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Maihofer AX, Ratanatharathorn A, Hemmings SMJ, Costenbader KH, Michopoulos V, Polimanti R, Rothbaum AO, Seedat S, Mikita EA, Smith AK, Salem RM, Shaffer RA, Wu T, Sebat J, Ressler KJ, Stein MB, Koenen KC, Wolf EJ, Sumner JA, Nievergelt CM. Effects of genetically predicted posttraumatic stress disorder on autoimmune phenotypes. Transl Psychiatry 2024; 14:172. [PMID: 38561342 PMCID: PMC10984931 DOI: 10.1038/s41398-024-02869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/21/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Observational studies suggest that posttraumatic stress disorder (PTSD) increases risk for various autoimmune diseases. Insights into shared biology and causal relationships between these diseases may inform intervention approaches to PTSD and co-morbid autoimmune conditions. We investigated the shared genetic contributions and causal relationships between PTSD, 18 autoimmune diseases, and 3 immune/inflammatory biomarkers. Univariate MiXeR was used to contrast the genetic architectures of phenotypes. Genetic correlations were estimated using linkage disequilibrium score regression. Bi-directional, two-sample Mendelian randomization (MR) was performed using independent, genome-wide significant single nucleotide polymorphisms; inverse variance weighted and weighted median MR estimates were evaluated. Sensitivity analyses for uncorrelated (MR PRESSO) and correlated horizontal pleiotropy (CAUSE) were also performed. PTSD was considerably more polygenic (10,863 influential variants) than autoimmune diseases (median 255 influential variants). However, PTSD evidenced significant genetic correlation with nine autoimmune diseases and three inflammatory biomarkers. PTSD had putative causal effects on autoimmune thyroid disease (p = 0.00009) and C-reactive protein (CRP) (p = 4.3 × 10-7). Inferences were not substantially altered by sensitivity analyses. Additionally, the PTSD-autoimmune thyroid disease association remained significant in multivariable MR analysis adjusted for genetically predicted inflammatory biomarkers as potential mechanistic pathway variables. No autoimmune disease had a significant causal effect on PTSD (all p values > 0.05). Although causal effect models were supported for associations of PTSD with CRP, shared pleiotropy was adequate to explain a putative causal effect of CRP on PTSD (p = 0.18). In summary, our results suggest a significant genetic overlap between PTSD, autoimmune diseases, and biomarkers of inflammation. PTSD has a putative causal effect on autoimmune thyroid disease, consistent with existing epidemiologic evidence. A previously reported causal effect of CRP on PTSD is potentially confounded by shared genetics. Together, results highlight the nuanced links between PTSD, autoimmune disorders, and associated inflammatory signatures, and suggest the importance of targeting related pathways to protect against disease and disability.
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Affiliation(s)
- Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA.
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA.
| | - Andrew Ratanatharathorn
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Sian M J Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- South African Medical Research Council/Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Karen H Costenbader
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vasiliki Michopoulos
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Renato Polimanti
- VA Connecticut Healthcare Center, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Alex O Rothbaum
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Research and Outcomes, Skyland Trail, Atlanta, GA, USA
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- South African Medical Research Council/Genomics of Brain Disorders Research Unit, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elizabeth A Mikita
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Richard A Shaffer
- Department of Epidemiology and Health Sciences, Naval Health Research Center, San Diego, CA, USA
| | - Tianying Wu
- Division of Epidemiology and Biostatistics, School of Public Health, San Diego State University, San Diego, CA, USA
- Moores Cancer Center, University of California, San Diego, San Diego, CA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Karestan C Koenen
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Erika J Wolf
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jennifer A Sumner
- Department of Psychology, University of California Los Angeles, Los Angeles, CA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
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2
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Lippincott MF, Schafer EC, Hindman AA, He W, Brauner R, Delaney A, Grinspon R, Hall JE, Hirschhorn JN, McElreavey K, Palmert MR, Rey R, Seminara SB, Salem RM, Chan YM. Contributions of common genetic variants to constitutional delay of puberty and idiopathic hypogonadotropic hypogonadism. J Clin Endocrinol Metab 2024:dgae166. [PMID: 38477512 DOI: 10.1210/clinem/dgae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
CONTEXT Constitutional delay of puberty (CDP) is highly heritable, but the genetic basis for CDP is largely unknown. Idiopathic hypogonadotropic hypogonadism (IHH) can be caused by rare genetic variants, but in about half of cases, no rare-variant cause is found. OBJECTIVE To determine whether common genetic variants that influence pubertal timing contribute to CDP and IHH. DESIGN Case-control study. PARTICIPANTS 80 individuals with CDP; 301 with normosmic IHH, and 348 with Kallmann syndrome; control genotyping data from unrelated studies. MAIN OUTCOME MEASURES Polygenic scores (PGS) based on genome-wide association studies for timing of male pubertal hallmarks and age at menarche (AAM). RESULTS The CDP cohort had higher PGS for male pubertal hallmarks and for AAM compared to controls (for male hallmarks, Cohen's d = 0.85, p = 1 × 10-16; for AAM, d = 0.67, p = 1 × 10-10). The normosmic IHH cohort also had higher PGS for male hallmarks compared to controls, but the difference was smaller (male hallmarks d = 0.20, p = 0.003; AAM d = 0.10, p = 0.055). No differences were seen for the KS cohort compared to controls (male hallmarks d = 0.04, p = 0.45; AAM d = -0.03, p = 0.86). CONCLUSIONS Common genetic variants that influence pubertal timing in the general population contribute strongly to the genetics of CDP, weakly to normosmic IHH, and potentially not at all to KS. These findings demonstrate that the common-variant genetics of CDP and normosmic IHH are largely but not entirely distinct.
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Affiliation(s)
- Margaret F Lippincott
- Harvard Center for Reproductive Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
| | - Evan C Schafer
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Anna A Hindman
- Harvard Center for Reproductive Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Wen He
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
| | - Raja Brauner
- Hôpital Fondation Adolphe de Rothschild and Université Paris Cité, Paris
| | - Angela Delaney
- Division of Endocrinology, Department of Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN
| | - Romina Grinspon
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Janet E Hall
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Joel N Hirschhorn
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
- Programs in Medical and Population Genetics (J.N.H., S.B.S., Y.-M.C.) and Metabolism (J.N.H.), Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Mark R Palmert
- Division of Endocrinology, Hospital for Sick Children; Departments of Pediatrics and Physiology, University of Toronto, Toronto, ON
| | - Rodolfo Rey
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Stephanie B Seminara
- Harvard Center for Reproductive Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
- Programs in Medical and Population Genetics (J.N.H., S.B.S., Y.-M.C.) and Metabolism (J.N.H.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Rany M Salem
- Herbert Wertheim School of Public Health & Human Longevity Science, University of San Diego, La Jolla, CA
| | - Yee-Ming Chan
- Departments of Medicine (M.F.L., S.B.S.), Pediatrics (J.N.H., Y.-M.C.), and Genetics (J.N.H.), Harvard Medical School, Boston, MA
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA
- Programs in Medical and Population Genetics (J.N.H., S.B.S., Y.-M.C.) and Metabolism (J.N.H.), Broad Institute of MIT and Harvard, Cambridge, MA
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Lawrence ES, Gu W, Bohlender RJ, Anza-Ramirez C, Cole AM, Yu JJ, Hu H, Heinrich EC, O’Brien KA, Vasquez CA, Cowan QT, Bruck PT, Mercader K, Alotaibi M, Long T, Hall JE, Moya EA, Bauk MA, Reeves JJ, Kong MC, Salem RM, Vizcardo-Galindo G, Macarlupu JL, Figueroa-Mujíca R, Bermudez D, Corante N, Gaio E, Fox KP, Salomaa V, Havulinna AS, Murray AJ, Malhotra A, Powel FL, Jain M, Komor AC, Cavalleri GL, Huff CD, Villafuerte FC, Simonson TS. Functional EPAS1/ HIF2A missense variant is associated with hematocrit in Andean highlanders. Sci Adv 2024; 10:eadj5661. [PMID: 38335297 PMCID: PMC10857371 DOI: 10.1126/sciadv.adj5661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.
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Affiliation(s)
- Elijah S. Lawrence
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cecilia Anza-Ramirez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Amy M. Cole
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - James J. Yu
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica C. Heinrich
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Katie A. O’Brien
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Carlos A. Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T. Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Patrick T. Bruck
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Kysha Mercader
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Tao Long
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - James E. Hall
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marco A. Bauk
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer J. Reeves
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mitchell C. Kong
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Rany M. Salem
- Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gustavo Vizcardo-Galindo
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jose-Luis Macarlupu
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Rómulo Figueroa-Mujíca
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Daniela Bermudez
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Noemi Corante
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Eduardo Gaio
- Laboratório de Fisiologia Respiratória, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Keolu P. Fox
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM-HiLIFE), Helsinki, Finland
| | - Andrew J. Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Atul Malhotra
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frank L. Powel
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mohit Jain
- Department of Medicine and Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco C. Villafuerte
- Laboratorio de Fisiología Comparada/Fisiología de del Transporte de Oxígeno-LID, Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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4
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Zhu J, Eliasen AU, Aris IM, Stinson SE, Holm JC, Hansen T, Hivert MF, Bønnelykke K, Salem RM, Hirschhorn JN, Chan YM. Pediatric Features of Genetic Predisposition to Polycystic Ovary Syndrome. J Clin Endocrinol Metab 2024; 109:380-388. [PMID: 37690116 PMCID: PMC10795915 DOI: 10.1210/clinem/dgad533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) has historically been conceptualized as a disorder of the reproductive system in women. However, offspring of women with PCOS begin to show metabolic features of PCOS in childhood, suggestive of childhood manifestations. OBJECTIVE To identify childhood manifestations of genetic risk for PCOS. METHODS We calculated a PCOS polygenic risk score (PRS) for 12 350 girls and boys in 4 pediatric cohorts-ALSPAC (UK), COPSAC (Denmark), Project Viva (USA), and The HOLBÆK Study (Denmark). We tested for association of the PRS with PCOS-related phenotypes throughout childhood and with age at pubarche and age at peak height velocity and meta-analyzed effects across cohorts using fixed-effect models. RESULTS Higher PRS for PCOS was associated with higher body mass index in midchildhood (0.05 kg/m2 increase per 1 SD of PRS, 95% CI 0.03, 0.07, P = 3 × 10-5) and higher risk of obesity in early childhood (OR 1.34, 95% CI 1.13, 1.59, P = .0009); both persisted through late adolescence (P all ≤.03). Higher PCOS PRS was associated with earlier age at pubarche (0.85-month decrease per 1 SD of PRS, 95% CI -1.44, -0.26, P = .005) and younger age at peak height velocity (0.64-month decrease per 1 SD of PRS, 95% CI -0.94, -0.33, P = 4 × 10-5). CONCLUSION Genetic risk factors for PCOS are associated with alterations in metabolic, growth, and developmental traits in childhood. Thus, PCOS may not simply be a condition that affects women of reproductive age but, rather, a possible manifestation of an underlying condition that affects both sexes starting in early life.
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Affiliation(s)
- Jia Zhu
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Anders U Eliasen
- Copenhagen Prospective Studies on Asthma in Childhood Research Center (COPSAC), Copenhagen University Hospital, Herlev-Gentofte, Copenhagen 2820, Denmark
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Izzuddin M Aris
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School, Harvard University and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Sara E Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jens-Christian Holm
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
- The Children's Obesity Clinic, Accredited European Centre for Obesity Management, Department of Pediatrics, Copenhagen University Hospital Holbæk, Holbæk 4300, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School, Harvard University and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood Research Center (COPSAC), Copenhagen University Hospital, Herlev-Gentofte, Copenhagen 2820, Denmark
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Joel N Hirschhorn
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yee-Ming Chan
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
- Programs in Metabolism and Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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5
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Talwar JV, Laub D, Pagadala MS, Castro A, Lewis M, Luebeck GE, Gorman BR, Pan C, Dong FN, Markianos K, Teerlink CC, Lynch J, Hauger R, Pyarajan S, Tsao PS, Morris GP, Salem RM, Thompson WK, Curtius K, Zanetti M, Carter H. Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility. Am J Hum Genet 2023; 110:1138-1161. [PMID: 37339630 PMCID: PMC10357503 DOI: 10.1016/j.ajhg.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
Autoimmunity and cancer represent two different aspects of immune dysfunction. Autoimmunity is characterized by breakdowns in immune self-tolerance, while impaired immune surveillance can allow for tumorigenesis. The class I major histocompatibility complex (MHC-I), which displays derivatives of the cellular peptidome for immune surveillance by CD8+ T cells, serves as a common genetic link between these conditions. As melanoma-specific CD8+ T cells have been shown to target melanocyte-specific peptide antigens more often than melanoma-specific antigens, we investigated whether vitiligo- and psoriasis-predisposing MHC-I alleles conferred a melanoma-protective effect. In individuals with cutaneous melanoma from both The Cancer Genome Atlas (n = 451) and an independent validation set (n = 586), MHC-I autoimmune-allele carrier status was significantly associated with a later age of melanoma diagnosis. Furthermore, MHC-I autoimmune-allele carriers were significantly associated with decreased risk of developing melanoma in the Million Veteran Program (OR = 0.962, p = 0.024). Existing melanoma polygenic risk scores (PRSs) did not predict autoimmune-allele carrier status, suggesting these alleles provide orthogonal risk-relevant information. Mechanisms of autoimmune protection were neither associated with improved melanoma-driver mutation association nor improved gene-level conserved antigen presentation relative to common alleles. However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte-conserved antigens and loss of heterozygosity of autoimmune alleles caused the greatest reduction in presentation for several conserved antigens across individuals with loss of HLA alleles. Overall, this study presents evidence that MHC-I autoimmune-risk alleles modulate melanoma risk unaccounted for by current PRSs.
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Affiliation(s)
- James V Talwar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - David Laub
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Meghana S Pagadala
- Biomedical Science Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - McKenna Lewis
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Georg E Luebeck
- Public Health Sciences Division, Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Cuiping Pan
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA
| | - Frederick N Dong
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Kyriacos Markianos
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02115, USA
| | - Craig C Teerlink
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Julie Lynch
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard Hauger
- VA San Diego Healthcare System, La Jolla, CA, USA; Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA; Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA, USA
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Philip S Tsao
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Wesley K Thompson
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK 74136, USA
| | - Kit Curtius
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Laboratory of Immunology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Division of Hematology and Oncology, University of California San Diego, La Jolla, CA 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
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6
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Bartell E, Lin K, Tsuo K, Gan W, Vedantam S, Cole JB, Baronas JM, Yengo L, Marouli E, Amariuta T, Chen Z, Li L, Renthal NE, Jacobsen CM, Salem RM, Walters RG, Hirschhorn JN. Genetics of skeletal proportions in two different populations. bioRxiv 2023:2023.05.22.541772. [PMID: 37292977 PMCID: PMC10245876 DOI: 10.1101/2023.05.22.541772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Human height can be divided into sitting height and leg length, reflecting growth of different parts of the skeleton whose relative proportions are captured by the ratio of sitting to total height (as sitting height ratio, SHR). Height is a highly heritable trait, and its genetic basis has been well-studied. However, the genetic determinants of skeletal proportion are much less well-characterized. Expanding substantially on past work, we performed a genome-wide association study (GWAS) of SHR in ∼450,000 individuals with European ancestry and ∼100,000 individuals with East Asian ancestry from the UK and China Kadoorie Biobanks. We identified 565 loci independently associated with SHR, including all genomic regions implicated in prior GWAS in these ancestries. While SHR loci largely overlap height-associated loci (P < 0.001), the fine-mapped SHR signals were often distinct from height. We additionally used fine-mapped signals to identify 36 credible sets with heterogeneous effects across ancestries. Lastly, we used SHR, sitting height, and leg length to identify genetic variation acting on specific body regions rather than on overall human height.
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7
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Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun 2023; 14:2744. [PMID: 37173324 PMCID: PMC10182072 DOI: 10.1038/s41467-023-38271-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.
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Affiliation(s)
- Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H Wu
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hyo Kim
- Undergraduate Bioengineering Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrea Castro
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Steven Cao
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Divya Kirani
- Undergraduate Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Au
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sandip Pravin Patel
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jill P Mesirov
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74136, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wesley K Thompson
- Division of Biostatistics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - J Silvio Gutkind
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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8
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Hill C, Duffy S, Kettyle LM, McGlynn L, Sandholm N, Salem RM, Thompson A, Swan EJ, Kilner J, Rossing P, Shiels PG, Lajer M, Groop PH, Maxwell AP, McKnight AJ. Differential Methylation of Telomere-Related Genes Is Associated with Kidney Disease in Individuals with Type 1 Diabetes. Genes (Basel) 2023; 14:genes14051029. [PMID: 37239390 DOI: 10.3390/genes14051029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
Diabetic kidney disease (DKD) represents a major global health problem. Accelerated ageing is a key feature of DKD and, therefore, characteristics of accelerated ageing may provide useful biomarkers or therapeutic targets. Harnessing multi-omics, features affecting telomere biology and any associated methylome dysregulation in DKD were explored. Genotype data for nuclear genome polymorphisms in telomere-related genes were extracted from genome-wide case-control association data (n = 823 DKD/903 controls; n = 247 end-stage kidney disease (ESKD)/1479 controls). Telomere length was established using quantitative polymerase chain reaction. Quantitative methylation values for 1091 CpG sites in telomere-related genes were extracted from epigenome-wide case-control association data (n = 150 DKD/100 controls). Telomere length was significantly shorter in older age groups (p = 7.6 × 10-6). Telomere length was also significantly reduced (p = 6.6 × 10-5) in DKD versus control individuals, with significance remaining after covariate adjustment (p = 0.028). DKD and ESKD were nominally associated with telomere-related genetic variation, with Mendelian randomisation highlighting no significant association between genetically predicted telomere length and kidney disease. A total of 496 CpG sites in 212 genes reached epigenome-wide significance (p ≤ 10-8) for DKD association, and 412 CpG sites in 193 genes for ESKD. Functional prediction revealed differentially methylated genes were enriched for Wnt signalling involvement. Harnessing previously published RNA-sequencing datasets, potential targets where epigenetic dysregulation may result in altered gene expression were revealed, useful as potential diagnostic and therapeutic targets for intervention.
