9334637 DOI: 10.1038/s42003-022-03702-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/12/2022] [Indexed: 01/04/2023] Open
Abstract
The genetic determinants of fasting glucose (FG) and fasting insulin (FI) have been studied mostly through genome arrays, resulting in over 100 associated variants. We extended this work with high-coverage whole genome sequencing analyses from fifteen cohorts in NHLBI's Trans-Omics for Precision Medicine (TOPMed) program. Over 23,000 non-diabetic individuals from five race-ethnicities/populations (African, Asian, European, Hispanic and Samoan) were included. Eight variants were significantly associated with FG or FI across previously identified regions MTNR1B, G6PC2, GCK, GCKR and FOXA2. We additionally characterize suggestive associations with FG or FI near previously identified SLC30A8, TCF7L2, and ADCY5 regions as well as APOB, PTPRT, and ROBO1. Functional annotation resources including the Diabetes Epigenome Atlas were compiled for each signal (chromatin states, annotation principal components, and others) to elucidate variant-to-function hypotheses. We provide a catalog of nucleotide-resolution genomic variation spanning intergenic and intronic regions creating a foundation for future sequencing-based investigations of glycemic traits.
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Affiliation(s)
- Daniel DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Emily M Russell
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kenneth E Westerman
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, 02114, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Timothy D Majarian
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Anne Jackson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natalie R Hasbani
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Paul S 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, 77030, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
- Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Bertha Hidalgo
- Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, 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, 90502, USA
| | - James A Perry
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Samantha Lent
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
| | - Ricardo D'Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arushi Varshney
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Leslie Lange
- Department of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Marcio Almeida
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | | | - Abigail S Baldridge
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Alain G Bertoni
- Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-, Salem, NC, 27157, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chung-Shiuan Chen
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, 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, 90502, USA
| | | | - Mark O Goodarzi
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Marguerite R Irvin
- Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Rita R Kalyani
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | | | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Douglas Loesch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - JoAnn E Manson
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Ryan L Minster
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55454, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | | | - Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21287, USA
| | - 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, USA
| | - Daniel E Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Huichun Xu
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - 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, 90502, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Stephen Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, 40506, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39211, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- National Heart Lung and Blood Institute and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan W Kim
- Psomagen, Inc, Rockville, MD, 20850, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Simin Liu
- Center for Global Cardiometabolic Health (CGCH), Boston, MA, 02215, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Stephen T McGarvey
- International Health Institute and Department of Epidemiology, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Geriatrics Research and Education Clinical Center, Baltimore VA Medical Center, Baltimore, MD, 21201, USA
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
- Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
- Department of Health Services, University of Washington, Seattle, WA, 98101, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Alan R Shuldiner
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21231, 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, 90502, USA
| | - Ramachandran S Vasan
- National Heart Lung and Blood Institute and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
- Evans Department of Medicine, Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, 02118, USA
- Evans Department of Medicine, Whitaker Cardiovascular Institute and Cardiology Section, Boston University School of Medicine, Boston, MA, 02118, USA
| | | | - Jose C Florez
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montreal, Montreal, Quebec, H3A 0G1, Canada
- Department of Medicine, McGill University, Montreal, Montreal, Quebec, H3A 0G1, Canada
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, 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, 90502, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, IN, 46202, USA.
- Department of Medicine, School of Medicine, Indiana University, IN, 46202, USA.
- Diabetes Translational Research Center, Indiana University, IN, 46202, USA.
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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13
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Chen W, Wang S, Tithi SS, Ellison DW, Schaid DJ, Wu G. A rare variant analysis framework using public genotype summary counts to prioritize disease-predisposition genes. Nat Commun 2022; 13:2592. [PMID: 35545612 PMCID: PMC9095601 DOI: 10.1038/s41467-022-30248-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/21/2022] [Indexed: 11/11/2022] Open
Abstract
Sequencing cases without matched healthy controls hinders prioritization of germline disease-predisposition genes. To circumvent this problem, genotype summary counts from public data sets can serve as controls. However, systematic inflation and false positives can arise if confounding factors are not controlled. We propose a framework, consistent summary counts based rare variant burden test (CoCoRV), to address these challenges. CoCoRV implements consistent variant quality control and filtering, ethnicity-stratified rare variant association test, accurate estimation of inflation factors, powerful FDR control, and detection of rare variant pairs in high linkage disequilibrium. When we applied CoCoRV to pediatric cancer cohorts, the top genes identified were cancer-predisposition genes. We also applied CoCoRV to identify disease-predisposition genes in adult brain tumors and amyotrophic lateral sclerosis. Given that potential confounding factors were well controlled after applying the framework, CoCoRV provides a cost-effective solution to prioritizing disease-risk genes enriched with rare pathogenic variants.