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Affiliation(s)
- Claire Hill
- Centre for Public Health, Queen's University of Belfast, Belfast BT12 6BA, UK
| | - Seamus Duffy
- Centre for Public Health, Queen's University of Belfast, Belfast BT12 6BA, UK
| | - Laura M Kettyle
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast BT9 7AE, UK
| | - Liane McGlynn
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, 00290 Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Alex Thompson
- School of Medicine, The Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Elizabeth J Swan
- Centre for Public Health, Queen's University of Belfast, Belfast BT12 6BA, UK
| | - Jill Kilner
- Centre for Public Health, Queen's University of Belfast, Belfast BT12 6BA, UK
| | - Peter Rossing
- Nordsjaellands Hospital, Hilleroed, Denmark and Health, Aarhus University, 8000 Aarhus, Denmark
- Steno Diabetes Center, 2730 Gentofte, Denmark
- Department of Clinical Medicine, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Paul G Shiels
- School of Molecular Biosciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Maria Lajer
- Steno Diabetes Center, 2730 Gentofte, Denmark
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, 00290 Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia
| | - Alexander Peter Maxwell
- Centre for Public Health, Queen's University of Belfast, Belfast BT12 6BA, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast BT9 7AB, UK
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University of Belfast, Belfast BT12 6BA, UK
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9
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Posis AIB, Bellettiere J, Salem RM, LaMonte MJ, Manson JE, Casanova R, LaCroix AZ, Shadyab AH. Associations of Accelerometer-Measured Physical Activity and Sedentary Time With All-Cause Mortality by Genetic Predisposition for Longevity. J Aging Phys Act 2023; 31:265-275. [PMID: 36002033 PMCID: PMC9950283 DOI: 10.1123/japa.2022-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022]
Abstract
The goal of this study was to examine associations between accelerometer-measured physical activity (PA) and sedentary time (ST) with mortality by a genetic risk score (GRS) for longevity. Among 5,446 women, (mean [SD]: age, 78.2 [6.6] years), 1,022 deaths were observed during 33,350 person-years of follow-up. Using multivariable Cox proportional hazards models, higher light PA and moderate to vigorous PA were associated with lower mortality across all GRS for longevity categories (low/medium/high; all ptrend < .001). Higher ST was associated with higher mortality (ptrend across all GRS categories < .001). Interaction tests for PA and ST with the GRS were not statistically significant. Findings support the importance of higher PA and lower ST for reducing mortality risk in older women, regardless of genetic predisposition for longevity.
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Affiliation(s)
- Alexander Ivan B. Posis
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - John Bellettiere
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Rany M. Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Michael J. LaMonte
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, State University of New York at Buffalo, Buffalo, NY, USA
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, MA, USA
| | - Ramon Casanova
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Andrea Z. LaCroix
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Aladdin H. Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
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10
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Smyth LJ, Dahlström EH, Syreeni A, Kerr K, Kilner J, Doyle R, Brennan E, Nair V, Fermin D, Nelson RG, Looker HC, Wooster C, Andrews D, Anderson K, McKay GJ, Cole JB, Salem RM, Conlon PJ, Kretzler M, Hirschhorn JN, Sadlier D, Godson C, Florez JC, Forsblom C, Maxwell AP, Groop PH, Sandholm N, McKnight AJ. Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease. Nat Commun 2022; 13:7891. [PMID: 36550108 PMCID: PMC9780337 DOI: 10.1038/s41467-022-34963-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Type 1 diabetes affects over nine million individuals globally, with approximately 40% developing diabetic kidney disease. Emerging evidence suggests that epigenetic alterations, such as DNA methylation, are involved in diabetic kidney disease. Here we assess differences in blood-derived genome-wide DNA methylation associated with diabetic kidney disease in 1304 carefully characterised individuals with type 1 diabetes and known renal status from two cohorts in the United Kingdom-Republic of Ireland and Finland. In the meta-analysis, we identify 32 differentially methylated CpGs in diabetic kidney disease in type 1 diabetes, 18 of which are located within genes differentially expressed in kidneys or correlated with pathological traits in diabetic kidney disease. We show that methylation at 21 of the 32 CpGs predict the development of kidney failure, extending the knowledge and potentially identifying individuals at greater risk for diabetic kidney disease in type 1 diabetes.
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Affiliation(s)
- Laura J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Emma H Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Katie Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Jill Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Ross Doyle
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Eoin Brennan
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Viji Nair
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Damian Fermin
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Christopher Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Darrell Andrews
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kerry Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Gareth J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Peter J Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital and Department of Medicine Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Joel N Hirschhorn
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Jose C Florez
- Programs in Metabolism and Medical & 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
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Alexander P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
| | - Amy Jayne McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
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11
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Maihofer AX, Engchuan W, Huguet G, Klein M, MacDonald JR, Shanta O, Thiruvahindrapuram B, Jean-Louis M, Saci Z, Jacquemont S, Scherer SW, Ketema E, Aiello AE, Amstadter AB, Avdibegović E, Babic D, Baker DG, Bisson JI, Boks MP, Bolger EA, Bryant RA, Bustamante AC, Caldas-de-Almeida JM, Cardoso G, Deckert J, Delahanty DL, Domschke K, Dunlop BW, Dzubur-Kulenovic A, Evans A, Feeny NC, Franz CE, Gautam A, Geuze E, Goci A, Hammamieh R, Jakovljevic M, Jett M, Jones I, Kaufman ML, Kessler RC, King AP, Kremen WS, Lawford BR, Lebois LAM, Lewis C, Liberzon I, Linnstaedt SD, Lugonja B, Luykx JJ, Lyons MJ, Mavissakalian MR, McLaughlin KA, McLean SA, Mehta D, Mellor R, Morris CP, Muhie S, Orcutt HK, Peverill M, Ratanatharathorn A, Risbrough VB, Rizzo A, Roberts AL, Rothbaum AO, Rothbaum BO, Roy-Byrne P, Ruggiero KJ, Rutten BPF, Schijven D, Seng JS, Sheerin CM, Sorenson MA, Teicher MH, Uddin M, Ursano RJ, Vinkers CH, Voisey J, Weber H, Winternitz S, Xavier M, Yang R, McD Young R, Zoellner LA, Salem RM, Shaffer RA, Wu T, Ressler KJ, Stein MB, Koenen KC, Sebat J, Nievergelt CM. Rare copy number variation in posttraumatic stress disorder. Mol Psychiatry 2022; 27:5062-5069. [PMID: 36131047 PMCID: PMC9763110 DOI: 10.1038/s41380-022-01776-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 01/27/2023]
Abstract
Posttraumatic stress disorder (PTSD) is a heritable (h2 = 24-71%) psychiatric illness. Copy number variation (CNV) is a form of rare genetic variation that has been implicated in the etiology of psychiatric disorders, but no large-scale investigation of CNV in PTSD has been performed. We present an association study of CNV burden and PTSD symptoms in a sample of 114,383 participants (13,036 cases and 101,347 controls) of European ancestry. CNVs were called using two calling algorithms and intersected to a consensus set. Quality control was performed to remove strong outlier samples. CNVs were examined for association with PTSD within each cohort using linear or logistic regression analysis adjusted for population structure and CNV quality metrics, then inverse variance weighted meta-analyzed across cohorts. We examined the genome-wide total span of CNVs, enrichment of CNVs within specified gene-sets, and CNVs overlapping individual genes and implicated neurodevelopmental regions. The total distance covered by deletions crossing over known neurodevelopmental CNV regions was significant (beta = 0.029, SE = 0.005, P = 6.3 × 10-8). The genome-wide neurodevelopmental CNV burden identified explains 0.034% of the variation in PTSD symptoms. The 15q11.2 BP1-BP2 microdeletion region was significantly associated with PTSD (beta = 0.0206, SE = 0.0056, P = 0.0002). No individual significant genes interrupted by CNV were identified. 22 gene pathways related to the function of the nervous system and brain were significant in pathway analysis (FDR q < 0.05), but these associations were not significant once NDD regions were removed. A larger sample size, better detection methods, and annotated resources of CNV are needed to explore this relationship further.
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Affiliation(s)
- Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA.
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA.
| | - Worrawat Engchuan
- The Hospital for Sick Children, Genetics and Genome Biology, Toronto, Ontario, Canada
- The Hospital for Sick Children, The Centre for Applied Genomics, Toronto, Ontario, Canada
| | - Guillaume Huguet
- Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
| | - Marieke Klein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey R MacDonald
- The Hospital for Sick Children, Genetics and Genome Biology, Toronto, Ontario, Canada
| | - Omar Shanta
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | | | - Martineau Jean-Louis
- Department of Pediatrics, Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
| | - Zohra Saci
- Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
| | - Sebastien Jacquemont
- Centre Hospitalier Universitaire Sainte-Justine Centre de Recherche, Montreal, Quebec, Canada
- Department of Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Vaud, Switzerland
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Stephen W Scherer
- The Hospital for Sick Children, Genetics and Genome Biology, Toronto, Ontario, Canada
- University of Toronto, McLaughlin Centre, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth Ketema
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Allison E Aiello
- Department of Epidemiology, Robert N Butler Columbia Aging Center, Columbia University, New York, NY, USA
| | - Ananda B Amstadter
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Esmina Avdibegović
- Department of Psychiatry, University Clinical Center of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Dragan Babic
- Department of Psychiatry, University Clinical Center of Mostar, Mostar, Bosnia and Herzegovina
| | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Jonathan I Bisson
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Marco P Boks
- Department of Psychiatry, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Elizabeth A Bolger
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Richard A Bryant
- Department of Psychology, University of New South Wales, Sydney, NSW, Australia
| | - Angela C Bustamante
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Graça Cardoso
- Lisbon Institute of Global Mental Health and Comprehensive Health Research Centre, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jurgen Deckert
- University Hospital of Wuerzburg, Center of Mental Health, Psychiatry, Psychosomatics and Psychotherapy, Wuerzburg, Germany
| | - Douglas L Delahanty
- Department of Psychological Sciences, Kent State University, Kent, OH, USA
- Research and Sponsored Programs, Kent State University, Kent, OH, USA
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Faculty of Medicine, Centre for Basics in Neuromodulation, University of Freiburg, Freiburg, Germany
| | - Boadie W Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Alma Dzubur-Kulenovic
- Department of Psychiatry, University Clinical Center of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Alexandra Evans
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Norah C Feeny
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Carol E Franz
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Aarti Gautam
- Walter Reed Army Institute of Research, Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Silver Spring, MD, USA
| | - Elbert Geuze
- Netherlands Ministry of Defence, Brain Research and Innovation Centre, Utrecht, the Netherlands
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Aferdita Goci
- Department of Psychiatry, University Clinical Centre of Kosovo, Prishtina, Kosovo
| | - Rasha Hammamieh
- Walter Reed Army Institute of Research, Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Silver Spring, MD, USA
| | - Miro Jakovljevic
- Department of Psychiatry, University Hospital Center of Zagreb, Zagreb, Croatia
| | - Marti Jett
- US Medical Research & Development Comm, Fort Detrick, MD, USA
- Walter Reed Army Institute of Research, Headquarter, Silver Spring, MD, USA
| | - Ian Jones
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Milissa L Kaufman
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Anthony P King
- Ohio State University, College of Medicine, Institute for Behavioral Medicine Research, Columbus, OH, USA
| | - William S Kremen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Bruce R Lawford
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Lauren A M Lebois
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Catrin Lewis
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Israel Liberzon
- Department of Psychiatry and Behavioral Sciences, Texas A&M University College of Medicine, Bryan, TX, USA
| | - Sarah D Linnstaedt
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bozo Lugonja
- MRC Centre for Psychiatric Genetics and Genomics, Cardiff University, National Centre for Mental Health, Cardiff, South Glamorgan, UK
| | - Jurjen J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Michael J Lyons
- Department of Psychological & Brain Sciences, Boston University, Boston, MA, USA
| | | | | | - Samuel A McLean
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Emergency Medicine, UNC Institute for Trauma Recovery, Chapel Hill, NC, USA
| | - Divya Mehta
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Queensland University of Technology, Centre for Genomics and Personalised Health, Kelvin Grove, QLD, Australia
| | - Rebecca Mellor
- Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, QLD, Australia
| | - Charles Phillip Morris
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Seid Muhie
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Holly K Orcutt
- Department of Psychology, Northern Illinois University, DeKalb, IL, USA
| | - Matthew Peverill
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Andrew Ratanatharathorn
- Department of Epidemiology, Columbia University Mailmain School of Public Health, New York, NY, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Albert Rizzo
- University of Southern California, Institute for Creative Technologies, Los Angeles, CA, USA
| | - Andrea L Roberts
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alex O Rothbaum
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Barbara O Rothbaum
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Peter Roy-Byrne
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Kenneth J Ruggiero
- Department of Nursing and Department of Psychiatry, Medical University of South Carolina, Charleston, SC, USA
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, Maastricht Universitair Medisch Centrum, School for Mental Health and Neuroscience, Maastricht, Limburg, the Netherlands
| | - Dick Schijven
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Julia S Seng
- University of Michigan, School of Nursing, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Women's and Gender Studies, University of Michigan, Ann Arbor, MI, USA
- University of Michigan, Institute for Research on Women and Gender, Ann Arbor, MI, USA
| | - Christina M Sheerin
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Michael A Sorenson
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Martin H Teicher
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Developmental Biopsychiatry Research Program, McLean Hospital, Belmont, MA, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Christiaan H Vinkers
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, the Netherlands
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Anatomy and Neurosciences, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Joanne Voisey
- School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Queensland University of Technology, Centre for Genomics and Personalised Health, Kelvin Grove, QLD, Australia
| | - Heike Weber
- University Hospital of Wuerzburg, Center of Mental Health, Psychiatry, Psychosomatics and Psychotherapy, Wuerzburg, Germany
| | - Sherry Winternitz
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Miguel Xavier
- Universidade Nova de Lisboa, Nova Medical School, Lisboa, Portugal
| | - Ruoting Yang
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ross McD Young
- Queensland University of Technology, School of Clinical Sciences, Kelvin Grove, QLD, Australia
- University of the Sunshine Coast, The Chancellory, Sippy Downs, QLD, Australia
| | - Lori A Zoellner
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Rany M Salem
- University of California San Diego, Herbert Wertheim School of Public Health and Human Longevity Science, La Jolla, CA, USA
| | - Richard A Shaffer
- Department of Epidemiology and Health Sciences, Naval Health Research Center, San Diego, CA, USA
| | - Tianying Wu
- Division of Epidemiology and Biostatistics, San Diego State University, School of Public Health, San Diego, CA, USA
- University of California, San Diego, Moores Cancer Center, San Diego, CA, USA
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- University of California San Diego, School of Public Health, La Jolla, CA, USA
| | - Karestan C Koenen
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. School of Public Health, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
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12
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Sandholm N, Cole JB, Nair V, Sheng X, Liu H, Ahlqvist E, van Zuydam N, Dahlström EH, Fermin D, Smyth LJ, Salem RM, Forsblom C, Valo E, Harjutsalo V, Brennan EP, McKay GJ, Andrews D, Doyle R, Looker HC, Nelson RG, Palmer C, McKnight AJ, Godson C, Maxwell AP, Groop L, McCarthy MI, Kretzler M, Susztak K, Hirschhorn JN, Florez JC, Groop PH. Genome-wide meta-analysis and omics integration identifies novel genes associated with diabetic kidney disease. Diabetologia 2022; 65:1495-1509. [PMID: 35763030 PMCID: PMC9345823 DOI: 10.1007/s00125-022-05735-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/30/2022] [Indexed: 11/29/2022]
Abstract
AIMS/HYPOTHESIS Diabetic kidney disease (DKD) is the leading cause of kidney failure and has a substantial genetic component. Our aim was to identify novel genetic factors and genes contributing to DKD by performing meta-analysis of previous genome-wide association studies (GWAS) on DKD and by integrating the results with renal transcriptomics datasets. METHODS We performed GWAS meta-analyses using ten phenotypic definitions of DKD, including nearly 27,000 individuals with diabetes. Meta-analysis results were integrated with estimated quantitative trait locus data from human glomerular (N=119) and tubular (N=121) samples to perform transcriptome-wide association study. We also performed gene aggregate tests to jointly test all available common genetic markers within a gene, and combined the results with various kidney omics datasets. RESULTS The meta-analysis identified a novel intronic variant (rs72831309) in the TENM2 gene associated with a lower risk of the combined chronic kidney disease (eGFR<60 ml/min per 1.73 m2) and DKD (microalbuminuria or worse) phenotype (p=9.8×10-9; although not withstanding correction for multiple testing, p>9.3×10-9). Gene-level analysis identified ten genes associated with DKD (COL20A1, DCLK1, EIF4E, PTPRN-RESP18, GPR158, INIP-SNX30, LSM14A and MFF; p<2.7×10-6). Integration of GWAS with human glomerular and tubular expression data demonstrated higher tubular AKIRIN2 gene expression in individuals with vs without DKD (p=1.1×10-6). The lead SNPs within six loci significantly altered DNA methylation of a nearby CpG site in kidneys (p<1.5×10-11). Expression of lead genes in kidney tubules or glomeruli correlated with relevant pathological phenotypes (e.g. TENM2 expression correlated positively with eGFR [p=1.6×10-8] and negatively with tubulointerstitial fibrosis [p=2.0×10-9], tubular DCLK1 expression correlated positively with fibrosis [p=7.4×10-16], and SNX30 expression correlated positively with eGFR [p=5.8×10-14] and negatively with fibrosis [p<2.0×10-16]). CONCLUSIONS/INTERPRETATION Altogether, the results point to novel genes contributing to the pathogenesis of DKD. DATA AVAILABILITY The GWAS meta-analysis results can be accessed via the type 1 and type 2 diabetes (T1D and T2D, respectively) and Common Metabolic Diseases (CMD) Knowledge Portals, and downloaded on their respective download pages ( https://t1d.hugeamp.org/downloads.html ; https://t2d.hugeamp.org/downloads.html ; https://hugeamp.org/downloads.html ).
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Affiliation(s)
- Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Viji Nair
- Michigan Medicine, Ann Arbor, MI, USA
| | - Xin Sheng
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Emma Ahlqvist
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University and Skåne University Hospital, Malmö, Sweden
| | - Natalie van Zuydam
- Pat Macpherson Centre for Pharmacogenetics & Pharmacogenomics, Cardiovascular & Diabetes Medicine, School of Medicine, University of Dundee, Dundee, UK
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emma H Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Laura J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Eoin P Brennan
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Gareth J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Darrell Andrews
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Ross Doyle
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Helen C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - Colin Palmer
- Pat Macpherson Centre for Pharmacogenetics & Pharmacogenomics, Cardiovascular & Diabetes Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Amy Jayne McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Alexander P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - Leif Groop
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University and Skåne University Hospital, Malmö, Sweden
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology & Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Joel N Hirschhorn
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA.
- Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA.
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, 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
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
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13
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Pagadala M, Wu V, Pérez-Guijarro E, Kim H, Castro A, Talwar J, Gonzalez-Colin C, Cao S, Schmiedel BJ, Sears T, Goudarzi S, Kirani D, Salem RM, Morris GP, Harismendy O, Patel SP, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Abstract 3825: Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
With the continued promise of immunotherapy as an avenue for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer risk screening and treatment strategies. Using genotypes from over 8,000 European individuals in The Cancer Genome Atlas and 137 heritable tumor immune phenotype components (IP components), we identified and investigated 532 TIME-SNPs. Focusing on 77 variants that were relevant to cancer risk, survival, or treatment response, we explored their potential to reveal novel targets for immunotherapy. Many variants overlapped regions with histone marks indicating active transcription, and influenced gene activities in specific immune cell subsets, such as macrophages and dendritic cells. TIME-SNPs implicated genes such as LAIR1, TREX1, CTSS, CTSW and LILRB2 were differentially expressed between responders and non-responders to immune-checkpoint blockade (ICB) in preclinical studies. Of these, LILRB2 and LAIR1 have already been identified as putative targets for immunotherapy. Here we found that inhibition of CTSS led to better tumor control and survival in murine models, alone or in combination with anti-PD-1. Collectively we show that through an integrative approach, it is possible to link host genetics to TIME characteristics, informing novel biomarkers for cancer risk and target identification in immunotherapy.
Citation Format: Meghana Pagadala, Victoria Wu, Eva Pérez-Guijarro, Hyo Kim, Andrea Castro, James Talwar, Cristian Gonzalez-Colin, Steven Cao, Benjamin J. Schmiedel, Timothy Sears, Shervin Goudarzi, Divya Kirani, Rany M. Salem, Gerald P. Morris, Olivier Harismendy, Sandip P. Patel, Jill P. Mesirov, Maurizio Zanetti, Chi-Ping Day, Chun C. Fan, Wesley K. Thompson, Glenn Merlino, J. Silvio Gutkind, Pandurangan Vijayanand, Hannah Carter. Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3825.
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Richard EL, McEvoy LK, Deary IJ, Davies G, Cao SY, Oren E, Alcaraz JE, LaCroix AZ, Bressler J, Salem RM. Markers of kidney function, genetic variation related to cognitive function, and cognitive performance in the UK Biobank. BMC Nephrol 2022; 23:159. [PMID: 35477353 PMCID: PMC9047316 DOI: 10.1186/s12882-022-02750-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic kidney disease has been linked to worse cognition. However, this association may be dependent on the marker of kidney function used, and studies assessing modification by genetics are lacking. This study examined associations between multiple measures of kidney function and assessed effect modification by a polygenic score for general cognitive function. METHODS In this cross-sectional study of up to 341,208 European ancestry participants from the UK Biobank study, we examined associations between albuminuria and estimated glomerular filtration rate based on creatinine (eGFRcre) or cystatin C (eGFRcys) with cognitive performance on tests of verbal-numeric reasoning, reaction time and visual memory. Adjustment for confounding factors was performed using multivariate regression and propensity-score matching. Interaction between kidney function markers and a polygenic risk score for general cognitive function was also assessed. RESULTS Albuminuria was associated with worse performance on tasks of verbal-numeric reasoning (β(points) = -0.09, p < 0.001), reaction time (β(milliseconds) = 7.06, p < 0.001) and visual memory (β(log errors) = 0.013, p = 0.01). A polygenic score for cognitive function modified the association between albuminuria and verbal-numeric reasoning with significantly lower scores in those with albuminuria and a lower polygenic score (p = 0.009). Compared to participants with eGFRcre ≥ 60 ml/min, those with eGFRcre < 60 ml/min had lower verbal-numeric reasoning scores and slower mean reaction times (verbal numeric reasoning β = -0.11, p < 0.001 and reaction time β = 6.08, p < 0.001 for eGFRcre < 60 vs eGFRcre ≥ 60). Associations were stronger using cystatin C-based eGFR than creatinine-based eGFR (verbal numeric reasoning β = -0.21, p < 0.001 and reaction time β = 11.21, p < 0.001 for eGFRcys < 60 vs eGFRcys ≥ 60). CONCLUSIONS Increased urine albumin is associated with worse cognition, but this may depend on genetic risk. Cystatin C-based eGFR may better predict cognitive performance than creatinine-based estimates.
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Affiliation(s)
- Erin L Richard
- Department of Family Medicine and Public Health, University of California San Diego, 9500 Gilman Dr, La Jolla, San Diego, CA, USA
- Department of Family Medicine and Public Health, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, School of Medicine, 9500 Gilman Dr, La Jolla, CA, 92093-0841, San Diego, USA
| | - Linda K McEvoy
- Department of Family Medicine and Public Health, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, School of Medicine, 9500 Gilman Dr, La Jolla, CA, 92093-0841, San Diego, USA
- Department of Radiology, University of California San Diego, 9500 Gilman Dr, La Jolla, San Diego, CA, USA
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Gail Davies
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Steven Y Cao
- Department of Family Medicine and Public Health, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, School of Medicine, 9500 Gilman Dr, La Jolla, CA, 92093-0841, San Diego, USA
| | - Eyal Oren
- Graduate School of Public Health, San Diego State University, 5500 Campanile Dr, San Diego, CA, USA
| | - John E Alcaraz
- Graduate School of Public Health, San Diego State University, 5500 Campanile Dr, San Diego, CA, USA
| | - Andrea Z LaCroix
- Department of Family Medicine and Public Health, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, School of Medicine, 9500 Gilman Dr, La Jolla, CA, 92093-0841, San Diego, USA
| | - Jan Bressler
- Human Genetics Center, Department of Epidemiology, School of Public Health, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rany M Salem
- Department of Family Medicine and Public Health, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, School of Medicine, 9500 Gilman Dr, La Jolla, CA, 92093-0841, San Diego, USA.
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Maihofer AX, Choi KW, Coleman JR, Daskalakis NP, Denckla CA, Ketema E, Morey RA, Polimanti R, Ratanatharathorn A, Torres K, Wingo AP, Zai CC, Aiello AE, Almli LM, Amstadter AB, Andersen SB, Andreassen OA, Arbisi PA, Ashley-Koch AE, Austin SB, Avdibegović E, Borglum AD, Babić D, Bækvad-Hansen M, Baker DG, Beckham JC, Bierut LJ, Bisson JI, Boks MP, Bolger EA, Bradley B, Brashear M, Breen G, Bryant RA, Bustamante AC, Bybjerg-Grauholm J, Calabrese JR, Caldas-de-Almeida JM, Chen CY, Dale AM, Dalvie S, Deckert J, Delahanty DL, Dennis MF, Disner SG, Domschke K, Duncan LE, Kulenović AD, Erbes CR, Evans A, Farrer LA, Feeny NC, Flory JD, Forbes D, Franz CE, Galea S, Garrett ME, Gautam A, Gelaye B, Gelernter J, Geuze E, Gillespie CF, Goçi A, Gordon SD, Guffanti G, Hammamieh R, Hauser MA, Heath AC, Hemmings SM, Hougaard DM, Jakovljević M, Jett M, Johnson EO, Jones I, Jovanovic T, Qin XJ, Karstoft KI, Kaufman ML, Kessler RC, Khan A, Kimbrel NA, King AP, Koen N, Kranzler HR, Kremen WS, Lawford BR, Lebois LA, Lewis C, Liberzon I, Linnstaedt SD, Logue MW, Lori A, Lugonja B, Luykx JJ, Lyons MJ, Maples-Keller JL, Marmar C, Martin NG, Maurer D, Mavissakalian MR, McFarlane A, McGlinchey RE, McLaughlin KA, McLean SA, Mehta D, Mellor R, Michopoulos V, Milberg W, Miller MW, Morris CP, Mors O, Mortensen PB, Nelson EC, Nordentoft M, Norman SB, O’Donnell M, Orcutt HK, Panizzon MS, Peters ES, Peterson AL, Peverill M, Pietrzak RH, Polusny MA, Rice JP, Risbrough VB, Roberts AL, Rothbaum AO, Rothbaum BO, Roy-Byrne P, Ruggiero KJ, Rung A, Rutten BP, Saccone NL, Sanchez SE, Schijven D, Seedat S, Seligowski AV, Seng JS, Sheerin CM, Silove D, Smith AK, Smoller JW, Sponheim SR, Stein DJ, Stevens JS, Teicher MH, Thompson WK, Trapido E, Uddin M, Ursano RJ, van den Heuvel LL, Van Hooff M, Vermetten E, Vinkers C, Voisey J, Wang Y, Wang Z, Werge T, Williams MA, Williamson DE, Winternitz S, Wolf C, Wolf EJ, Yehuda R, Young KA, Young RM, Zhao H, Zoellner LA, Haas M, Lasseter H, Provost AC, Salem RM, Sebat J, Shaffer RA, Wu T, Ripke S, Daly MJ, Ressler KJ, Koenen KC, Stein MB, Nievergelt CM. Enhancing Discovery of Genetic Variants for Posttraumatic Stress Disorder Through Integration of Quantitative Phenotypes and Trauma Exposure Information. Biol Psychiatry 2022; 91:626-636. [PMID: 34865855 PMCID: PMC8917986 DOI: 10.1016/j.biopsych.2021.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/25/2021] [Accepted: 09/21/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Posttraumatic stress disorder (PTSD) is heritable and a potential consequence of exposure to traumatic stress. Evidence suggests that a quantitative approach to PTSD phenotype measurement and incorporation of lifetime trauma exposure (LTE) information could enhance the discovery power of PTSD genome-wide association studies (GWASs). METHODS A GWAS on PTSD symptoms was performed in 51 cohorts followed by a fixed-effects meta-analysis (N = 182,199 European ancestry participants). A GWAS of LTE burden was performed in the UK Biobank cohort (N = 132,988). Genetic correlations were evaluated with linkage disequilibrium score regression. Multivariate analysis was performed using Multi-Trait Analysis of GWAS. Functional mapping and annotation of leading loci was performed with FUMA. Replication was evaluated using the Million Veteran Program GWAS of PTSD total symptoms. RESULTS GWASs of PTSD symptoms and LTE burden identified 5 and 6 independent genome-wide significant loci, respectively. There was a 72% genetic correlation between PTSD and LTE. PTSD and LTE showed largely similar patterns of genetic correlation with other traits, albeit with some distinctions. Adjusting PTSD for LTE reduced PTSD heritability by 31%. Multivariate analysis of PTSD and LTE increased the effective sample size of the PTSD GWAS by 20% and identified 4 additional loci. Four of these 9 PTSD loci were independently replicated in the Million Veteran Program. CONCLUSIONS Through using a quantitative trait measure of PTSD, we identified novel risk loci not previously identified using prior case-control analyses. PTSD and LTE have a high genetic overlap that can be leveraged to increase discovery power through multivariate methods.
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Wang H, Rosenthal BS, Makowski C, Lo M, Andreassen OA, Salem RM, McEvoy LK, Fiecas M, Chen C. Causal association of cognitive reserve on Alzheimer's disease with putative sex difference. Alzheimers Dement (Amst) 2021; 13:e12270. [PMID: 35005200 PMCID: PMC8719428 DOI: 10.1002/dad2.12270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/13/2021] [Accepted: 11/15/2021] [Indexed: 11/08/2022]
Abstract
INTRODUCTION Sex-dependent risk factors may underlie sex differences in Alzheimer's disease (AD). METHODS Using sex-stratified genome-wide association studies (GWAS) of AD, we evaluated associations of 12 traits with AD through polygenic risk scores (PRS) and Mendelian randomization (MR), and explored joint genetic architecture among significant traits by genomic structural equation modeling and network analysis. RESULTS AD was associated with lower PRS for premorbid cognitive performance, intelligence, and educational attainment. MR showed a causal role for the cognition-related traits in AD, particularly among females. Their joint genetic components encompassed RNA processing, neuron projection development, and cell cycle pathways that overlap with cellular senescence. Cholesterol and C-reactive protein showed pleiotropy but no causality with AD. DISCUSSION Lower cognitive reserve is causally related to AD. The stronger causal link between cognitive performance and AD in females, despite similar PRS between sexes, suggest these differences may result from gene-environmental interactions accumulated over the lifespan.
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Affiliation(s)
- Hao Wang
- Center for Multimodal Imaging and GeneticsDepartment of RadiologyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Brin Sara Rosenthal
- Center for Computational Biology and BioinformaticsUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Carolina Makowski
- Center for Multimodal Imaging and GeneticsDepartment of RadiologyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Min‐Tzu Lo
- Center for Multimodal Imaging and GeneticsDepartment of RadiologyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Ole A. Andreassen
- NORMENT CentreDivision of Mental Health and AddictionUniversity of Oslo and Oslo University HospitalOsloNorway
| | - Rany M. Salem
- Department of Family Medicine and Public HealthDivision of EpidemiologyUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Linda K. McEvoy
- Center for Multimodal Imaging and GeneticsDepartment of RadiologyUniversity of California San DiegoLa JollaCaliforniaUSA
- Herbert Wertheim School of Public Health and Human Longevity ScienceUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Mark Fiecas
- School of Public HealthDivision of BiostatisticsUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Chi‐Hua Chen
- Center for Multimodal Imaging and GeneticsDepartment of RadiologyUniversity of California San DiegoLa JollaCaliforniaUSA
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Richard EL, McEvoy LK, Cao SY, Oren E, Alcaraz JE, LaCroix AZ, Salem RM. Biomarkers of kidney function and cognitive ability: A Mendelian randomization study. J Neurol Sci 2021; 430:118071. [PMID: 34534883 PMCID: PMC8635776 DOI: 10.1016/j.jns.2021.118071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/28/2021] [Accepted: 09/04/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Estimated glomerular filtration rate (eGFR), albuminuria and serum uric acid (SUA) are markers of kidney function that have been associated with cognitive ability. However, whether these associations are causal is unclear. METHODS We performed one-sample Mendelian randomization (MR) to estimate the effects of kidney function markers on cognitive performance using data from the UK Biobank. Polygenic scores for SUA, urine albumin to creatinine ratio (ACR), estimated glomerular filtration rate based on serum creatinine (eGFRcre) and serum cystatin C (eGFRcys) were used as instrumental variables, and cognitive function outcomes included tests of verbal-numeric reasoning, reaction time, visual memory, and numeric memory. RESULTS We found no evidence of a causal effect of genetically determined SUA, eGFRcre or eGFRcys on cognitive function outcomes. There was no association between a polygenic score for ACR and verbal-numeric reasoning or numeric memory. However, there was suggestive evidence of a relationship between genetically increased ACR and slower reaction time and worse visual memory. ACR was no longer significantly associated with visual memory in analyses using an unweighted polygenic score and in analyses stratified by sex and age category. Pleiotropy adjusted estimates were directionally consistent with those of the principal analysis but overlapped with the null. CONCLUSIONS This MR study does not support causal effects of SUA, eGFRcre or eGFRcys on cognitive performance. Genetically increased ACR was associated with slower processing speed and visual memory, but results need confirmation in independent samples.
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Affiliation(s)
- Erin L Richard
- Department of Family Medicine and Public Health, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA; Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA.
| | - Linda K McEvoy
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA; Department of Radiology, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA
| | - Steven Y Cao
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA
| | - Eyal Oren
- Graduate School of Public Health, San Diego State University, 5500 Campanile Dr, San Diego, CA, USA
| | - John E Alcaraz
- Graduate School of Public Health, San Diego State University, 5500 Campanile Dr, San Diego, CA, USA
| | - Andrea Z LaCroix
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, USA
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Wang H, Lo MT, Rosenthal SB, Makowski C, Andreassen OA, Salem RM, McEvoy LK, Fiecas M, Chen CH. Similar Genetic Architecture of Alzheimer's Disease and Differential APOE Effect Between Sexes. Front Aging Neurosci 2021; 13:674318. [PMID: 34122051 PMCID: PMC8194397 DOI: 10.3389/fnagi.2021.674318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/27/2021] [Indexed: 01/09/2023] Open
Abstract
Sex differences have been observed in the clinical manifestations of Alzheimer’s disease (AD) and elucidating their genetic basis is an active research topic. Based on autosomal genotype data of 7,216 men and 10,680 women, including 8,136 AD cases and 9,760 controls, we explored sex-related genetic heterogeneity in AD by investigating SNP heritability, genetic correlation, as well as SNP- and gene-based genome-wide analyses. We found similar SNP heritability (men: 19.5%; women: 21.5%) and high genetic correlation (Rg = 0.96) between the sexes. The heritability of APOE ε4-related risks for AD, after accounting for effects of all SNPs excluding chromosome 19, was nominally, but not significantly, higher in women (10.6%) than men (9.7%). In age-stratified analyses, ε3/ε4 was associated with a higher risk of AD among women than men aged 65–75 years, but not in the full sample. Apart from APOE, no new significant locus was identified in sex-stratified gene-based analyses. Our result of the high genetic correlation indicates overall similar genetic architecture of AD in both sexes at the genome-wide averaged level. Our study suggests that clinically observed sex differences may arise from sex-specific variants with small effects or more complicated mechanisms involving epigenetic alterations, sex chromosomes, or gene-environment interactions.
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Affiliation(s)
- Hao Wang
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, San Diego, CA, United States
| | - Min-Tzu Lo
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, San Diego, CA, United States
| | - Sara Brin Rosenthal
- Center for Computational Biology and Bioinformatics, University of California, San Diego, San Diego, CA, United States
| | - Carolina Makowski
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, San Diego, CA, United States
| | - Ole A Andreassen
- Division of Mental Health and Addiction, NORMENT Centre, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Rany M Salem
- Department of Family Medicine and Public Health, Division of Epidemiology, University of California, San Diego, San Diego, CA, United States
| | - Linda K McEvoy
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, San Diego, CA, United States.,Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, San Diego, CA, United States
| | - Mark Fiecas
- School of Public Health, Division of Biostatistics, University of Minnesota, Minneapolis, MN, United States
| | - Chi-Hua Chen
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, San Diego, CA, United States
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Smyth LJ, Kilner J, Nair V, Liu H, Brennan E, Kerr K, Sandholm N, Cole J, Dahlström E, Syreeni A, Salem RM, Nelson RG, Looker HC, Wooster C, Anderson K, McKay GJ, Kee F, Young I, Andrews D, Forsblom C, Hirschhorn JN, Godson C, Groop PH, Maxwell AP, Susztak K, Kretzler M, Florez JC, McKnight AJ. Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study. Clin Epigenetics 2021; 13:99. [PMID: 33933144 PMCID: PMC8088646 DOI: 10.1186/s13148-021-01081-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence suggests epigenetic changes in DNA methylation may have a causal role in both T1DM and DKD. The aim of this exploratory investigation was to assess differences in blood-derived DNA methylation patterns between individuals with T1DM-ESKD and individuals with long-duration T1DM but no evidence of kidney disease upon repeated testing to identify potential blood-based biomarkers. Blood-derived DNA from individuals (107 cases, 253 controls and 14 experimental controls) were bisulphite treated before DNA methylation patterns from both groups were generated and analysed using Illumina's Infinium MethylationEPIC BeadChip arrays (n = 862,927 sites). Differentially methylated CpG sites (dmCpGs) were identified (false discovery rate adjusted p ≤ × 10-8 and fold change ± 2) by comparing methylation levels between ESKD cases and T1DM controls at single site resolution. Gene annotation and functionality was investigated to enrich and rank methylated regions associated with ESKD in T1DM. RESULTS Top-ranked genes within which several dmCpGs were located and supported by functional data with methylation look-ups in other cohorts include: AFF3, ARID5B, CUX1, ELMO1, FKBP5, HDAC4, ITGAL, LY9, PIM1, RUNX3, SEPTIN9 and UPF3A. Top-ranked enrichment pathways included pathways in cancer, TGF-β signalling and Th17 cell differentiation. CONCLUSIONS Epigenetic alterations provide a dynamic link between an individual's genetic background and their environmental exposures. This robust evaluation of DNA methylation in carefully phenotyped individuals has identified biomarkers associated with ESKD, revealing several genes and implicated key pathways associated with ESKD in individuals with T1DM.