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Affiliation(s)
- Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Shuoguo Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- 150 Second Street, Cambridge, MA, USA
| | - Saima Sultana Tithi
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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14
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Swislocki AL. Glucose Trajectory: More than Changing Glucose Tolerance with Age? Metab Syndr Relat Disord 2022; 20:313-320. [DOI: 10.1089/met.2021.0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Arthur L.M. Swislocki
- Medical Service, VA Northern California Health Care System (612/111), Martinez, California, USA
- Division of Endocrinology and Metabolism, Department of Internal Medicine, UC Davis School of Medicine, Sacramento, California, USA
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15
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Sun Q, Graff M, Rowland B, Wen J, Huang L, Miller-Fleming TW, Haessler J, Preuss MH, Chai JF, Lee MP, Avery CL, Cheng CY, Franceschini N, Sim X, Cox NJ, Kooperberg C, North KE, Li Y, Raffield LM. Analyses of biomarker traits in diverse UK biobank participants identify associations missed by European-centric analysis strategies. J Hum Genet 2022; 67:87-93. [PMID: 34376796 PMCID: PMC8792153 DOI: 10.1038/s10038-021-00968-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/09/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
Despite the dramatic underrepresentation of non-European populations in human genetics studies, researchers continue to exclude participants of non-European ancestry, as well as variants rare in European populations, even when these data are available. This practice perpetuates existing research disparities and can lead to important and large effect size associations being missed. Here, we conducted genome-wide association studies (GWAS) of 31 serum and urine biomarker quantitative traits in African (n = 9354), East Asian (n = 2559), and South Asian (n = 9823) ancestry UK Biobank (UKBB) participants. We adjusted for all known GWAS catalog variants for each trait, as well as novel signals identified in a recent European ancestry-focused analysis of UKBB participants. We identify 7 novel signals in African ancestry and 2 novel signals in South Asian ancestry participants (p < 1.61E-10). Many of these signals are highly plausible, including a cis pQTL for the gene encoding gamma-glutamyl transferase and PIEZO1 and G6PD variants with impacts on HbA1c through likely erythrocytic mechanisms. This work illustrates the importance of using the genetic data we already have in diverse populations, with novel discoveries possible in even modest sample sizes.
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Affiliation(s)
- Quan Sun
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Bryce Rowland
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Le Huang
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Tyne W Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Moa P Lee
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
- Carolina Center of Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
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16
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Barroso I. The importance of increasing population diversity in genetic studies of type 2 diabetes and related glycaemic traits. Diabetologia 2021; 64:2653-2664. [PMID: 34595549 PMCID: PMC8563561 DOI: 10.1007/s00125-021-05575-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/07/2021] [Indexed: 12/11/2022]
Abstract
Type 2 diabetes has a global prevalence, with epidemiological data suggesting that some populations have a higher risk of developing this disease. However, to date, most genetic studies of type 2 diabetes and related glycaemic traits have been performed in individuals of European ancestry. The same is true for most other complex diseases, largely due to use of 'convenience samples'. Rapid genotyping of large population cohorts and case-control studies from existing collections was performed when the genome-wide association study (GWAS) 'revolution' began, back in 2005. Although global representation has increased in the intervening 15 years, further expansion and inclusion of diverse populations in genetic and genomic studies is still needed. In this review, I discuss the progress made in incorporating multi-ancestry participants in genetic analyses of type 2 diabetes and related glycaemic traits, and associated opportunities and challenges. I also discuss how increased representation of global diversity in genetic and genomic studies is required to fulfil the promise of precision medicine for all.
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Affiliation(s)
- Inês Barroso
- Exeter Centre of Excellence for Diabetes research (EXCEED), University of Exeter Medical School, Exeter, UK.
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17
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Stilp AM, Emery LS, Broome JG, Buth EJ, Khan AT, Laurie CA, Wang FF, Wong Q, Chen D, D’Augustine CM, Heard-Costa NL, Hohensee CR, Johnson WC, Juarez LD, Liu J, Mutalik KM, Raffield LM, Wiggins KL, de Vries PS, Kelly TN, Kooperberg C, Natarajan P, Peloso GM, Peyser PA, Reiner AP, Arnett DK, Aslibekyan S, Barnes KC, Bielak LF, Bis JC, Cade BE, Chen MH, Correa A, Cupples LA, de Andrade M, Ellinor PT, Fornage M, Franceschini N, Gan W, Ganesh SK, Graffelman J, Grove ML, Guo X, Hawley NL, Hsu WL, Jackson RD, Jaquish CE, Johnson AD, Kardia SLR, Kelly S, Lee J, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, North KE, Nouraie SM, Oelsner EC, Pankratz N, Rich SS, Rotter JI, Smith JA, Taylor KD, Vasan RS, Weeks DE, Weiss ST, Wilson CG, Yanek LR, Psaty BM, Heckbert SR, Laurie CC. A System for Phenotype Harmonization in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Program. Am J Epidemiol 2021; 190:1977-1992. [PMID: 33861317 PMCID: PMC8485147 DOI: 10.1093/aje/kwab115] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 11/12/2022] Open
Abstract
Genotype-phenotype association studies often combine phenotype data from multiple studies to increase statistical power. Harmonization of the data usually requires substantial effort due to heterogeneity in phenotype definitions, study design, data collection procedures, and data-set organization. Here we describe a centralized system for phenotype harmonization that includes input from phenotype domain and study experts, quality control, documentation, reproducible results, and data-sharing mechanisms. This system was developed for the National Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine (TOPMed) program, which is generating genomic and other -omics data for more than 80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants (recruited in 1948-2012) from up to 17 studies per phenotype. Here we discuss challenges in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include 1) the software code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify, or extend these harmonizations to additional studies, and 2) the results of labeling thousands of phenotype variables with controlled vocabulary terms.
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Affiliation(s)
- Adrienne M Stilp
- Correspondence to Dr. Adrienne Stilp, Department of Biostatistics, School of Public Health, University of Washington, Box 359461, Seattle, WA 98195 (e-mail: )
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18
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Selvin E. Hemoglobin A 1c-Using Epidemiology to Guide Medical Practice: Kelly West Award Lecture 2020. Diabetes Care 2021; 44:dci210035. [PMID: 34548283 PMCID: PMC8929182 DOI: 10.2337/dci21-0035] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 02/03/2023]
Abstract
The discovery that HbA1c was a valid and reliable measure of average glucose exposure was one of the most important advances in diabetes care. HbA1c was rapidly adopted for monitoring glucose control and is now recommended for the diagnosis of diabetes. HbA1c has several advantages over glucose. Glucose assessment requires fasting, has poor preanalytic stability, and is not standardized; concentrations are acutely altered by a number of factors; and measurement can vary depending on sample type (e.g., plasma or whole blood) and source (e.g., capillary, venous, interstitial). HbA1c does not require fasting, reflects chronic exposure to glucose over the past 2-3 months, and has low within-person variability, and assays are well standardized. One reason HbA1c is widely accepted as a prognostic and diagnostic biomarker is that epidemiologic studies have demonstrated robust links between HbA1c and complications, with stronger associations than those observed for usual measures of glucose. Clinical trials have also demonstrated that lowering HbA1c slows or prevents the development of microvascular disease. As with all laboratory tests, there are some clinical situations in which HbA1c is unreliable (e.g., certain hemoglobin variants, alterations in red blood cell turnover). Recent studies demonstrate that fructosamine and glycated albumin may be substituted as measures of hyperglycemia in these settings. Other approaches to monitoring glucose have recently been introduced, including continuous glucose monitoring, although this technology relies on interstitial glucose and epidemiologic evidence supporting its routine use has not yet been established for most clinical settings. In summary, a large body of epidemiologic evidence has convincingly established HbA1c as a cornerstone of modern diabetes care.