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Affiliation(s)
- L J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
| | - J Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - V Nair
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - H Liu
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E Brennan
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - K Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - N Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J Cole
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - E Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - A Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R M Salem
- Department of Family Medicine and Public Health, UC San Diego, San Diego, CA, USA
| | - R G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - H C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - C Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - K Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - F Kee
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - I Young
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - D Andrews
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - C Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J N Hirschhorn
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C Godson
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - P H Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - A P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.,Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - K Susztak
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - M Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - J C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - A J McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
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Richard EL, McEvoy LK, Oren E, Alcaraz JE, Laughlin GA, LaCroix AZ, Salem RM. Markers of Kidney Function and Longitudinal Cognitive Ability Among Older Community-Dwelling Adults: The Rancho Bernardo Study. J Alzheimers Dis 2021; 83:319-331. [PMID: 34334390 PMCID: PMC8555353 DOI: 10.3233/jad-201605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Reduced kidney function has been associated with cognitive decline. Most studies have examined a single marker of kidney function and have limited duration of follow-up. OBJECTIVE This study evaluated associations between markers of kidney function (urine albumin, estimated glomerular filtration rate [eGFR], and hyperuricemia) with cognitive performance over time. METHODS This is a longitudinal study of 1,634 community-dwelling adults (mean age = 71.7 years), with kidney function markers and cognitive ability measured at baseline (1992-1996) and at up to five additional time points with a maximum of 23.4 years (mean = 8.1 years) of follow-up. Associations between kidney function and cognitive performance were assessed using linear mixed effects models. Testing for interaction by sex was conducted. RESULTS Albuminuria (urine albumin-to-creatinine ratio [ACR]≥30 mg/g) was associated with steeper annual declines in global cognitive function (MMSE, β= -0.12, p = 0.003), executive function (Trails B, β= 4.50, p < 0.0001) and episodic memory (Buschke total recall, β= -0.62, p = 0.02) scores in men. Results were similar when cognitive test scores were regressed on latent trajectory classes of ACR. In men, hyperuricemia (serum uric acid [SUA]≥6.8 mg/dl for men and SUA≥6.0 mg/dl for women) was associated with lower baseline MMSE (β= -0.70, p = 0.009) scores but not with MMSE change over time. No such associations were detected in women. There were no significant associations between eGFR and cognitive performance for either sex. CONCLUSION In older men, albuminuria is an independent predictor of subsequent cognitive decline. More investigations are needed to explain the observed sex differences and the potential relationship between hyperuricemia and poorer global cognition.
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Affiliation(s)
- Erin L Richard
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Linda K McEvoy
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, USA
| | - Eyal Oren
- Graduate School of Public Health, San Diego State University, San Diego, CA, USA
| | - John E Alcaraz
- Graduate School of Public Health, San Diego State University, San Diego, CA, USA
| | - Gail A Laughlin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Andrea Z LaCroix
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Rany M Salem
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
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21
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Salem RM, Todd JN, Sandholm N, Cole JB, Chen WM, Andrews D, Pezzolesi MG, McKeigue PM, Hiraki LT, Qiu C, Nair V, Di Liao C, Cao JJ, Valo E, Onengut-Gumuscu S, Smiles AM, McGurnaghan SJ, Haukka JK, Harjutsalo V, Brennan EP, van Zuydam N, Ahlqvist E, Doyle R, Ahluwalia TS, Lajer M, Hughes MF, Park J, Skupien J, Spiliopoulou A, Liu A, Menon R, Boustany-Kari CM, Kang HM, Nelson RG, Klein R, Klein BE, Lee KE, Gao X, Mauer M, Maestroni S, Caramori ML, de Boer IH, Miller RG, Guo J, Boright AP, Tregouet D, Gyorgy B, Snell-Bergeon JK, Maahs DM, Bull SB, Canty AJ, Palmer CNA, Stechemesser L, Paulweber B, Weitgasser R, Sokolovska J, Rovīte V, Pīrāgs V, Prakapiene E, Radzeviciene L, Verkauskiene R, Panduru NM, Groop LC, McCarthy MI, Gu HF, Möllsten A, Falhammar H, Brismar K, Martin F, Rossing P, Costacou T, Zerbini G, Marre M, Hadjadj S, McKnight AJ, Forsblom C, McKay G, Godson C, Maxwell AP, Kretzler M, Susztak K, Colhoun HM, Krolewski A, Paterson AD, Groop PH, Rich SS, Hirschhorn JN, Florez JC. Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen. J Am Soc Nephrol 2019; 30:2000-2016. [PMID: 31537649 DOI: 10.1681/asn.2019030218] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Although diabetic kidney disease demonstrates both familial clustering and single nucleotide polymorphism heritability, the specific genetic factors influencing risk remain largely unknown. METHODS To identify genetic variants predisposing to diabetic kidney disease, we performed genome-wide association study (GWAS) analyses. Through collaboration with the Diabetes Nephropathy Collaborative Research Initiative, we assembled a large collection of type 1 diabetes cohorts with harmonized diabetic kidney disease phenotypes. We used a spectrum of ten diabetic kidney disease definitions based on albuminuria and renal function. RESULTS Our GWAS meta-analysis included association results for up to 19,406 individuals of European descent with type 1 diabetes. We identified 16 genome-wide significant risk loci. The variant with the strongest association (rs55703767) is a common missense mutation in the collagen type IV alpha 3 chain (COL4A3) gene, which encodes a major structural component of the glomerular basement membrane (GBM). Mutations in COL4A3 are implicated in heritable nephropathies, including the progressive inherited nephropathy Alport syndrome. The rs55703767 minor allele (Asp326Tyr) is protective against several definitions of diabetic kidney disease, including albuminuria and ESKD, and demonstrated a significant association with GBM width; protective allele carriers had thinner GBM before any signs of kidney disease, and its effect was dependent on glycemia. Three other loci are in or near genes with known or suggestive involvement in this condition (BMP7) or renal biology (COLEC11 and DDR1). CONCLUSIONS The 16 diabetic kidney disease-associated loci may provide novel insights into the pathogenesis of this condition and help identify potential biologic targets for prevention and treatment.
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Affiliation(s)
- Rany M Salem
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California
| | - Jennifer N Todd
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts.,Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Center for Genomic Medicine and
| | - Niina Sandholm
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine and
| | - Joanne B Cole
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts.,Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Center for Genomic Medicine and
| | - Wei-Min Chen
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Darrell Andrews
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Marcus G Pezzolesi
- Division of Nephrology and Hypertension, Diabetes and Metabolism Center, University of Utah, Salt Lake City, Utah
| | - Paul M McKeigue
- Usher Institute of Population Health Sciences and Informatics and
| | - Linda T Hiraki
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chengxiang Qiu
- Departments of Medicine and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Viji Nair
- Division of Nephrology, Department of Internal Medicine and
| | - Chen Di Liao
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jing Jing Cao
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Erkka Valo
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine and
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | | | - Stuart J McGurnaghan
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jani K Haukka
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine and
| | - Valma Harjutsalo
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine and.,The Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Eoin P Brennan
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Natalie van Zuydam
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Emma Ahlqvist
- Department of Genomics, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Ross Doyle
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | | | - Maria Lajer
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Maria F Hughes
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Jihwan Park
- Departments of Medicine and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jan Skupien
- Joslin Diabetes Center, Boston, Massachusetts
| | | | | | - Rajasree Menon
- Division of Nephrology, Department of Internal Medicine and.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | | | - Hyun M Kang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona
| | - Ronald Klein
- University of Wisconsin-Madison, Madison, Wisconsin
| | | | | | - Xiaoyu Gao
- The George Washington University, Washington, DC
| | | | - Silvia Maestroni
- Complications of Diabetes Unit, Division of Immunology, Transplantation and Infectious Diseases, Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | | | | | - Rachel G Miller
- University of Pittsburgh Public Health, Pittsburgh, Pennsylvania
| | - Jingchuan Guo
- University of Pittsburgh Public Health, Pittsburgh, Pennsylvania
| | | | - David Tregouet
- INSERM UMR_S 1166, Sorbonne Université, UPMC Univ Paris 06, Paris, France.,ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Beata Gyorgy
- INSERM UMR_S 1166, Sorbonne Université, UPMC Univ Paris 06, Paris, France.,ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | | | - David M Maahs
- Department of Pediatrics-Endocrinology, Stanford University, Stanford, California
| | - Shelley B Bull
- The Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Angelo J Canty
- Department of Mathematics and Statistics, McMaster University, Hamilton, Ontario, Canada
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Lars Stechemesser
- First Department of Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Bernhard Paulweber
- First Department of Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Raimund Weitgasser
- First Department of Medicine, Paracelsus Medical University, Salzburg, Austria.,Department of Medicine, Diakonissen-Wehrle Hospital, Salzburg, Austria
| | | | - Vita Rovīte
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Valdis Pīrāgs
- University of Latvia, Riga, Latvia.,Pauls Stradins University Hospital, Riga, Latvia
| | | | - Lina Radzeviciene
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rasa Verkauskiene
- Institute of Endocrinology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Nicolae Mircea Panduru
- Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,2nd Clinical Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Leif C Groop
- Department of Genomics, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK.,Genentech, 1 DNA Way, South San Francisco, California
| | - Harvest F Gu
- Department of Clinical Science, Intervention and Technology and.,School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Anna Möllsten
- Division of Pediatrics, Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Henrik Falhammar
- Department of Molecular Medicine and Surgery, Rolf Luft Center for Diabetes Research and Endocrinology, Karolinska Institutet, Stockholm, Sweden.,Department of Endocrinology, Diabetes and Metabolism, Karolinska University Hospital, Stockholm, Sweden
| | - Kerstin Brismar
- Department of Molecular Medicine and Surgery, Rolf Luft Center for Diabetes Research and Endocrinology, Karolinska Institutet, Stockholm, Sweden.,Department of Endocrinology, Diabetes and Metabolism, Karolinska University Hospital, Stockholm, Sweden
| | - Finian Martin
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Gentofte, Denmark.,University of Copenhagen, Copenhagen, Denmark
| | - Tina Costacou
- University of Pittsburgh Public Health, Pittsburgh, Pennsylvania
| | - Gianpaolo Zerbini
- Complications of Diabetes Unit, Division of Immunology, Transplantation and Infectious Diseases, Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Michel Marre
- Department of Diabetology, Endocrinology and Nutrition, Bichat Hospital, DHU FIRE, Assistance Publique-Hôpitaux de Paris, Paris, France.,UFR de Médecine, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,INSERM UMRS 1138, Cordeliers Research Center, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France
| | - Samy Hadjadj
- Department of Endocrinology and Diabetology, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,INSERM CIC 1402, Poitiers, France.,L'institut du thorax, INSERM, CNRS, CHU Nantes, Nantes, France
| | - Amy J McKnight
- Centre for Public Health, Queens University of Belfast, Northern Ireland, UK
| | - Carol Forsblom
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine and.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine and
| | - Gareth McKay
- Centre for Public Health, Queens University of Belfast, Northern Ireland, UK
| | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - A Peter Maxwell
- Centre for Public Health, Queens University of Belfast, Northern Ireland, UK
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine and.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Katalin Susztak
- Departments of Medicine and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Helen M Colhoun
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Per-Henrik Groop
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland.,Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine and.,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia; and
| | - Stephen S Rich
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Joel N Hirschhorn
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts.,Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts; .,Center for Genomic Medicine and.,Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
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22
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Astley CM, Todd JN, Salem RM, Vedantam S, Ebbeling CB, Huang PL, Ludwig DS, Hirschhorn JN, Florez JC. Genetic Evidence That Carbohydrate-Stimulated Insulin Secretion Leads to Obesity. Clin Chem 2019; 64:192-200. [PMID: 29295838 DOI: 10.1373/clinchem.2017.280727] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/17/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND A fundamental precept of the carbohydrate-insulin model of obesity is that insulin secretion drives weight gain. However, fasting hyperinsulinemia can also be driven by obesity-induced insulin resistance. We used genetic variation to isolate and estimate the potentially causal effect of insulin secretion on body weight. METHODS Genetic instruments of variation of insulin secretion [assessed as insulin concentration 30 min after oral glucose (insulin-30)] were used to estimate the causal relationship between increased insulin secretion and body mass index (BMI), using bidirectional Mendelian randomization analysis of genome-wide association studies. Data sources included summary results from the largest published metaanalyses of predominantly European ancestry for insulin secretion (n = 26037) and BMI (n = 322154), as well as individual-level data from the UK Biobank (n = 138541). Data from the Cardiology and Metabolic Patient Cohort study at Massachusetts General Hospital (n = 1675) were used to validate genetic associations with insulin secretion and to test the observational association of insulin secretion and BMI. RESULTS Higher genetically determined insulin-30 was strongly associated with higher BMI (β = 0.098, P = 2.2 × 10-21), consistent with a causal role in obesity. Similar positive associations were noted in sensitivity analyses using other genetic variants as instrumental variables. By contrast, higher genetically determined BMI was not associated with insulin-30. CONCLUSIONS Mendelian randomization analyses provide evidence for a causal relationship of glucose-stimulated insulin secretion on body weight, consistent with the carbohydrate-insulin model of obesity.
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Affiliation(s)
- Christina M Astley
- Department of Medicine, Division of Endocrinology, Boston Children's Hospital, Boston, MA.,Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA.,Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA
| | - Jennifer N Todd
- Department of Medicine, Division of Endocrinology, Boston Children's Hospital, Boston, MA.,Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA.,Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA.,Diabetes Unit and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Rany M Salem
- Department of Family Medicine and Public Health, University of California, San Diego, CA
| | - Sailaja Vedantam
- Department of Medicine, Division of Endocrinology, Boston Children's Hospital, Boston, MA.,Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA
| | - Cara B Ebbeling
- Department of Medicine, Division of Endocrinology, Boston Children's Hospital, Boston, MA.,Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA
| | - Paul L Huang
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA.,Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - David S Ludwig
- Department of Medicine, Division of Endocrinology, Boston Children's Hospital, Boston, MA; .,Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA
| | - Joel N Hirschhorn
- Department of Medicine, Division of Endocrinology, Boston Children's Hospital, Boston, MA; .,Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA.,Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA
| | - Jose C Florez
- Departments of Medicine and Pediatrics, Harvard Medical School, Boston, MA; .,Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA.,Diabetes Unit and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA
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23
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Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, Satpathy AT, Kartha VK, Salem RM, Hirschhorn JN, Finucane HK, Aryee MJ, Buenrostro JD, Sankaran VG. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet 2019; 51:683-693. [PMID: 30858613 PMCID: PMC6441389 DOI: 10.1038/s41588-019-0362-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 01/28/2019] [Indexed: 11/16/2022]
Abstract
Widespread linkage disequilibrium and incomplete annotation of cell-to-cell state variation represent substantial challenges to elucidating mechanisms of trait-associated genetic variation. Here, we perform genetic fine-mapping for blood cell traits in the UK Biobank to identify putative causal variants. These variants are enriched in genes encoding for proteins in trait-relevant biological pathways and in accessible chromatin of hematopoietic progenitors. For regulatory variants, we explore patterns of developmental enhancer activity, predict molecular mechanisms, and identify likely target genes. In several instances, we localize multiple independent variants to the same regulatory element or gene. We further observe that variants with pleiotropic effects preferentially act in common progenitor populations to direct the production of distinct lineages. Finally, we leverage fine-mapped variants in conjunction with continuous epigenomic annotations to identify trait-cell type enrichments within closely related populations and in single cells. Our study provides a comprehensive framework for single-variant and single-cell analyses of genetic associations. Fine mapping of blood cell traits in UK Biobank identifies putative causal variants and enrichment of fine-mapped variants in accessible chromatin of hematopoietic progenitor cells. The study provides an analytical framework for single-variant and single-cell analyses of genetic associations.
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Affiliation(s)
- Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Caleb A Lareau
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael H Guo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Christian Benner
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vinay K Kartha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Rany M Salem
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Schmidt Fellows Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
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24
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Marty Pyke R, Thompson WK, Salem RM, Font-Burgada J, Zanetti M, Carter H. Evolutionary Pressure against MHC Class II Binding Cancer Mutations. Cell 2018; 175:1991. [DOI: 10.1016/j.cell.2018.11.050] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Marty Pyke R, Thompson WK, Salem RM, Font-Burgada J, Zanetti M, Carter H. Evolutionary Pressure against MHC Class II Binding Cancer Mutations. Cell 2018; 175:416-428.e13. [PMID: 30245014 PMCID: PMC6482006 DOI: 10.1016/j.cell.2018.08.048] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/07/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
Abstract
The anti-cancer immune response against mutated peptides of potential immunological relevance (neoantigens) is primarily attributed to MHC-I-restricted cytotoxic CD8+ T cell responses. MHC-II-restricted CD4+ T cells also drive anti-tumor responses, but their relation to neoantigen selection and tumor evolution has not been systematically studied. Modeling the potential of an individual's MHC-II genotype to present 1,018 driver mutations in 5,942 tumors, we demonstrate that the MHC-II genotype constrains the mutational landscape during tumorigenesis in a manner complementary to MHC-I. Mutations poorly bound to MHC-II are positively selected during tumorigenesis, even more than mutations poorly bound to MHC-I. This emphasizes the importance of CD4+ T cells in anti-tumor immunity. In addition, we observed less inter-patient variation in mutation presentation for MHC-II than for MHC-I. These differences were reflected by age at diagnosis, which was correlated with presentation by MHC-I only. Collectively, our results emphasize the central role of MHC-II presentation in tumor evolution.
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Affiliation(s)
- Rachel Marty Pyke
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Wesley Kurt Thompson
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Rany M Salem
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA
| | - Joan Font-Burgada
- Department of Pharmacology, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; CIFAR, MaRS Centre, West Tower, 661 University Ave., Suite 505, Toronto, ON, Canada.
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26
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Shadyab AH, Terkeltaub R, Kooperberg C, Reiner A, Eaton CB, Jackson RD, Krok-Schoen JL, Salem RM, LaCroix AZ. Prospective associations of C-reactive protein (CRP) levels and CRP genetic risk scores with risk of total knee and hip replacement for osteoarthritis in a diverse cohort. Osteoarthritis Cartilage 2018; 26:1038-1044. [PMID: 29758352 PMCID: PMC6050083 DOI: 10.1016/j.joca.2018.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/18/2018] [Accepted: 05/03/2018] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To examine associations of high-sensitivity C-reactive protein (CRP) levels and polygenic CRP genetic risk scores (GRS) with risk of end-stage hip or knee osteoarthritis (OA), defined as incident total hip (THR) or knee replacement (TKR) for OA. DESIGN This study included a cohort of postmenopausal white, African American, and Hispanic women from the Women's Health Initiative. Women were followed from baseline to date of THR or TKR, death, or December 31, 2014. Medicare claims data identified THR and TKR. Hs-CRP and genotyping data were collected at baseline. Three CRP GRS were constructed: 1) a 4-SNP GRS comprised of genetic variants representing variation in the CRP gene among European populations; 2) a multilocus 18-SNP GRS of genetic variants significantly associated with CRP levels in a meta-analysis of genome-wide association studies; and 3) a 5-SNP GRS of genetic variants significantly associated with CRP levels among African American women. RESULTS In analyses conducted separately among each race and ethnic group, there were no significant associations of ln hs-CRP with risk of THR or TKR, after adjusting for age, body mass index, lifestyle characteristics, chronic diseases, hormone therapy use, and non-steroidal anti-inflammatory drug use. CRP GRS were not associated with risk of THR or TKR in any ethnic group. CONCLUSIONS Serum levels of ln hs-CRP and genetically-predicted CRP levels were not associated with risk of THR or TKR for OA among a diverse cohort of women.