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Affiliation(s)
- Elizabeth Selvin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- The Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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19
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Leak-Johnson T, Yan F, Daniels P. What the Jackson Heart Study Has Taught Us About Diabetes and Cardiovascular Disease in the African American Community: a 20-year Appreciation. Curr Diab Rep 2021; 21:39. [PMID: 34495422 DOI: 10.1007/s11892-021-01413-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW The burden of cardiometabolic diseases such as cardiovascular disease (CVD) and type 2 diabetes (T2D) is pronounced among African Americans. Research has shown that behavioral, social, metabolic, psychosocial, and genetic risk factors of CVD and T2D are closely interwoven. Approximately 20 years ago, the Jackson Heart Study (JHS) was established to investigate this constellation of risk factors. RECENT FINDINGS Findings from neighborhood studies emphasize the importance of social cohesion and physical environment in the context CVD and T2D risk. Socioeconomic status factors such as income and education were significant predictors for CVD and T2D. Behavioral studies indicate that modifiable risk factors such as smoking, physical inactivity, lack of sleep, and poor nutrition are associated with CVD risk and all-cause mortality. Mental health also was found to be associated with CVD and T2D. Genetic influences are associated with disease etiology. This review summarizes the joint contributions of CVD and cardiometabolic risk factors in an African American population.
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Affiliation(s)
- Tennille Leak-Johnson
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
- Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA.
| | - Fengxia Yan
- The Research Design and Biostatistics Core, Morehouse School of Medicine, Atlanta, GA, USA
- Community Health & Preventive Medicine, Morehouse School of Medicine, Atlanta, GA, USA
| | - Pamela Daniels
- The Research Design and Biostatistics Core, Morehouse School of Medicine, Atlanta, GA, 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: 298] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [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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21
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Wu JD, Liang DL, Xie Y, Chen MY, Chen HH, Sun D, Hu HQ. Association Between Hemoglobin Glycation Index and Risk of Cardiovascular Disease and All Cause Mortality in Type 2 Diabetic Patients: A Meta-Analysis. Front Cardiovasc Med 2021; 8:690689. [PMID: 34124211 PMCID: PMC8193090 DOI: 10.3389/fcvm.2021.690689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022] Open
Abstract
Background: The hemoglobin glycation index (HGI) has been proposed as a marker to quantify inter-individual variation in hemoglobin glycosylation. However, whether HGI is associated with an increased risk of diabetic complications independent of glycated hemoglobin (HbA1c) remains unclear. This meta-analysis aimed to determine the association between HGI and the risk of all cause mortality and composite cardiovascular disease (CVD). Methods: PubMed, and EMBASE databases were searched for related studies up to March 31, 2021. Observational studies reported associations between HGI levels and composite CVD and all cause mortality were included for meta-analysis. A random effect model was used to calculate the hazard ratios (HRs) and 95% confidence intervals (CI) for higher HGI. Results: A total of five studies, comprising 22,035 patients with type two diabetes mellitus were included for analysis. The median follow-up duration was 5.0 years. After adjusted for multiple conventional cardiovascular risk factors, an increased level of HGI was associated with a higher risk of composite CVD (per 1 SD increment: HR = 1.14, 95% CI = 1.04–1.26) and all cause mortality (per 1 SD increment: HR = 1.18, 95% CI = 1.05–1.32). However, when further adjusted for HbA1c, the association between HGI and risk of composite CVD (per 1 SD increment of HGI: HR = 1.01, 95% CI = 0.93–1.10) and all cause mortality (per 1 SD increment of HGI: HR = 1.03, 95% CI = 0.96–1.10) became insignificant. Conclusions: High HGI was associated with an increased risk of composite CVD and all cause mortality after adjustment for multiple conventional cardiovascular risk factors. However, the association was mainly mediating by the level of HbA1c.