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Affiliation(s)
- Aladdin H. Shadyab
- Division of Epidemiology, Department of Family Medicine and Public Health, University of California San Diego School of Medicine, La Jolla, CA
| | - Robert Terkeltaub
- VA San Diego Healthcare System/University of California San Diego, La Jolla, CA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alexander Reiner
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Charles B. Eaton
- Center for Primary Care and Prevention, Memorial Hospital of Rhode Island and Department of Family Medicine, Warren Alpert Medical School, Brown University, Providence, RI
| | - Rebecca D. Jackson
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Jessica L. Krok-Schoen
- Division of Medical Dietetics and Health Sciences, School of Health and Rehabilitation Sciences, College of Medicine, The Ohio State University, Columbus, OH
| | - Rany M. Salem
- Division of Epidemiology, Department of Family Medicine and Public Health, University of California San Diego School of Medicine, La Jolla, CA
| | - Andrea Z. LaCroix
- Division of Epidemiology, Department of Family Medicine and Public Health, University of California San Diego School of Medicine, La Jolla, CA
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27
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van Zuydam NR, Ahlqvist E, Sandholm N, Deshmukh H, Rayner NW, Abdalla M, Ladenvall C, Ziemek D, Fauman E, Robertson NR, McKeigue PM, Valo E, Forsblom C, Harjutsalo V, Perna A, Rurali E, Marcovecchio ML, Igo RP, Salem RM, Perico N, Lajer M, Käräjämäki A, Imamura M, Kubo M, Takahashi A, Sim X, Liu J, van Dam RM, Jiang G, Tam CHT, Luk AOY, Lee HM, Lim CKP, Szeto CC, So WY, Chan JCN, Ang SF, Dorajoo R, Wang L, Clara TSH, McKnight AJ, Duffy S, Pezzolesi MG, Marre M, Gyorgy B, Hadjadj S, Hiraki LT, Ahluwalia TS, Almgren P, Schulz CA, Orho-Melander M, Linneberg A, Christensen C, Witte DR, Grarup N, Brandslund I, Melander O, Paterson AD, Tregouet D, Maxwell AP, Lim SC, Ma RCW, Tai ES, Maeda S, Lyssenko V, Tuomi T, Krolewski AS, Rich SS, Hirschhorn JN, Florez JC, Dunger D, Pedersen O, Hansen T, Rossing P, Remuzzi G, Brosnan MJ, Palmer CNA, Groop PH, Colhoun HM, Groop LC, McCarthy MI. A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes. Diabetes 2018; 67:1414-1427. [PMID: 29703844 PMCID: PMC6014557 DOI: 10.2337/db17-0914] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 03/30/2018] [Indexed: 01/10/2023]
Abstract
Identification of sequence variants robustly associated with predisposition to diabetic kidney disease (DKD) has the potential to provide insights into the pathophysiological mechanisms responsible. We conducted a genome-wide association study (GWAS) of DKD in type 2 diabetes (T2D) using eight complementary dichotomous and quantitative DKD phenotypes: the principal dichotomous analysis involved 5,717 T2D subjects, 3,345 with DKD. Promising association signals were evaluated in up to 26,827 subjects with T2D (12,710 with DKD). A combined T1D+T2D GWAS was performed using complementary data available for subjects with T1D, which, with replication samples, involved up to 40,340 subjects with diabetes (18,582 with DKD). Analysis of specific DKD phenotypes identified a novel signal near GABRR1 (rs9942471, P = 4.5 × 10-8) associated with microalbuminuria in European T2D case subjects. However, no replication of this signal was observed in Asian subjects with T2D or in the equivalent T1D analysis. There was only limited support, in this substantially enlarged analysis, for association at previously reported DKD signals, except for those at UMOD and PRKAG2, both associated with estimated glomerular filtration rate. We conclude that, despite challenges in addressing phenotypic heterogeneity, access to increased sample sizes will continue to provide more robust inference regarding risk variant discovery for DKD.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Case-Control Studies
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/epidemiology
- Diabetes Mellitus, Type 2/genetics
- Diabetic Nephropathies/epidemiology
- Diabetic Nephropathies/genetics
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Humans
- Kidney Failure, Chronic/complications
- Kidney Failure, Chronic/epidemiology
- Kidney Failure, Chronic/genetics
- Male
- Middle Aged
- Polymorphism, Single Nucleotide
- Renal Insufficiency, Chronic/complications
- Renal Insufficiency, Chronic/epidemiology
- Renal Insufficiency, Chronic/genetics
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Affiliation(s)
- Natalie R van Zuydam
- Wellcome Centre Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Emma Ahlqvist
- Diabetes and Endocrinology, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Diabetes and Obesity Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | | | - N William Rayner
- Wellcome Centre Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Human Genetics Programme, Wellcome Sanger Institute, University of Cambridge, Cambridge, U.K
| | - Moustafa Abdalla
- Wellcome Centre Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- Department of Statistics, University of Oxford, Oxford, U.K
| | - Claes Ladenvall
- Diabetes and Endocrinology, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Daniel Ziemek
- Inflammation and Immunology Research Unit, Pfizer, Berlin, Germany
| | - Eric Fauman
- Computational Target Validation, Pfizer, Cambridge, MA
| | - Neil R Robertson
- Wellcome Centre Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
| | - Paul M McKeigue
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, U.K
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Diabetes and Obesity Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Diabetes and Obesity Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Diabetes and Obesity Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | | | - Annalisa Perna
- Clinical Research Center for Rare Diseases "Aldo e Cele Daccò," Istituto di Ricerche Farmacologiche "Mario Negri," Bergamo, Italy
| | - Erica Rurali
- Clinical Research Center for Rare Diseases "Aldo e Cele Daccò," Istituto di Ricerche Farmacologiche "Mario Negri," Bergamo, Italy
| | | | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH
| | - Rany M Salem
- Department of Family Medicine and Public Health, University of California, San Diego, San Diego, CA
| | - Norberto Perico
- Clinical Research Center for Rare Diseases "Aldo e Cele Daccò," Istituto di Ricerche Farmacologiche "Mario Negri," Bergamo, Italy
| | - Maria Lajer
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Annemari Käräjämäki
- Department of Primary Health Care, Vaasa Central Hospital, Vaasa, Finland
- Diabetes Center, Vaasa Health Care Center, Vaasa, Finland
| | - Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Takahashi
- Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Suita, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Guozhi Jiang
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Claudia H T Tam
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrea O Y Luk
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | - Heung Man Lee
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
- Integrated Bioinformatics Laboratory for Cancer and Metabolic Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Cadmon K P Lim
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Cheuk Chun Szeto
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Wing Yee So
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Juliana C N Chan
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Su Fen Ang
- Clinical Research Unit, Khoo Teck Puat Hospital, National Healthcare Group, Singapore
| | - Rajkumar Dorajoo
- Division of Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ling Wang
- Division of Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Tan Si Hua Clara
- Clinical Research Unit, Khoo Teck Puat Hospital, National Healthcare Group, Singapore
| | | | - Seamus Duffy
- Centre for Public Health, Queen's University Belfast, Belfast, U.K
| | | | - Marcus G Pezzolesi
- Division of Nephrology and Hypertension and Diabetes & Metabolism Research Center, University of Utah Health, Salt Lake City, UT
| | | | - Michel Marre
- Sorbonnes Université, University Pierre and Marie Curie, INSERM UMRS 1166, Institute for Cardiometabolism and Nutrition, Department of Genomics and Pathophysiology of Cardiovascular Diseases, Paris, France
| | - Beata Gyorgy
- Sorbonnes Université, University Pierre and Marie Curie, INSERM UMRS 1166, Institute for Cardiometabolism and Nutrition, Department of Genomics and Pathophysiology of Cardiovascular Diseases, Paris, France
| | - Samy Hadjadj
- Endocrinology-Diabetology, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
- Clinical Investigation Center 1402 and U1082, INSERM, University of Poitiers, Poitiers, France
- Faculté de Médecine et de Pharmacie, University of Poitiers, Poitiers, France
| | - Linda T Hiraki
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | | | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Almgren
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Christina-Alexandra Schulz
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Marju Orho-Melander
- Diabetes and Cardiovascular Disease-Genetic Epidemiology, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Allan Linneberg
- Research Centre for Prevention and Health, Capital Region of Denmark, Glostrup, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cramer Christensen
- Department of Internal Medicine and Endocrinology, Vejle Hospital, Vejle, Denmark
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivan Brandslund
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Andrew D Paterson
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - David Tregouet
- Sorbonnes Université, University Pierre and Marie Curie, INSERM UMRS 1166, Institute for Cardiometabolism and Nutrition, Department of Genomics and Pathophysiology of Cardiovascular Diseases, Paris, France
| | | | - Su Chi Lim
- Diabetes Centre, Clinical Research Unit, Department of Medicine, Khoo Teck Puat Hospital, National Healthcare Group, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ronald C W Ma
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong, China
- Integrated Bioinformatics Laboratory for Cancer and Metabolic Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Cardiovascular & Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Valeriya Lyssenko
- Diabetes and Endocrinology, Department of Clinical Sciences, Lund University, Malmö, Sweden
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway
| | - Tiinamaija Tuomi
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Diabetes and Obesity Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Abdominal Center Endocrinology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Joel N Hirschhorn
- Center for Basic and Translational Obesity Research and Division of Endocrinology, Boston Children's Hospital, Boston, MA
- Programs in Medical and Population Genetics and Metabolism, Broad Institute, Cambridge, MA
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Jose C Florez
- Programs in Medical and Population Genetics and Metabolism, Broad Institute, Cambridge, MA
- Diabetes Clinical Research Center, Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - David Dunger
- Department of Paediatrics, University of Cambridge, Cambridge, U.K
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, U.K
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Peter Rossing
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Giuseppe Remuzzi
- Clinical Research Center for Rare Diseases "Aldo e Cele Daccò," Istituto di Ricerche Farmacologiche "Mario Negri," Bergamo, Italy
- Unit of Nephrology and Dialysis, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | | | - Mary Julia Brosnan
- Cardiovascular, Metabolic and Endocrine Diseases Research Unit, Pfizer, Cambridge, MA
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, U.K
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Diabetes and Obesity Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Helen M Colhoun
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, U.K
| | - Leif C Groop
- Diabetes and Endocrinology, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark I McCarthy
- Wellcome Centre Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, U.K
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, U.K
- National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, U.K
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28
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Sandholm N, Van Zuydam N, Ahlqvist E, Juliusdottir T, Deshmukh HA, Rayner NW, Di Camillo B, Forsblom C, Fadista J, Ziemek D, Salem RM, Hiraki LT, Pezzolesi M, Trégouët D, Dahlström E, Valo E, Oskolkov N, Ladenvall C, Marcovecchio ML, Cooper J, Sambo F, Malovini A, Manfrini M, McKnight AJ, Lajer M, Harjutsalo V, Gordin D, Parkkonen M, Tuomilehto J, Lyssenko V, McKeigue PM, Rich SS, Brosnan MJ, Fauman E, Bellazzi R, Rossing P, Hadjadj S, Krolewski A, Paterson AD, Florez JC, Hirschhorn JN, Maxwell AP, Dunger D, Cobelli C, Colhoun HM, Groop L, McCarthy MI, Groop PH. The Genetic Landscape of Renal Complications in Type 1 Diabetes. J Am Soc Nephrol 2016; 28:557-574. [PMID: 27647854 DOI: 10.1681/asn.2016020231] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/17/2016] [Indexed: 12/14/2022] Open
Abstract
Diabetes is the leading cause of ESRD. Despite evidence for a substantial heritability of diabetic kidney disease, efforts to identify genetic susceptibility variants have had limited success. We extended previous efforts in three dimensions, examining a more comprehensive set of genetic variants in larger numbers of subjects with type 1 diabetes characterized for a wider range of cross-sectional diabetic kidney disease phenotypes. In 2843 subjects, we estimated that the heritability of diabetic kidney disease was 35% (P=6.4×10-3). Genome-wide association analysis and replication in 12,540 individuals identified no single variants reaching stringent levels of significance and, despite excellent power, provided little independent confirmation of previously published associated variants. Whole-exome sequencing in 997 subjects failed to identify any large-effect coding alleles of lower frequency influencing the risk of diabetic kidney disease. However, sets of alleles increasing body mass index (P=2.2×10-5) and the risk of type 2 diabetes (P=6.1×10-4) associated with the risk of diabetic kidney disease. We also found genome-wide genetic correlation between diabetic kidney disease and failure at smoking cessation (P=1.1×10-4). Pathway analysis implicated ascorbate and aldarate metabolism (P=9.0×10-6), and pentose and glucuronate interconversions (P=3.0×10-6) in pathogenesis of diabetic kidney disease. These data provide further evidence for the role of genetic factors influencing diabetic kidney disease in those with type 1 diabetes and highlight some key pathways that may be responsible. Altogether these results reveal important biology behind the major cause of kidney disease.
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Affiliation(s)
- Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Natalie Van Zuydam
- Wellcome Trust Centre for Human Genetics,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom.,Medical Research Institute
| | - Emma Ahlqvist
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Harshal A Deshmukh
- Division of Population Health Sciences, University of Dundee, Dundee, United Kingdom
| | - N William Rayner
- Wellcome Trust Centre for Human Genetics,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom.,Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Joao Fadista
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Daniel Ziemek
- Computational Sciences, Pfizer Worldwide Research and Development, Berlin, Germany
| | - Rany M Salem
- Departments of Genetics,Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts.,Divisions of Endocrinology and Genetics, Boston Children's Hospital, Boston, Massachusetts
| | - Linda T Hiraki
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marcus Pezzolesi
- Section on Genetics and Epidemiology, Joslin Diabetes Center, Boston, Massachusetts
| | - David Trégouët
- Sorbonne Universities, Pierre et Marie Curie University (UPMC) and National Institute for Health and Medical Research, Mixed Research Unit in Health (UMR_S) 1166, Paris, France.,Institute for Cardiometabolism and Nutrition, Genomics and pathophysiology of Cardiovascular diseases, Paris, France
| | - Emma Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Erkka Valo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Nikolay Oskolkov
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Jason Cooper
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Francesco Sambo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Alberto Malovini
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.,Laboratory of Informatics and Systems Engineering for Clinical Research, Scientific Institute for Research, Hospitalization and Health Care, IRCCS (Instituto di Ricovero e Cura a Carattere Scientifico); Salvatore Maugeri Foundation, Pavia, Italy
| | - Marco Manfrini
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Amy Jayne McKnight
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, United Kingdom
| | - Maria Lajer
- Diabetic Complications, Steno Diabetes Center, Gentofte, Denmark
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,The Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Daniel Gordin
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Maija Parkkonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | | | - Jaakko Tuomilehto
- The Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.,Centre for Vascular Prevention, Danube University Krems, Krems, Austria
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden.,Diabetic Complications, Steno Diabetes Center, Gentofte, Denmark
| | - Paul M McKeigue
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Eric Fauman
- Computational Sciences, Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | - Riccardo Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Peter Rossing
- Diabetic Complications, Steno Diabetes Center, Gentofte, Denmark.,Department of Health, Aarhus University, Aarhus, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Samy Hadjadj
- Functional Research Unit of Medicine and Pharmacy, University of Poitiers, Poitiers, France.,Department of Endocrinology-Diabetology and Center of Clinical Investigation, Poitiers University Hospital, Poitiers, France.,Institute National pour la Santé et la Recherche Médicale, National Institute for Health and Medical Research, Center of Clinical Investigation 1402 and Unit 1082, Poitiers, France
| | - Andrzej Krolewski
- Section on Genetics and Epidemiology, Joslin Diabetes Center, Boston, Massachusetts
| | - Andrew D Paterson
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Jose C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts.,Diabetes Unit and Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Joel N Hirschhorn
- Departments of Genetics,Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts.,Divisions of Endocrinology and Genetics, Boston Children's Hospital, Boston, Massachusetts
| | - Alexander P Maxwell
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom; and
| | | | - David Dunger
- Department of Paediatrics, Institute of Metabolic Science, and
| | - Claudio Cobelli
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Helen M Colhoun
- Division of Population Health Sciences, University of Dundee, Dundee, United Kingdom
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom.,Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, United Kingdom
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Baker IDI (International Diabetes Institute) Heart and Diabetes Institute, Melbourne, Victoria, Australia
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29
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Guo MH, Dauber A, Lippincott MF, Chan YM, Salem RM, Hirschhorn JN. Determinants of Power in Gene-Based Burden Testing for Monogenic Disorders. Am J Hum Genet 2016; 99:527-539. [PMID: 27545677 DOI: 10.1016/j.ajhg.2016.06.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/28/2016] [Indexed: 12/11/2022] Open
Abstract
Whole-exome sequencing has enabled new approaches for discovering genes associated with monogenic disorders. One such approach is gene-based burden testing, in which the aggregate frequency of "qualifying variants" is compared between case and control subjects for each gene. Despite substantial successes of this approach, the genetic causes for many monogenic disorders remain unknown or only partially known. It is possible that particular genetic architectures lower rates of discovery, but the influence of these factors on power has not been rigorously evaluated. Here, we leverage large-scale exome-sequencing data to create an empirically based simulation framework to evaluate the impact of key parameters (background variation rates, locus heterogeneity, mode of inheritance, penetrance) on power in gene-based burden tests in the context of monogenic disorders. Our results demonstrate that across genes, there is a wide range in sample sizes needed to achieve power due to differences in the background rate of rare variants in each gene. Increasing locus heterogeneity results in rapid increases in sample sizes needed to achieve adequate power, particularly when individual genes contribute to less than 5% of cases under a dominant model. Interestingly, incomplete penetrance as low as 10% had little effect on power due to the low prevalence of monogenic disorders. Our results suggest that moderate incomplete penetrance is not an obstacle in this gene-based burden testing approach but that dominant disorders with high locus heterogeneity will require large sample sizes. Our simulations also provide guidance on sample size needs and inform study design under various genetic architectures.
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Affiliation(s)
- Michael H Guo
- Division of Endocrinology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Andrew Dauber
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Margaret F Lippincott
- Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yee-Ming Chan
- Division of Endocrinology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Reproductive Sciences Center and Reproductive Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rany M Salem
- Division of Endocrinology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joel N Hirschhorn
- Division of Endocrinology, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA.
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30
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Boettger LM, Salem RM, Handsaker RE, Peloso GM, Kathiresan S, Hirschhorn JN, McCarroll SA. Recurring exon deletions in the HP (haptoglobin) gene contribute to lower blood cholesterol levels. Nat Genet 2016; 48:359-66. [PMID: 26901066 PMCID: PMC4811681 DOI: 10.1038/ng.3510] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/20/2016] [Indexed: 02/08/2023]
Abstract
Two exons of the human haptoglobin (HP) gene exhibit copy number variation that affects HP multimerization and underlies one of the first protein polymorphisms identified in humans. The evolutionary origins and medical significance of this polymorphism have been uncertain. Here we show that this variation has likely arisen from the recurring reversion of an ancient hominin-specific duplication of these exons. Though this polymorphism has been largely invisible to genome-wide genetic studies to date, we describe a way to analyze it by imputation from SNP haplotypes and find among 22,288 individuals that these HP exonic deletions associate with reduced LDL and total cholesterol levels. We show that these deletions, and a SNP that affects HP expression, are the likely drivers of the strong but complex association of cholesterol levels to SNPs near HP. Recurring exonic deletions in the haptoglobin gene likely enhance human health by lowering cholesterol levels in the blood.
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Affiliation(s)
- Linda M Boettger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rany M Salem
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Robert E Handsaker
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gina M Peloso
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Joel N Hirschhorn
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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31
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Todd JN, Dahlström EH, Salem RM, Sandholm N, Forsblom C, McKnight AJ, Maxwell AP, Brennan E, Sadlier D, Godson C, Groop PH, Hirschhorn JN, Florez JC. Genetic Evidence for a Causal Role of Obesity in Diabetic Kidney Disease. Diabetes 2015; 64:4238-46. [PMID: 26307587 PMCID: PMC4657582 DOI: 10.2337/db15-0254] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 08/19/2015] [Indexed: 12/20/2022]
Abstract
Obesity has been posited as an independent risk factor for diabetic kidney disease (DKD), but establishing causality from observational data is problematic. We aimed to test whether obesity is causally related to DKD using Mendelian randomization, which exploits the random assortment of genes during meiosis. In 6,049 subjects with type 1 diabetes, we used a weighted genetic risk score (GRS) comprised of 32 validated BMI loci as an instrument to test the relationship of BMI with macroalbuminuria, end-stage renal disease (ESRD), or DKD defined as presence of macroalbuminuria or ESRD. We compared these results with cross-sectional and longitudinal observational associations. Longitudinal analysis demonstrated a U-shaped relationship of BMI with development of macroalbuminuria, ESRD, or DKD over time. Cross-sectional observational analysis showed no association with overall DKD, higher odds of macroalbuminuria (for every 1 kg/m(2) higher BMI, odds ratio [OR] 1.05, 95% CI 1.03-1.07, P < 0.001), and lower odds of ESRD (OR 0.95, 95% CI 0.93-0.97, P < 0.001). Mendelian randomization analysis showed a 1 kg/m(2) higher BMI conferring an increased risk in macroalbuminuria (OR 1.28, 95% CI 1.11-1.45, P = 0.001), ESRD (OR 1.43, 95% CI 1.20-1.72, P < 0.001), and DKD (OR 1.33, 95% CI 1.17-1.51, P < 0.001). Our results provide genetic evidence for a causal link between obesity and DKD in type 1 diabetes. As obesity prevalence rises, this finding predicts an increase in DKD prevalence unless intervention should occur.
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Affiliation(s)
- Jennifer N Todd
- Division of Endocrinology, Boston Children's Hospital, Boston, MA Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Emma H Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland Research Programs Unit, Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
| | - Rany M Salem
- Division of Endocrinology, Boston Children's Hospital, Boston, MA Department of Pediatrics, Harvard Medical School, Boston, MA Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland Research Programs Unit, Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Amy J McKnight
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland
| | - Alexander P Maxwell
- Nephrology Research, Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland
| | - Eoin Brennan
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Denise Sadlier
- Mater Misericordiae University Hospital, Dublin, Ireland
| | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute, School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Joel N Hirschhorn
- Division of Endocrinology, Boston Children's Hospital, Boston, MA Department of Pediatrics, Harvard Medical School, Boston, MA Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Jose C Florez
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA Department of Medicine, Harvard Medical School, Boston, MA Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
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32
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Giani FC, Fiorini C, Wakabayashi A, Ludwig LS, Salem RM, Jobaliya CD, Regan SN, Ulirsch JC, Liang G, Steinberg-Shemer O, Guo MH, Esko T, Tong W, Brugnara C, Hirschhorn JN, Weiss MJ, Zon LI, Chou ST, French DL, Musunuru K, Sankaran VG. Targeted Application of Human Genetic Variation Can Improve Red Blood Cell Production from Stem Cells. Cell Stem Cell 2015; 18:73-78. [PMID: 26607381 DOI: 10.1016/j.stem.2015.09.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 07/11/2015] [Accepted: 09/20/2015] [Indexed: 12/25/2022]
Abstract
Multipotent and pluripotent stem cells are potential sources for cell and tissue replacement therapies. For example, stem cell-derived red blood cells (RBCs) are a potential alternative to donated blood, but yield and quality remain a challenge. Here, we show that application of insight from human population genetic studies can enhance RBC production from stem cells. The SH2B3 gene encodes a negative regulator of cytokine signaling and naturally occurring loss-of-function variants in this gene increase RBC counts in vivo. Targeted suppression of SH2B3 in primary human hematopoietic stem and progenitor cells enhanced the maturation and overall yield of in-vitro-derived RBCs. Moreover, inactivation of SH2B3 by CRISPR/Cas9 genome editing in human pluripotent stem cells allowed enhanced erythroid cell expansion with preserved differentiation. Our findings therefore highlight the potential for combining human genome variation studies with genome editing approaches to improve cell and tissue production for regenerative medicine.
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Affiliation(s)
- Felix C Giani
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Neonatology, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aoi Wakabayashi
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Neonatology, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Rany M Salem
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chintan D Jobaliya
- Departments of Pathology and Laboratory Medicine and Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie N Regan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ge Liang
- Departments of Pathology and Laboratory Medicine and Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Orna Steinberg-Shemer
- Departments of Pathology and Laboratory Medicine and Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael H Guo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tõnu Esko
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Tong
- Departments of Pathology and Laboratory Medicine and Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Leonard I Zon
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stella T Chou
- Departments of Pathology and Laboratory Medicine and Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deborah L French
- Departments of Pathology and Laboratory Medicine and Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kiran Musunuru
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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33
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Swan EJ, Salem RM, Sandholm N, Tarnow L, Rossing P, Lajer M, Groop PH, Maxwell AP, McKnight AJ. Genetic risk factors affecting mitochondrial function are associated with kidney disease in people with Type 1 diabetes. Diabet Med 2015; 32:1104-9. [PMID: 25819010 PMCID: PMC4504747 DOI: 10.1111/dme.12763] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/24/2015] [Indexed: 01/13/2023]
Abstract
AIM To evaluate the association with diabetic kidney disease of single nucleotide polymorphisms (SNPs) that may contribute to mitochondrial dysfunction. METHODS The mitochondrial genome and 1039 nuclear genes that are integral to mitochondrial function were investigated using a case (n = 823 individuals with diabetic kidney disease) vs. control (n = 903 individuals with diabetes and no renal disease) approach. All people included in the analysis were of white European origin and were diagnosed with Type 1 diabetes before the age of 31 years. Replication was conducted in 5093 people with similar phenotypes to those of the discovery collection. Association analyses were performed using the plink genetic analysis toolset, with adjustment for relevant covariates. RESULTS A total of 25 SNPs were evaluated in the mitochondrial genome, but none were significantly associated with diabetic kidney disease or end-stage renal disease. A total of 38 SNPs in nuclear genes influencing mitochondrial function were nominally associated with diabetic kidney disease and 16 SNPS were associated with end-stage renal disease, secondary to diabetic kidney disease, with meta-analyses confirming the same direction of effect. Three independent signals (seven SNPs) were common to the replication data for both phenotypes with Type 1 diabetes and persistent proteinuria or end-stage renal disease. CONCLUSIONS Our results suggest that SNPs in nuclear genes that influence mitochondrial function are significantly associated with diabetic kidney disease in a white European population.
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Affiliation(s)
- E J Swan
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - R M Salem
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - N Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland
- Department of Medicine, Division of Nephrology, Helsinki University Central Hospital, Helsinki, Finland
| | - L Tarnow
- Nordsjaellands Hospital, Hilleroed, Denmark and Health, Aarhus University, Aarhus, Denmark
- Steno Diabetes Centre, Gentofte, Denmark
| | - P Rossing
- Steno Diabetes Centre, Gentofte, Denmark
| | - M Lajer
- Steno Diabetes Centre, Gentofte, Denmark
| | - P H Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Centre, Helsinki, Finland
- Department of Medicine, Division of Nephrology, Helsinki University Central Hospital, Helsinki, Finland
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - A P Maxwell
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, UK
| | - A J McKnight
- Centre for Public Health, Queen's University of Belfast, Belfast, UK
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Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, Nutile T, Jackson AU, Schurmann C, Smith AV, Zhang W, Okada Y, Stančáková A, Faul JD, Zhao W, Bartz TM, Concas MP, Franceschini N, Enroth S, Vitart V, Trompet S, Guo X, Chasman DI, O'Connel JR, Corre T, Nongmaithem SS, Chen Y, Mangino M, Ruggiero D, Traglia M, Farmaki AE, Kacprowski T, Bjonnes A, van der Spek A, Wu Y, Giri AK, Yanek LR, Wang L, Hofer E, Rietveld CA, McLeod O, Cornelis MC, Pattaro C, Verweij N, Baumbach C, Abdellaoui A, Warren HR, Vuckovic D, Mei H, Bouchard C, Perry JRB, Cappellani S, Mirza SS, Benton MC, Broeckel U, Medland SE, Lind PA, Malerba G, Drong A, Yengo L, Bielak LF, Zhi D, van der Most PJ, Shriner D, Mägi R, Hemani G, Karaderi T, Wang Z, Liu T, Demuth I, Zhao JH, Meng W, Lataniotis L, van der Laan SW, Bradfield JP, Wood AR, Bonnefond A, Ahluwalia TS, Hall LM, Salvi E, Yazar S, Carstensen L, de Haan HG, Abney M, Afzal U, Allison MA, Amin N, Asselbergs FW, Bakker SJL, Barr RG, Baumeister SE, Benjamin DJ, Bergmann S, Boerwinkle E, Bottinger EP, Campbell A, Chakravarti A, Chan Y, Chanock SJ, Chen C, Chen YDI, Collins FS, Connell J, Correa A, Cupples LA, Smith GD, Davies G, Dörr M, Ehret G, Ellis SB, Feenstra B, Feitosa MF, Ford I, Fox CS, Frayling TM, Friedrich N, Geller F, Scotland G, Gillham-Nasenya I, Gottesman O, Graff M, Grodstein F, Gu C, Haley C, Hammond CJ, Harris SE, Harris TB, Hastie ND, Heard-Costa NL, Heikkilä K, Hocking LJ, Homuth G, Hottenga JJ, Huang J, Huffman JE, Hysi PG, Ikram MA, Ingelsson E, Joensuu A, Johansson Å, Jousilahti P, Jukema JW, Kähönen M, Kamatani Y, Kanoni S, Kerr SM, Khan NM, Koellinger P, Koistinen HA, Kooner MK, Kubo M, Kuusisto J, Lahti J, Launer LJ, Lea RA, Lehne B, Lehtimäki T, Liewald DCM, Lind L, Loh M, Lokki ML, London SJ, Loomis SJ, Loukola A, Lu Y, Lumley T, Lundqvist A, Männistö S, Marques-Vidal P, Masciullo C, Matchan A, Mathias RA, Matsuda K, Meigs JB, Meisinger C, Meitinger T, Menni C, Mentch FD, Mihailov E, Milani L, Montasser ME, Montgomery GW, Morrison A, Myers RH, Nadukuru R, Navarro P, Nelis M, Nieminen MS, Nolte IM, O'Connor GT, Ogunniyi A, Padmanabhan S, Palmas WR, Pankow JS, Patarcic I, Pavani F, Peyser PA, Pietilainen K, Poulter N, Prokopenko I, Ralhan S, Redmond P, Rich SS, Rissanen H, Robino A, Rose LM, Rose R, Sala C, Salako B, Salomaa V, Sarin AP, Saxena R, Schmidt H, Scott LJ, Scott WR, Sennblad B, Seshadri S, Sever P, Shrestha S, Smith BH, Smith JA, Soranzo N, Sotoodehnia N, Southam L, Stanton AV, Stathopoulou MG, Strauch K, Strawbridge RJ, Suderman MJ, Tandon N, Tang ST, Taylor KD, Tayo BO, Töglhofer AM, Tomaszewski M, Tšernikova N, Tuomilehto J, Uitterlinden AG, Vaidya D, van Hylckama Vlieg A, van Setten J, Vasankari T, Vedantam S, Vlachopoulou E, Vozzi D, Vuoksimaa E, Waldenberger M, Ware EB, Wentworth-Shields W, Whitfield JB, Wild S, Willemsen G, Yajnik CS, Yao J, Zaza G, Zhu X, Project TBJ, Salem RM, Melbye M, Bisgaard H, Samani NJ, Cusi D, Mackey DA, Cooper RS, Froguel P, Pasterkamp G, Grant SFA, Hakonarson H, Ferrucci L, Scott RA, Morris AD, Palmer CNA, Dedoussis G, Deloukas P, Bertram L, Lindenberger U, Berndt SI, Lindgren CM, Timpson NJ, Tönjes A, Munroe PB, Sørensen TIA, Rotimi CN, Arnett DK, Oldehinkel AJ, Kardia SLR, Balkau B, Gambaro G, Morris AP, Eriksson JG, Wright MJ, Martin NG, Hunt SC, Starr JM, Deary IJ, Griffiths LR, Tiemeier H, Pirastu N, Kaprio J, Wareham NJ, Pérusse L, Wilson JG, Girotto G, Caulfield MJ, Raitakari O, Boomsma DI, Gieger C, van der Harst P, Hicks AA, Kraft P, Sinisalo J, Knekt P, Johannesson M, Magnusson PKE, Hamsten A, Schmidt R, Borecki IB, Vartiainen E, Becker DM, Bharadwaj D, Mohlke KL, Boehnke M, van Duijn CM, Sanghera DK, Teumer A, Zeggini E, Metspalu A, Gasparini P, Ulivi S, Ober C, Toniolo D, Rudan I, Porteous DJ, Ciullo M, Spector TD, Hayward C, Dupuis J, Loos RJF, Wright AF, Chandak GR, Vollenweider P, Shuldiner A, Ridker PM, Rotter JI, Sattar N, Gyllensten U, North KE, Pirastu M, Psaty BM, Weir DR, Laakso M, Gudnason V, Takahashi A, Chambers JC, Kooner JS, Strachan DP, Campbell H, Hirschhorn JN, Perola M, Polašek O, Wilson JF. Directional dominance on stature and cognition in diverse human populations. Nature 2015; 523:459-462. [PMID: 26131930 PMCID: PMC4516141 DOI: 10.1038/nature14618] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/28/2015] [Indexed: 01/13/2023]
Abstract
Homozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10(-300), 2.1 × 10(-6), 2.5 × 10(-10) and 1.8 × 10(-10), respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months' less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.