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Affiliation(s)
- Jian-di Wu
- Department of Cardiology, The Second People's Hospital of Foshan, Foshan, China
| | - Dong-Liang Liang
- Department of Cardiology, The Second People's Hospital of Foshan, Foshan, China
| | - Yue Xie
- Department of Cardiology, The Second People's Hospital of Foshan, Foshan, China
| | - Mei-Yu Chen
- Department of Cardiology, The Second People's Hospital of Foshan, Foshan, China
| | - Hai-Hong Chen
- Department of Cardiology, The Second People's Hospital of Foshan, Foshan, China
| | - Dan Sun
- Department of Cardiology, The Second People's Hospital of Foshan, Foshan, China
| | - Hui-Qi Hu
- Department of Cardiology, The Second People's Hospital of Foshan, Foshan, China
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22
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Hu Y, Stilp AM, McHugh CP, Rao S, Jain D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH, Yanek LR, Wheeler M, Yao Y, Ren C, Broome J, Moon JY, de Vries PS, Hobbs BD, Sun Q, Surendran P, Brody JA, Blackwell TW, Choquet H, Ryan K, Duggirala R, Heard-Costa N, Wang Z, Chami N, Preuss MH, Min N, Ekunwe L, Lange LA, Cushman M, Faraday N, Curran JE, Almasy L, Kundu K, Smith AV, Gabriel S, Rotter JI, Fornage M, Lloyd-Jones DM, Vasan RS, Smith NL, North KE, Boerwinkle E, Becker LC, Lewis JP, Abecasis GR, Hou L, O'Connell JR, Morrison AC, Beaty TH, Kaplan R, Correa A, Blangero J, Jorgenson E, Psaty BM, Kooperberg C, Walton RT, Kleinstiver BP, Tang H, Loos RJF, Soranzo N, Butterworth AS, Nickerson D, Rich SS, Mitchell BD, Johnson AD, Auer PL, Li Y, Mathias RA, Lettre G, Pankratz N, Laurie CC, Laurie CA, Bauer DE, Conomos MP, Reiner AP. Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. Am J Hum Genet 2021; 108:874-893. [PMID: 33887194 DOI: 10.1016/j.ajhg.2021.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders.
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Affiliation(s)
- Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - John Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | | | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marsha Wheeler
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Jai Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Paul S 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 77030, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Thomas W Blackwell
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Nancy Heard-Costa
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nancy Min
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Lynette Ekunwe
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mary Cushman
- Department of Medicine, Larner College of Medicine at the University of Vermont, Burlington, VT 05405, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and Department of Genetics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kousik Kundu
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - Albert V Smith
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, 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 90502, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | | | - Ramachandran S Vasan
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA; Departments of Cardiology and Preventive Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98105, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eric Boerwinkle
- 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 77030, USA
| | - Lewis C Becker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Goncalo R Abecasis
- TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Lifang Hou
- Northwestern University, Chicago, IL 60208, USA
| | - Jeffrey R O'Connell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, 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 77030, USA
| | - Terri H Beaty
- School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78539, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94601, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98105, USA
| | - Russell T Walton
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Soranzo
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Department of Human Genetics, Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge CB1 8RN, UK
| | - Debbie Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes & Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01701, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA
| | - Yun Li
- Departments of Biostatistics, Genetics, Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA 21205, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Faculté de Médecine, Université de Montréal, Montréal, QC H1T 1C8, Canada
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA.
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23
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Khosla L, Bhat S, Fullington LA, Horlyck-Romanovsky MF. HbA 1c Performance in African Descent Populations in the United States With Normal Glucose Tolerance, Prediabetes, or Diabetes: A Scoping Review. Prev Chronic Dis 2021; 18:E22. [PMID: 33705304 PMCID: PMC7986971 DOI: 10.5888/pcd18.200365] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction African descent populations in the United States have high rates of type 2 diabetes and are incorrectly represented as a single group. Current glycated hemoglobin A1c (HbA1c) cutoffs (5.7% to <6.5% for prediabetes; ≥6.5% for type 2 diabetes) may perform suboptimally in evaluating glycemic status among African descent groups. We conducted a scoping review of US-based evidence documenting HbA1c performance to assess glycemic status among African American, Afro-Caribbean, and African people. Methods A PubMed, Scopus, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) search (January 2020) yielded 3,238 articles published from January 2000 through January 2020. After review of titles, abstracts, and full texts, 12 met our criteria. HbA1c results were compared with other ethnic groups or validated against the oral glucose tolerance test (OGTT), fasting plasma glucose (FPG), or previous diagnosis. We classified study results by the risk of false positives and risk of false negatives in assessing glycemic status. Results In 5 studies of African American people, the HbA1c test increased risk of false positives compared with White populations, regardless of glycemic status. Three studies of African Americans found that HbA1c of 5.7% to less than 6.5% or HbA1c of 6.5% or higher generally increased risk of overdiagnosis compared with OGTT or previous diagnosis. In one study of Afro-Caribbean people, HbA1c of 6.5% or higher detected fewer type 2 diabetes cases because of a greater risk of false negatives. Compared with OGTT, HbA1c tests in 4 studies of Africans found that HbA1c of 5.7% to less than 6.5% or HbA1c of 6.5% or higher leads to underdiagnosis. Conclusion HbA1c criteria inadequately characterizes glycemic status among heterogeneous African descent populations. Research is needed to determine optimal HbA1c cutoffs or other test strategies that account for risk profiles unique to African American, Afro-Caribbean, and African people living in the United States.