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Affiliation(s)
- Peter K Joshi
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, 02141, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge Center 7, Cambridge, 02242, MA, USA
- Department of Genetics, Harvard Medical School, 25 Shattuck St, Boston, 02115, MA, USA
| | - Hannele Mattsson
- Unit of Public Health Genomics, National Institute for Health and Welfare, P.O. Box 104, Helsinki, FI-00251, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, P.O. Box 20, Helsinki, FI-00014, Finland
| | - Niina Eklund
- Unit of Public Health Genomics, National Institute for Health and Welfare, P.O. Box 104, Helsinki, FI-00251, Finland
| | - Ilaria Gandin
- Department of Medical Sciences, University of Trieste, Strada di Fiume 447 - Osp. di Cattinara, Trieste, 34149, Italy
| | - Teresa Nutile
- Institute of Genetics and Biophysics "A. Buzzati-Traverso" CNR, via Pietro Castellino, 111, Naples, 80131, Italy
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
| | - Albert V Smith
- Icelandic Heart Association, Holtasmari 1, 201, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UB1 3HW, UK
| | - Yukinori Okada
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8510, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Alena Stančáková
- Department of Medicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Jessica D Faul
- Institute for Social Research, University of Michigan, 426 Thompson Street, 48104, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, 1415 Washington Heights, 48109, Ann Arbor, MI, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, 98101, WA, USA
| | - Maria Pina Concas
- Institute of Population Genetics, National Research Council, Trav. La Crucca n. 3 - Reg. Baldinca, Sassari, 07100, Italy
| | - Nora Franceschini
- Epidemiology, University of North Carolina, 137 E. Franklin St., Suite 306, 27599-8050, Chapel Hill, USA
| | - Stefan Enroth
- Immunology, Genetics & Pathology, Uppsala University, Husargatan 3, Box 815, Uppsala, SE-751 08, Sweden
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Stella Trompet
- Department of Gerontology and Geriatrics, Leiden University Medical Center , PO Box 9600, Leiden, Netherlands
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences , Los Angeles Biomedical Research Institute, 1124 W. Carson Street, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, 900 Commonwealth Avenue, East, Harvard Medical School, Boston, Boston, MA 02215, USA
| | - Jeffery R O'Connel
- Division of Endocrinology, Diabetes, and Nutrition and Program for Personalised and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, 685 Baltimore St. MSTF, Baltimore, 21201, USA
| | - Tanguy Corre
- Department of Medical Genetics, University of Lausanne, Rue du Bugnon 27, Lausanne, 1005, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - batiment génopode, Lausanne, 1015, Switzerland
| | - Suraj S Nongmaithem
- Genomic Research on Complex Diseases (GRC) Group, CSIR-Centre for Cellular and Molecular Biology, Habshiguda, Uppal Road, Hyderabad, 500007, India
| | - Yuning Chen
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, 02118, MA, USA
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, South Wing, Block D, 3rd Floor, Westminster Bridge Road, London, SE1 7EH, UK
- NIHR Biomedical Research Centre , Guy's and St. Thomas' Foundation Trust, Westminster Bridge Road, London, SE1 7EH, UK
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics "A. Buzzati-Traverso" CNR, via Pietro Castellino, 111, Naples, 80131, Italy
| | - Michela Traglia
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, Milano, 20132, Italy
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, Harokopio University of Athens, 70, El. Venizelou Ave, Athens, 17671, Greece
| | - Tim Kacprowski
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15A, Greifswald, 17475, Germany
| | - Andrew Bjonnes
- Center for Human Genetic Research , 55 Fruit Street, Massachusetts General Hospital, 2114, USA
| | - Ashley van der Spek
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, 27599, NC, USA
| | - Anil K Giri
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Lisa R Yanek
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, 21287, Maryland, USA
| | - Lihua Wang
- Department of Genetics, Washington University School of Medicine, 4444 Forest Park Boulevard, Saint Louis, 63108, MO, USA
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, Graz, A-8036, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz2, Graz, A-8036, Austria
| | - Cornelius A Rietveld
- Erasmus School of Economics, Erasmus University Rotterdam, Burgemeester Oudlaan 50, Rotterdam, 3000 DR, The Netherlands
| | - Olga McLeod
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, CMM L8:03, Karolinska University Hospital, Solna, Stockholm, 171 76, Sweden
| | - Marilyn C Cornelis
- Channing Division of Network Medicine, Brigham & Women's Hospital, 181 Longwood, Boston, 02115, USA
- Nutrition, Harvard School of Public Health, 401 Park Drive, Boston, 02215, USA
| | - Cristian Pattaro
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Niek Verweij
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Hanzeplein 1, Groningen, 9700RB, The Netherlands
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, 1081 BT, Amsterdam, Netherlands
| | - Helen R Warren
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Dragana Vuckovic
- Department of Medical Sciences, University of Trieste, Strada di Fiume 447 - Osp. di Cattinara, Trieste, 34149, Italy
| | - Hao Mei
- Department of Medicine, University of Mississippi Medical Center, 2500 N. State St., Jackson, 39216, MS, USA
| | - Claude Bouchard
- Pennington Biomedical Research Center, 6400 Perkins Rd, Baton Rouge, LA 70808, USA
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Stefania Cappellani
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", via dell'Istria 65, Trieste, 34137, Italy
| | - Saira S Mirza
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Miles C Benton
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, GPO Box 2434, Brisbane Qld 4001, Brisbane, Australia
| | - Ulrich Broeckel
- Department of Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, 53226, WI, USA
| | - Sarah E Medland
- Quantitative Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Australia
| | - Penelope A Lind
- Quantitative Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Australia
| | - Giovanni Malerba
- Dipartimento di Scienze della Vita e della Riproduzione, University of Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Alexander Drong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Loic Yengo
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Lille 2 University, 1 Rue du Professeur Calmette, 59000, Lille, France
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan, 1415 Washington Heights, 48109, Ann Arbor, MI, USA
| | - Degui Zhi
- Department of Biostatistics, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, 35294, AL, USA
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, P.O. box 30.001, 9700 RB, Groningen, The Netherlands
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Building 12A/Room 4047, 12 South Dr., Bethesda, 20892, Maryland, USA
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Tugce Karaderi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, 20850, MD, USA
- Cancer Genomics Research Laboratory, National Cancer Institute, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick,MD, USA
| | - Tian Liu
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Lentzeallee 94, Berlin, 14195, Germany
- Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 72, Berlin, 14195, Germany
| | - Ilja Demuth
- Charité Research Group on Geriatrics, Charité - Universitätsmedizin Berlin, Reinickendorferstr. 61, 13347, Berlin, Germany
- Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Weihua Meng
- Division of Population Health Sciences, Medical Research Institute, University of Dundee, Ninewells hospital and School of Medicine, Dundee, DD2 4BF, Scotland
| | - Lazaros Lataniotis
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Sander W van der Laan
- Experimental Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Jonathan P Bradfield
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Amelie Bonnefond
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Lille 2 University, 1 Rue du Professeur Calmette, 59000, Lille, France
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Pediatric Asthma Center, Gentofte Hospital, The Capital Region, Copenhagen, Denmark
- Novo Nordisk Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1, Copenhagen, 2100, Denmark
| | - Leanne M Hall
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UK
| | - Erika Salvi
- Department of Health Sciences, University of Milan, via A. di Rudinì 8, 20142 Milan, Italy
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, 2 Verdun St, Perth, 6009, Australia
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Denmark
| | - Hugoline G de Haan
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300RC, The Netherlands
| | - Mark Abney
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA
| | - Uzma Afzal
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UB1 3HW, UK
| | - Matthew A Allison
- Department of Family and Preventive Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Catharijnesingel 52, Utrecht, 3501 DG, The Netherlands
- Institute of Cardiovascular Science, faculty of Population Health Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Stephan J L Bakker
- University of Groningen, University Medical Center Groningen, Department of Internal Medicine, Hanzeplein 1, Groningen, 9700RB, The Netherlands
| | - R Graham Barr
- Department of Medicine, Columbia University, 622 W. 168th Street, New York, 10032, NY, USA
| | - Sebastian E Baumeister
- Institute for Community Medicine, University Medicine Greifswald, W.-Rathenau-Str. 48, Greifswald, 17475, Germany
| | - Daniel J Benjamin
- Department of Economics, Cornell University, 480 Uris Hall, Ithaca, NY, 14853, USA
- Department of Economics and Center for Economic and Social Research, University of Southern California, 314C Dauterive Hall, 635 Downey Way, Los Angeles, CA, 90089, USA
| | - Sven Bergmann
- Department of Medical Genetics, University of Lausanne, Rue du Bugnon 27, Lausanne, 1005, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge - batiment génopode, Lausanne, 1015, Switzerland
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, 1200 Pressler St., Suite 453E, Houston, Texas, 77030, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, MD, USA
| | - Yingleong Chan
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, 02141, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge Center 7, Cambridge, 02242, MA, USA
- Department of Genetics, Harvard Medical School, 25 Shattuck St, Boston, 02115, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, 20850, MD, USA
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, 665 Huntington Ave, Boston, 02115, USA
| | - Y-D Ida Chen
- Institute for Translational Genomics and Population Sciences , Los Angeles Biomedical Research Institute, 1124 W. Carson Street, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Francis S Collins
- Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, 20892, MD, USA
| | - John Connell
- College of Medicine, Dentistry and Nursing, Ninewells Hospital and Medical School, College Office, Level 10, Dundee, DD1 9SY, UK
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, 2500 N. State St., Jackson, 39216, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, 02118, MA, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, 73 Mt. Wayte Ave, Framingham, 01702, MA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Gail Davies
- Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Marcus Dörr
- Department of Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Str. NK, Greifswald, 17475, Germany
| | - Georg Ehret
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205, MD, USA
- Cardiology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil, 4, Genève 14, 1211, Switzerland
| | - Stephen B Ellis
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Denmark
| | - Mary F Feitosa
- Department of Genetics, Washington University School of Medicine, 4444 Forest Park Boulevard, Saint Louis, 63108, MO, USA
| | - Ian Ford
- Robertson Centre, University of Glasgow, Boyd Orr Building, Glasgow, G12 8QQ, Scotland
| | - Caroline S Fox
- National Heart, Lung, and Blood Institute's Framingham Heart Study, 73 Mt. Wayte Ave, Framingham, 01702, MA, USA
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School , 75 Francis St, Boston, 02115, MA, USA
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Str. NK, 17475, Greifswald, Germany
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Denmark
| | - Generation Scotland
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Irina Gillham-Nasenya
- Department of Twin Research & Genetic Epidemiology, King's College London, South Wing, Block D, 3rd Floor, Westminster Bridge Road, London, SE1 7EH, UK
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
| | - Misa Graff
- Epidemiology, University of North Carolina, 137 E Franklin St., Suite 306, USA
| | - Francine Grodstein
- Nutrition, Harvard School of Public Health, 401 Park Drive, Boston, 02215, USA
| | - Charles Gu
- Division of Biostatistics, Washington University, 660 S Euclid, St Louis, 63110, MO, USA
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland
| | - Christopher J Hammond
- Department of Twin Research & Genetic Epidemiology, King's College London, South Wing, Block D, 3rd Floor, Westminster Bridge Road, London, SE1 7EH, UK
| | - Sarah E Harris
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Tamara B Harris
- National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas D Hastie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Nancy L Heard-Costa
- National Heart, Lung, and Blood Institute's Framingham Heart Study, 73 Mt. Wayte Ave, Framingham, 01702, MA, USA
- Department of Neurology, Boston University School of Medicine, 72 E Concord St, Boston, 02118, MA, USA
| | - Kauko Heikkilä
- Department of Public Health, University of Helsinki, Hjelt Institute, P.O.Box 41, Mannerheimintie 172, Helsinki, FI-00014, Finland
| | - Lynne J Hocking
- Musculoskeletal Research Programme, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15A, Greifswald, 17475, Germany
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, 1081 BT, Amsterdam, Netherlands
| | - Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated with Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, 200025 China
| | - Jennifer E Huffman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, South Wing, Block D, 3rd Floor, Westminster Bridge Road, London, SE1 7EH, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
- Department of Radiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anni Joensuu
- Unit of Public Health Genomics, National Institute for Health and Welfare, P.O. Box 104, Helsinki, FI-00251, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, P.O. Box 20, Helsinki, FI-00014, Finland
| | - Åsa Johansson
- Immunology, Genetics & Pathology, Uppsala University, Husargatan 3, Box 815, Uppsala, SE-751 08, Sweden
- Uppsala Clinical Research Center, Uppsala University, Uppsala, SE-75237, Sweden
| | - Pekka Jousilahti
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - J Wouter Jukema
- Department of Cardiology C5-P , Leiden University Medical Center, PO Box 9600, Leiden, Netherlands
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, P.O. Box 2000, Tampere, 33521, Finland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Shona M Kerr
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Nazir M Khan
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Philipp Koellinger
- Erasmus School of Economics, Erasmus University Rotterdam, Burgemeester Oudlaan 50, Rotterdam, 3000 DR, The Netherlands
| | - Heikki A Koistinen
- Diabetes Prevention Unit, National Institute for Health and Welfare, P.O. Box 30, FI-00271 Helsinki, Finland
- Department of Medicine, Division of Endocrinology, Helsinki University Central Hospital, P.O.Box 340, Haartmaninkatu 4, Helsinki, FI-00029, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, FI-00290, Finland
| | - Manraj K Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UB1 3HW, UK
| | - Michiaki Kubo
- Laboratory for Genotyping Development RCfIMS, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Jari Lahti
- Institute of Behavioural Sciences, University of Helsinki, P.O. Box 9, FI-00014 University of Helsinki, Helsinki, Finland
- Folkhälsan Reasearch Centre, PB 63, Helsinki, FI-00014 University of Helsinki, Finland
| | - Lenore J Launer
- National Institutes on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Rodney A Lea
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, GPO Box 2434, Brisbane Qld 4001, Brisbane, Australia
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and School of Medicine University of Tampere, Tampere, 33520, Finland
| | - David C M Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Lars Lind
- Department of Medical Sciences, University Hospital, Uppsala, 75185, Sweden
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Marja-Liisa Lokki
- Transplantation laboratory, Haartman Institute, University of Helsinki, P.O. Box 21, Helsinki, FI-00014, Finland
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, RTP, NC, USA
| | - Stephanie J Loomis
- Ophthalmology, Massachusetts Eye and Ear, 243 Charles St, Boston, 02114, USA
| | - Anu Loukola
- Department of Public Health, University of Helsinki, Hjelt Institute, P.O.Box 41, Mannerheimintie 172, Helsinki, FI-00014, Finland
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
| | - Thomas Lumley
- Department of Statistics, University of Auckland, 303.325 Science Centre, Private Bag 92019, Auckland, 1142, New Zealand
| | - Annamari Lundqvist
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Satu Männistö
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Pedro Marques-Vidal
- Department of Internal Medicine, University Hospital, Route du Bugnon 44, Lausanne, 1011, Switzerland
| | - Corrado Masciullo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, Milano, 20132, Italy
| | - Angela Matchan
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Rasika A Mathias
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, 21287, Maryland, USA
- Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, 21224, USA
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital , 50 Staniford St, Boston, 02114, MA, USA
| | - Christa Meisinger
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764 Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, München, 81675, Germany
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, South Wing, Block D, 3rd Floor, Westminster Bridge Road, London, SE1 7EH, UK
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition and Program for Personalised and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, 685 Baltimore St. MSTF, Baltimore, 21201, USA
| | - Grant W Montgomery
- Molecular Epidemiology, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Australia
| | - Alanna Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, 1200 Pressler St., Suite 453E, Houston, Texas, 77030, USA
| | - Richard H Myers
- Genome Science Institute, Boston University School of Medicine, 72 East Concord Street, E-304, Boston, 2118, MA, USA
| | - Rajiv Nadukuru
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Mari Nelis
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Markku S Nieminen
- HUCH Heart and Lung center, Helsinki University Central Hospital, P.O. Box 340, Helsinki, FI-00029, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, P.O. box 30.001, 9700 RB, Groningen, The Netherlands
| | - George T O'Connor
- National Heart, Lung, and Blood Institute's Framingham Heart Study, 73 Mt. Wayte Ave, Framingham, 01702, MA, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, 72 E Concord St, Boston, 02118, MA, USA
| | | | | | - Walter R Palmas
- Department of Medicine, Columbia University, 622 W. 168th Street, New York, 10032, NY, USA
| | - James S Pankow
- Division of Epidemiology and Community Health , University of Minnesota , 1300 S 2nd Street, Minneapolis, 55454, USA
| | - Inga Patarcic
- Centre for Global Health and Department of Public Health, School of Medicine, University of Split, Soltanska 2, 21000 Split, Croatia
| | - Francesca Pavani
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, 1415 Washington Heights, 48109, Ann Arbor, MI, USA
| | - Kirsi Pietilainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, P.O. Box 20, Helsinki, FI-00014, Finland
- Department of Medicine, Division of Endocrinology, Helsinki University Central Hospital, P.O.Box 340, Haartmaninkatu 4, Helsinki, FI-00029, Finland
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, P.O.Box 63, Haartmaninkatu 8, FI-00014, Helsinki, Finland
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College London, London, W2 1LA, UK
| | - Inga Prokopenko
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, SW7 2AZ, UK
| | - Sarju Ralhan
- Department of Cardiology and Cardio thoracic Surgery Hero DMC Heart Institute, Civil Lines, 141001, Ludhiana, India
| | - Paul Redmond
- Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Stephen S Rich
- Department Public Health Sciences, University of Virginia School of Medicine, 3232 West Complex, Charlottesville, 22908, USA
| | - Harri Rissanen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Antonietta Robino
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", via dell'Istria 65, Trieste, 34137, Italy
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, 900 Commonwealth Avenue, East, Harvard Medical School, Boston, Boston, MA 02215, USA
| | - Richard Rose
- Department of Psychological & Brain Sciences, Indiana University Bloomington, 1101 E. 10th St., Bloomington, IN 47405, USA
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, Milano, 20132, Italy
| | | | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Antti-Pekka Sarin
- Unit of Public Health Genomics, National Institute for Health and Welfare, P.O. Box 104, Helsinki, FI-00251, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, P.O. Box 20, Helsinki, FI-00014, Finland
| | - Richa Saxena
- Center for Human Genetic Research , 55 Fruit Street, Massachusetts General Hospital, 2114, USA
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Medical University Graz, Harrachgasse 21, Graz, A-8010, Austria
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - William R Scott
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UB1 3HW, UK
| | - Bengt Sennblad
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, CMM L8:03, Karolinska University Hospital, Solna, Stockholm, 171 76, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sudha Seshadri
- National Heart, Lung, and Blood Institute's Framingham Heart Study, 73 Mt. Wayte Ave, Framingham, 01702, MA, USA
- Department of Neurology, Boston University School of Medicine, 72 E Concord St, Boston, 02118, MA, USA
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College London, London, W2 1LA, UK
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC) Group, CSIR-Centre for Cellular and Molecular Biology, Habshiguda, Uppal Road, Hyderabad, 500007, India
| | - Blair H Smith
- University of Dundee, Kirsty Semple Way, Dundee, DD2 4DB, UK
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, 1415 Washington Heights, 48109, Ann Arbor, MI, USA
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, 98101, WA, USA
| | - Lorraine Southam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Alice V Stanton
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
| | - Maria G Stathopoulou
- UMR INSERM U1122; IGE-PCV "Interactions Gène-Environnement en Physiopathologie Cardio-Vasculaire", INSERM, University of Lorraine, 30 Rue Lionnois, Nancy, 54000, France
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Rona J Strawbridge
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, CMM L8:03, Karolinska University Hospital, Solna, Stockholm, 171 76, Sweden