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Affiliation(s)
- Lakshay Khosla
- Department of Health and Nutrition Sciences, Brooklyn College, City University of New York, Brooklyn, New York.,College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, New York
| | - Sonali Bhat
- Department of Health and Nutrition Sciences, Brooklyn College, City University of New York, Brooklyn, New York.,College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, New York
| | - Lee Ann Fullington
- Library Department, Brooklyn College, City University of New York, Brooklyn, New York
| | - Margrethe F Horlyck-Romanovsky
- Department of Health and Nutrition Sciences, Brooklyn College, City University of New York, Brooklyn, New York.,Center for Systems and Community Design, Graduate School of Public Health and Health Policy, City University of New York, New York, New York.,City University of New York, Brooklyn College, 2900 Bedford Ave, Brooklyn, NY 11210.
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24
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Comprehensive characterization of protein-protein interactions perturbed by disease mutations. Nat Genet 2021; 53:342-353. [PMID: 33558758 DOI: 10.1038/s41588-020-00774-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
Technological and computational advances in genomics and interactomics have made it possible to identify how disease mutations perturb protein-protein interaction (PPI) networks within human cells. Here, we show that disease-associated germline variants are significantly enriched in sequences encoding PPI interfaces compared to variants identified in healthy participants from the projects 1000 Genomes and ExAC. Somatic missense mutations are also significantly enriched in PPI interfaces compared to noninterfaces in 10,861 tumor exomes. We computationally identified 470 putative oncoPPIs in a pan-cancer analysis and demonstrate that oncoPPIs are highly correlated with patient survival and drug resistance/sensitivity. We experimentally validate the network effects of 13 oncoPPIs using a systematic binary interaction assay, and also demonstrate the functional consequences of two of these on tumor cell growth. In summary, this human interactome network framework provides a powerful tool for prioritization of alleles with PPI-perturbing mutations to inform pathobiological mechanism- and genotype-based therapeutic discovery.
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25
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Zhou Y, Zhao J, Fang J, Martin W, Li L, Nussinov R, Chan TA, Eng C, Cheng F. My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. Genome Biol 2021; 22:53. [PMID: 33514395 PMCID: PMC7845113 DOI: 10.1186/s13059-021-02269-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerating the development of precision cancer medicine protocols. MPM contains 490,245 mutations from over 10,800 tumor exomes across 33 cancer types in The Cancer Genome Atlas mapped to 94,563 structure-resolved/predicted protein-protein interaction interfaces ("edgetic") and 311,022 functional sites ("nodetic"), including ligand-protein binding sites and 8 types of protein posttranslational modifications. In total, 8884 survival results and 1,271,132 drug responses are obtained for these mapped interactions. MPM is available at https://mutanome.lerner.ccf.org .
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Junfei Zhao
- Department of Systems Biology, Herbert Irving Comprehensive Center, Columbia University, New York, NY, 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, 10032, USA
| | - Jiansong Fang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - William Martin
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH, 43210, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Timothy A Chan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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26
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Sofer T, Guo N. Rare variants association testing for a binary outcome when pooling individual level data from heterogeneous studies. Genet Epidemiol 2020; 45:115-127. [PMID: 33094516 DOI: 10.1002/gepi.22359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 02/04/2023]
Abstract
Whole genome sequencing (WGS) and whole exome sequencing studies are used to test the association of rare genetic variants with health traits. Many existing WGS efforts now aggregate data from heterogeneous groups, for example, combining sets of individuals of European and African ancestries. We here investigate the statistical implications on rare variant association testing with a binary trait when combining together heterogeneous studies, defined as studies with potentially different disease proportion and different frequency of variant carriers. We study and compare in simulations the Type 1 error control and power of the naïve score test, the saddlepoint approximation to the score test, and the BinomiRare test in a range of settings, focusing on low numbers of variant carriers. We show that Type 1 error control and power patterns depend on both the number of carriers of the rare allele and on disease prevalence in each of the studies. We develop recommendations for association analysis of rare genetic variants. (1) The Score test is preferred when the case proportion in the sample is 50%. (2) Do not down-sample controls to balance case-control ratio, because it reduces power. Rather, use a test that controls the Type 1 error. (3) Conduct stratified analysis in parallel with combined analysis. Aggregated testing may have lower power when the variant effect size differs between strata.
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Affiliation(s)
- Tamar Sofer
- Departments of Medicine and of Biostatistics, Harvard University, Boston, Massachusetts, USA.,Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Na Guo
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts, USA
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27
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Fernandez-Rhodes L, Young KL, Lilly AG, Raffield LM, Highland HM, Wojcik GL, Agler C, M Love SA, Okello S, Petty LE, Graff M, Below JE, Divaris K, North KE. Importance of Genetic Studies of Cardiometabolic Disease in Diverse Populations. Circ Res 2020; 126:1816-1840. [PMID: 32496918 PMCID: PMC7285892 DOI: 10.1161/circresaha.120.315893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have revolutionized our understanding of the genetic underpinnings of cardiometabolic disease. Yet, the inadequate representation of individuals of diverse ancestral backgrounds in these studies may undercut their ultimate potential for both public health and precision medicine. The goal of this review is to describe the imperativeness of studying the populations who are most affected by cardiometabolic disease, to the aim of better understanding the genetic underpinnings of the disease. We support this premise by describing the current variation in the global burden of cardiometabolic disease and emphasize the importance of building a globally and ancestrally representative genetics evidence base for the identification of population-specific variants, fine-mapping, and polygenic risk score estimation. We discuss the important ethical, legal, and social implications of increasing ancestral diversity in genetic studies of cardiometabolic disease and the challenges that arise from the (1) lack of diversity in current reference populations and available analytic samples and the (2) unequal generation of health-associated genomic data and their prediction accuracies. Despite these challenges, we conclude that additional, unprecedented opportunities lie ahead for public health genomics and the realization of precision medicine, provided that the gap in diversity can be systematically addressed. Achieving this goal will require concerted efforts by social, academic, professional and regulatory stakeholders and communities, and these efforts must be based on principles of equity and social justice.
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Affiliation(s)
- Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Cary Agler
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Shelly-Ann M Love
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Samson Okello
- Department of Internal Medicine, Mbarara University of Science and Technology, Uganda
- University of Virginia, Charlottesville, VA
- Harvard TH Chan School of Public Health, Boston, MA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Kimon Divaris
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Center for Genome Sciences, Chapel Hill, NC
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28
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Leong A, Lim VJY, Wang C, Chai JF, Dorajoo R, Heng CK, van Dam RM, Koh WP, Yuan JM, Jonas JB, Wang YX, Wei WB, Liu J, Reilly DF, Wong TY, Cheng CY, Sim X. Association of G6PD variants with hemoglobin A1c and impact on diabetes diagnosis in East Asian individuals. BMJ Open Diabetes Res Care 2020; 8:8/1/e001091. [PMID: 32209585 PMCID: PMC7103857 DOI: 10.1136/bmjdrc-2019-001091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/20/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Hemoglobin A1c (HbA1c) accuracy is important for diabetes diagnosis and estimation of overall glycemia. The G6PD-Asahi variant which causes glucose-6-phosphate dehydrogenase (G6PD) deficiency has been shown to lower HbA1c independently of glycemia in African ancestry populations. As different G6PD variants occur in Asian ancestry, we sought to identify Asian-specific G6PD variants associated with HbA1c. RESEARCH DESIGN AND METHODS In eight Asian population-based cohorts, we performed imputation on the X chromosome using the 1000 Genomes reference panel and tested for association with HbA1c (10 005 East Asians and 2051 South Asians). Results were meta-analyzed across studies. We compared the proportion of individuals classified as having diabetes/pre-diabetes by fasting glucose ≥100 mg/dL or HbA1c ≥5.7% units among carriers and non-carriers of HbA1c-associated variants. RESULTS The strongest association was a missense variant (G6PD-Canton, rs72554665, minor allele frequency=2.2%, effect in men=-0.76% unit, 95% CI -0.88 to -0.64, p=1.25×10-27, n=2844). Conditional analyses identified a secondary distinct signal, missense variant (G6PD-Kaiping, rs72554664, minor allele frequency=1.6%, effect in men=-1.12 % unit, 95% CI -1.32 to -0.92, p=3.12×10-15, pconditional_Canton=7.57×10-11). Adjusting for glucose did not attenuate their effects. The proportion of individuals with fasting glucose ≥100 mg/dL did not differ by carrier status of G6PD-Canton (p=0.21). Whereas the proportion of individuals with HbA1c ≥5.7% units was lower in carriers (5%) compared with non-carriers of G6PD-Canton (30%, p=0.03). CONCLUSIONS We identified two G6PD variants in East Asian men associated with non-glycemic lowering of HbA1c. Carriers of these variants are more likely to be underdiagnosed for diabetes or pre-diabetes than non-carriers if screened by HbA1c without confirmation by direct glucose measurements.
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Affiliation(s)
- Aaron Leong
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Victor Jun Yu Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Woon-Puay Koh
- Health Services and Systems Research, Duke NUS Medical School, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Baden-Württemberg, Germany
- Ophthalmology and Visual Sciences Key Laboratory, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ya Xing Wang
- Ophthalmology and Visual Sciences Key Laboratory, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wen-Bin Wei
- Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Dermot F Reilly
- Genetics, Merck Sharp and Dohme IA, Kenilworth, New Jersey, USA
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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29
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Huerta-Chagoya A, Moreno-Macías H, Sevilla-González M, Rodríguez-Guillén R, Ordóñez-Sánchez ML, Gómez-Velasco D, Muñóz-Hernández L, Segura-Kato Y, Arellano-Campos O, Cruz-Bautista I, Aguilar-Salinas CA, Tusié-Luna T. Contribution of Known Genetic Risk Variants to Dyslipidemias and Type 2 Diabetes in Mexico: A Population-Based Nationwide Study. Genes (Basel) 2020; 11:genes11010114. [PMID: 31968565 PMCID: PMC7016795 DOI: 10.3390/genes11010114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/13/2022] Open
Abstract
Dyslipidemias are common risk factors for the development of chronic disorders including type 2 diabetes (T2D). Over 100 associated loci have been identified but few reports have evaluated the population attributable fraction captured by them in population-based nationwide surveys. Therefore, we determined the population contribution of a set of known genetic risk variants to the development of dyslipidemias and T2D in Mexico. This study included 1665 participants from a Mexican National Health Survey carried out in the year 2000. It is a probabilistic complex sample survey of households, which comprises representative data at a national level. 103 previously reported SNPs associated with different dyslipidemias or T2D were genotyped and used to compute polygenic risk scores. We found that the previously known variants associated with dyslipidemias explain at most 7% of the total risk variance of lipid levels. In contrast, the known genetic risk component for T2D explained a negligible amount of variance (0.1%). Notably, variants derived from the Native-American ancestry have the strongest effect and contribute with a high proportion of the variance. These results support the need for additional studies aimed to identify specific genetic risk variants for Mexican population.
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Affiliation(s)
- Alicia Huerta-Chagoya
- CONACYT, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 03940, Mexico;
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | | | - Magdalena Sevilla-González
- Clinical and Traslational Epidemiological Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Rosario Rodríguez-Guillén
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - María L. Ordóñez-Sánchez
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Donají Gómez-Velasco
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Liliana Muñóz-Hernández
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Yayoi Segura-Kato
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Olimpia Arellano-Campos
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Ivette Cruz-Bautista
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Carlos A. Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico 14080, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, Mexico 04510, Mexico
- Correspondence: ; Tel.: +52-55-5655-0011
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