| | - Matthew J Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Nikhil Tandon
- Department of Endocrinology, All India Institute of Medical Sciences, Ansari Nagar East, New Delhi, 110029, India
| | - Sian-Tsun Tang
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences , Los Angeles Biomedical Research Institute, 1124 W. Carson Street, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Bamidele O Tayo
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, USA
| | - Anna Maria Töglhofer
- Institute of Molecular Biology and Biochemistry, Medical University Graz, Harrachgasse 21, Graz, A-8010, Austria
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UK
- NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UK
| | - Natalia Tšernikova
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010 Estonia
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, P.O. Box 30, FI-00271 Helsinki, Finland
- Centre for Vascular Prevention, Danube-University Krems, 3500 Krems, Austria
- Diabetes Research Group, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Dhananjay Vaidya
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, 21287, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, 21205, USA
| | - Astrid van Hylckama Vlieg
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300RC, The Netherlands
| | - Jessica van Setten
- Experimental Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Tuula Vasankari
- Finnish Lung Health Association, Sibeliuksenkatu 11 A 1, Helsinki, FI-00250, Finland
| | - Sailaja Vedantam
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, 02141, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge Center 7, Cambridge, 02242, MA, USA
- Department of Genetics, Harvard Medical School, 25 Shattuck St, Boston, 02115, MA, USA
| | - Efthymia Vlachopoulou
- Transplantation laboratory, Haartman Institute, University of Helsinki, P.O. Box 21, Helsinki, FI-00014, Finland
| | - Diego Vozzi
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", via dell'Istria 65, Trieste, 34137, Italy
| | - Eero Vuoksimaa
- Department of Public Health, University of Helsinki, Hjelt Institute, P.O.Box 41, Mannerheimintie 172, Helsinki, FI-00014, Finland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
| | - Erin B Ware
- Department of Epidemiology, University of Michigan, 1415 Washington Heights, 48109, Ann Arbor, MI, USA
| | | | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Australia
| | - Sarah Wild
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, 1081 BT, Amsterdam, Netherlands
| | | | - Jie Yao
- Institute for Translational Genomics and Population Sciences , Los Angeles Biomedical Research Institute, 1124 W. Carson Street, Torrance, 90502, USA
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, Piazzale A. Stefani 1, Verona, 37124, Italy
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, USA
| | - The BioBank Japan Project
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Rany M Salem
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, 02141, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge Center 7, Cambridge, 02242, MA, USA
- Department of Genetics, Harvard Medical School, 25 Shattuck St, Boston, 02115, MA, USA
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Artillerivej 5, Copenhagen, 2300, Denmark
- Department of Medicine, Stanford University, 300 Pasteur Drive, Stanford, 94305, CA, USA
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Pediatric Asthma Center, Gentofte Hospital, The Capital Region, Copenhagen, Denmark
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, BHF Cardiovascular Research Centre, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UK
- NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, Glenfield Hospital, Groby Road, Leicester, LE3 9QP, UK
| | - Daniele Cusi
- Department of Health Sciences, University of Milan, via A. di Rudinì 8, 20142 Milan, Italy
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, 2 Verdun St, Perth, 6009, Australia
| | - Richard S Cooper
- Department of Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, USA
| | - Philippe Froguel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Lille 2 University, 1 Rue du Professeur Calmette, 59000, Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, SW7 2AZ, UK
| | - Gerard Pasterkamp
- Experimental Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Struan F A Grant
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National institute on Aging, Baltimore, 21225, Maryland, USA
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Andrew D Morris
- Jacqui Wood Cancer Centre, Medical Research Insitute, University of Dundee, Ninewells hospital and School of Medicine, Dundee, DD1 9SY, Scotland
| | - Colin N A Palmer
- Centre for Pharmacogenetics and Pharmacogenomics, Medical Research Institute, University of Dundee, Ninewells hospital and School of Medicine, Dundee, DD1 9SY, Scotland
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, 70, El. Venizelou Ave, Athens, 17671, Greece
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Lars Bertram
- Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 72, Berlin, 14195, Germany
- Faculty of Medicine, Imperial College London, Charing Cross Campus - St Dunstan's Road, London, W6 8RP, UK
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Lentzeallee 94, Berlin, 14195, Germany
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, 20850, MD, USA
| | - Cecilia M Lindgren
- Program in Medical and Population Genetics, Broad Institute, Cambridge Center 7, Cambridge, 02242, MA, USA
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Thorkild I A Sørensen
- Novo Nordisk Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 1, Copenhagen, 2100, Denmark
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospital , The Capital Region, Copenhagen, 2000, Denmark
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Building 12A/Room 4047, 12 South Dr., Bethesda, 20892, Maryland, USA
| | - Donna K Arnett
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, 35294, AL, USA
| | - Albertine J Oldehinkel
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, P.O. box 30.001, Groningen, 9700 RB, The Netherlands
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, 1415 Washington Heights, 48109, Ann Arbor, MI, USA
| | - Beverley Balkau
- Epidemiology of diabetes, obesity and chronic kidney disease over the lifecourse, Inserm, CESP Center for Research in Epidemiology and Population Health U1018, 16 Avenue Paul Vaillant Couturier, Villejuif, 94807, France
| | - Giovanni Gambaro
- Dipartimento di Scienze Mediche, Catholic University of the Sacred Heart, Via G. Moscati 31/34, Roma, 00168, Italy
| | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Duncan Building, Daulby Stree, Liverpool, L69 3GA, UK
| | - Johan G Eriksson
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, P.O. Box 20, University of Helsinki, Helsinki, FI-00014, Finland
- Vasa Central Hospital, Sandviksgatan 2-4, Vasa, 65130, Finland
- Folkhälsan Reasearch Centre, PB 63, University of Helsinki, Helsinki, FI-00014, Finland
- Unit of General Practice, Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, FI-00290, Finland
| | - Margie J Wright
- Neuro-Imaging Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006 Australia
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, Brisbane, 4006, Australia
| | - Steven C Hunt
- Cardiovascular Genetics Division, University of Utah, 420 Chipeta Way, Room 1160, Salt Lake City, 84117, Utah, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Lyn R Griffiths
- Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, GPO Box 2434, Brisbane Qld 4001, Brisbane, Australia
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Nicola Pirastu
- Department of Medical Sciences, University of Trieste, Strada di Fiume 447 - Osp. di Cattinara, Trieste, 34149, Italy
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", via dell'Istria 65, Trieste, 34137, Italy
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, P.O. Box 20, Helsinki, FI-00014, Finland
- Department of Public Health, University of Helsinki, Hjelt Institute, P.O.Box 41, Mannerheimintie 172, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare (THL), P.O.Box 30, Mannerheimintie 166, Helsinki, FI-00271, Finland
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Louis Pérusse
- Department of kinesiology, Laval University, 2300 rue de la Terrasse, Quebec, G1V 0A6, Canada
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, 2500 N. State St., Jackson, 39216, MS, USA
| | - Giorgia Girotto
- Department of Medical Sciences, University of Trieste, Strada di Fiume 447 - Osp. di Cattinara, Trieste, 34149, Italy
| | - Mark J Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Olli Raitakari
- Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, 20521, Finland
- Research Center of Applied and Preventive Cardiovascular medicine, University of Turku, Turku, 20521, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Van der Boechorststraat 1, 1081 BT, Amsterdam, Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany
| | - Pim van der Harst
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Hanzeplein 1, Groningen, 9700RB, The Netherlands
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Catharijnesingel 52, Utrecht, 3501 DG, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, Groningen, 9700RB, The Netherlands
| | - Andrew A Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy - Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, 665 Huntington Ave, Boston, 02115, USA
| | - Juha Sinisalo
- HUCH Heart and Lung center, Helsinki University Central Hospital, P.O. Box 340, Helsinki, FI-00029, Finland
| | - Paul Knekt
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Box 6501, Stockholm, SE-113 83, Sweden
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Box 281, Stockholm, SE-171 77, Sweden
| | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, CMM L8:03, Karolinska University Hospital, Solna, Stockholm, 171 76, Sweden
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Auenbruggerplatz 22, Graz, A-8036, Austria
| | - Ingrid B Borecki
- Department of Genetics and Biostatistics, Washington University School of Medicine, 4444 Forest Park Boulevard, Saint Louis, 63108, MO, USA
| | - Erkki Vartiainen
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Diane M Becker
- The GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, 21287, Maryland, USA
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, 21205, Maryland, USA
| | - Dwaipayan Bharadwaj
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, 27599, NC, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, Rotterdam, 3000 CA, The Netherlands
| | - Dharambir K Sanghera
- Department of Pediatrics, University of Oklahoma Health Sciences Center, 940 Stanton Young Boulevard, Oklahoma City, 73104, OK , USA
- Department of Pharmaceutical Sciences , University of Oklahoma Health Sceienecs Center, Oklahoma City , 73104, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, W.-Rathenau-Str. 48, Greifswald, 17475, Germany
| | - Eleftheria Zeggini
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010 Estonia
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", via dell'Istria 65, Trieste, 34137, Italy
| | - Sheila Ulivi
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", via dell'Istria 65, Trieste, 34137, Italy
| | - Carole Ober
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Via Olgettina 58, Milano, 20132, Italy
| | - Igor Rudan
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Marina Ciullo
- Institute of Genetics and Biophysics "A. Buzzati-Traverso" CNR, via Pietro Castellino, 111, Naples, 80131, Italy
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, South Wing, Block D, 3rd Floor, Westminster Bridge Road, London, SE1 7EH, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, 02118, MA, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, 73 Mt. Wayte Ave, Framingham, 01702, MA, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, 10029, USA
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC) Group, CSIR-Centre for Cellular and Molecular Biology, Habshiguda, Uppal Road, Hyderabad, 500007, India
- Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Peter Vollenweider
- Department of Internal Medicine, University Hospital, Route du Bugnon 44, Lausanne, 1011, Switzerland
| | - Alan Shuldiner
- Division of Endocrinology, Diabetes, and Nutrition and Program for Personalised and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, 685 Baltimore St. MSTF, Baltimore, 21201, USA
- Program for Personalised and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, 685 Baltimore St. MSTF, Baltimore, 21201, USA
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, 685 W Baltimore MSTF, Baltimore, 21201, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, 900 Commonwealth Avenue, East, Harvard Medical School, Boston, Boston, MA 02215, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences , Los Angeles Biomedical Research Institute, 1124 W. Carson Street, Torrance, 90502, USA
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, 90502, USA
| | - Naveed Sattar
- BHF centre, University of Glasgow, 126 University Avenue, Glasgow, G12 8TA, Scotland
| | - Ulf Gyllensten
- Immunology, Genetics & Pathology, Uppsala University, Husargatan 3, Box 815, Uppsala, SE-751 08, Sweden
| | - Kari E North
- Epidemiology, University of North Carolina, 137 E Franklin St., Suite 306, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, 137 E. Franklin St., Suite 306, Chapel Hill, USA
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council, Trav. La Crucca n. 3 - Reg. Baldinca, Sassari, 07100, Italy
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, 98101, WA, USA
- Group Health Research Institute, Group Health Cooperative, 1730 Minor Ave, Suite 1360, Seattle, 98101, WA, USA
| | - David R Weir
- Institute for Social Research, University of Michigan, 426 Thompson Street, 48104, Ann Arbor, MI, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Holtasmari 1, 201, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, Imperial College London, Praed Street, London, W2 1NY, UK
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UB1 3HW, UK
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, Imperial College London, Praed Street, London, W2 1NY, UK
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Harry Campbell
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Joel N Hirschhorn
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, 02141, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge Center 7, Cambridge, 02242, MA, USA
- Department of Genetics, Harvard Medical School, 25 Shattuck St, Boston, 02115, MA, USA
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Unit of Public Health Genomics, National Institute for Health and Welfare, P.O. Box 104, Helsinki, FI-00251, Finland
| | - Ozren Polašek
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
- Centre for Global Health and Department of Public Health, School of Medicine, University of Split, Soltanska 2, 21000 Split, Croatia
| | - James F Wilson
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, Edinburgh, UK
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Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE, Mägi R, Strawbridge RJ, Pers TH, Fischer K, Justice AE, Workalemahu T, Wu JMW, Buchkovich ML, Heard-Costa NL, Roman TS, Drong AW, Song C, Gustafsson S, Day FR, Esko T, Fall T, Kutalik Z, Luan J, Randall JC, Scherag A, Vedantam S, Wood AR, Chen J, Fehrmann R, Karjalainen J, Kahali B, Liu CT, Schmidt EM, Absher D, Amin N, Anderson D, Beekman M, Bragg-Gresham JL, Buyske S, Demirkan A, Ehret GB, Feitosa MF, Goel A, Jackson AU, Johnson T, Kleber ME, Kristiansson K, Mangino M, Mateo Leach I, Medina-Gomez C, Palmer CD, Pasko D, Pechlivanis S, Peters MJ, Prokopenko I, Stančáková A, Ju Sung Y, Tanaka T, Teumer A, Van Vliet-Ostaptchouk JV, Yengo L, Zhang W, Albrecht E, Ärnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Böhringer S, Bonnet F, Böttcher Y, Bruinenberg M, Carba DB, Caspersen IH, Clarke R, Warwick Daw E, Deelen J, Deelman E, Delgado G, Doney ASF, Eklund N, Erdos MR, Estrada K, Eury E, Friedrich N, Garcia ME, Giedraitis V, Gigante B, Go AS, Golay A, Grallert H, Grammer TB, Gräßler J, Grewal J, Groves CJ, Haller T, Hallmans G, Hartman CA, Hassinen M, Hayward C, Heikkilä K, Herzig KH, Helmer Q, Hillege HL, Holmen O, Hunt SC, Isaacs A, Ittermann T, James AL, Johansson I, Juliusdottir T, Kalafati IP, Kinnunen L, Koenig W, Kooner IK, Kratzer W, Lamina C, Leander K, Lee NR, Lichtner P, Lind L, Lindström J, Lobbens S, Lorentzon M, Mach F, Magnusson PKE, Mahajan A, McArdle WL, Menni C, Merger S, Mihailov E, Milani L, Mills R, Moayyeri A, Monda KL, Mooijaart SP, Mühleisen TW, Mulas A, Müller G, Müller-Nurasyid M, Nagaraja R, Nalls MA, Narisu N, Glorioso N, Nolte IM, Olden M, Rayner NW, Renstrom F, Ried JS, Robertson NR, Rose LM, Sanna S, Scharnagl H, Scholtens S, Sennblad B, Seufferlein T, Sitlani CM, Vernon Smith A, Stirrups K, Stringham HM, Sundström J, Swertz MA, Swift AJ, Syvänen AC, Tayo BO, Thorand B, Thorleifsson G, Tomaschitz A, Troffa C, van Oort FVA, Verweij N, Vonk JM, Waite LL, Wennauer R, Wilsgaard T, Wojczynski MK, Wong A, Zhang Q, Hua Zhao J, Brennan EP, Choi M, Eriksson P, Folkersen L, Franco-Cereceda A, Gharavi AG, Hedman ÅK, Hivert MF, Huang J, Kanoni S, Karpe F, Keildson S, Kiryluk K, Liang L, Lifton RP, Ma B, McKnight AJ, McPherson R, Metspalu A, Min JL, Moffatt MF, Montgomery GW, Murabito JM, Nicholson G, Nyholt DR, Olsson C, Perry JRB, Reinmaa E, Salem RM, Sandholm N, Schadt EE, Scott RA, Stolk L, Vallejo EE, Westra HJ, Zondervan KT, Amouyel P, Arveiler D, Bakker SJL, Beilby J, Bergman RN, Blangero J, Brown MJ, Burnier M, Campbell H, Chakravarti A, Chines PS, Claudi-Boehm S, Collins FS, Crawford DC, Danesh J, de Faire U, de Geus EJC, Dörr M, Erbel R, Eriksson JG, Farrall M, Ferrannini E, Ferrières J, Forouhi NG, Forrester T, Franco OH, Gansevoort RT, Gieger C, Gudnason V, Haiman CA, Harris TB, Hattersley AT, Heliövaara M, Hicks AA, Hingorani AD, Hoffmann W, Hofman A, Homuth G, Humphries SE, Hyppönen E, Illig T, Jarvelin MR, Johansen B, Jousilahti P, Jula AM, Kaprio J, Kee F, Keinanen-Kiukaanniemi SM, Kooner JS, Kooperberg C, Kovacs P, Kraja AT, Kumari M, Kuulasmaa K, Kuusisto J, Lakka TA, Langenberg C, Le Marchand L, Lehtimäki T, Lyssenko V, Männistö S, Marette A, Matise TC, McKenzie CA, McKnight B, Musk AW, Möhlenkamp S, Morris AD, Nelis M, Ohlsson C, Oldehinkel AJ, Ong KK, Palmer LJ, Penninx BW, Peters A, Pramstaller PP, Raitakari OT, Rankinen T, Rao DC, Rice TK, Ridker PM, Ritchie MD, Rudan I, Salomaa V, Samani NJ, Saramies J, Sarzynski MA, Schwarz PEH, Shuldiner AR, Staessen JA, Steinthorsdottir V, Stolk RP, Strauch K, Tönjes A, Tremblay A, Tremoli E, Vohl MC, Völker U, Vollenweider P, Wilson JF, Witteman JC, Adair LS, Bochud M, Boehm BO, Bornstein SR, Bouchard C, Cauchi S, Caulfield MJ, Chambers JC, Chasman DI, Cooper RS, Dedoussis G, Ferrucci L, Froguel P, Grabe HJ, Hamsten A, Hui J, Hveem K, Jöckel KH, Kivimaki M, Kuh D, Laakso M, Liu Y, März W, Munroe PB, Njølstad I, Oostra BA, Palmer CNA, Pedersen NL, Perola M, Pérusse L, Peters U, Power C, Quertermous T, Rauramaa R, Rivadeneira F, Saaristo TE, Saleheen D, Sinisalo J, Eline Slagboom P, Snieder H, Spector TD, Thorsteinsdottir U, Stumvoll M, Tuomilehto J, Uitterlinden AG, Uusitupa M, van der Harst P, Veronesi G, Walker M, Wareham NJ, Watkins H, Wichmann HE, Abecasis GR, Assimes TL, Berndt SI, Boehnke M, Borecki IB, Deloukas P, Franke L, Frayling TM, Groop LC, Hunter DJ, Kaplan RC, O’Connell JR, Qi L, Schlessinger D, Strachan DP, Stefansson K, van Duijn CM, Willer CJ, Visscher PM, Yang J, Hirschhorn JN, Carola Zillikens M, McCarthy MI, Speliotes EK, North KE, Fox CS, Barroso I, Franks PW, Ingelsson E, Heid IM, Loos RJF, Cupples LA, Morris AP, Lindgren CM, Mohlke KL. New genetic loci link adipose and insulin biology to body fat distribution. Nature 2015; 518:187-196. [PMID: 25673412 PMCID: PMC4338562 DOI: 10.1038/nature14132] [Citation(s) in RCA: 1046] [Impact Index Per Article: 116.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/02/2014] [Indexed: 12/17/2022]
Abstract
Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, we conducted genome-wide association meta-analyses of waist and hip circumference-related traits in up to 224,459 individuals. We identified 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (WHRadjBMI) and an additional 19 loci newly associated with related waist and hip circumference measures (P<5×10−8). Twenty of the 49 WHRadjBMI loci showed significant sexual dimorphism, 19 of which displayed a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation, and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.
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Loh PR, Tucker G, Bulik-Sullivan BK, Vilhjálmsson BJ, Finucane HK, Salem RM, Chasman DI, Ridker PM, Neale BM, Berger B, Patterson N, Price AL. Efficient Bayesian mixed-model analysis increases association power in large cohorts. Nat Genet 2015; 47:284-90. [PMID: 25642633 PMCID: PMC4342297 DOI: 10.1038/ng.3190] [Citation(s) in RCA: 830] [Impact Index Per Article: 92.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Linear mixed models are a powerful statistical tool for identifying genetic associations and avoiding confounding. However, existing methods are computationally intractable in large cohorts and may not optimize power. All existing methods require time cost O(MN(2)) (where N is the number of samples and M is the number of SNPs) and implicitly assume an infinitesimal genetic architecture in which effect sizes are normally distributed, which can limit power. Here we present a far more efficient mixed-model association method, BOLT-LMM, which requires only a small number of O(MN) time iterations and increases power by modeling more realistic, non-infinitesimal genetic architectures via a Bayesian mixture prior on marker effect sizes. We applied BOLT-LMM to 9 quantitative traits in 23,294 samples from the Women's Genome Health Study (WGHS) and observed significant increases in power, consistent with simulations. Theory and simulations show that the boost in power increases with cohort size, making BOLT-LMM appealing for genome-wide association studies in large cohorts.
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Affiliation(s)
- Po-Ru Loh
- 1] Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - George Tucker
- 1] Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. [2] Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA
| | - Brendan K Bulik-Sullivan
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bjarni J Vilhjálmsson
- 1] Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Hilary K Finucane
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rany M Salem
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Department of Endocrinology, Children's Hospital Boston, Boston, Massachusetts, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Benjamin M Neale
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bonnie Berger
- 1] Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA
| | - Nick Patterson
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Alkes L Price
- 1] Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [3] Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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Sambo F, Malovini A, Sandholm N, Stavarachi M, Forsblom C, Mäkinen VP, Harjutsalo V, Lithovius R, Gordin D, Parkkonen M, Saraheimo M, Thorn LM, Tolonen N, Wadén J, He B, Osterholm AM, Tuomilehto J, Lajer M, Salem RM, McKnight AJ, Tarnow L, Panduru NM, Barbarini N, Di Camillo B, Toffolo GM, Tryggvason K, Bellazzi R, Cobelli C, Groop PH. Novel genetic susceptibility loci for diabetic end-stage renal disease identified through robust naive Bayes classification. Diabetologia 2014; 57:1611-22. [PMID: 24871321 DOI: 10.1007/s00125-014-3256-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
Abstract
AIMS/HYPOTHESIS Diabetic nephropathy is a major diabetic complication, and diabetes is the leading cause of end-stage renal disease (ESRD). Family studies suggest a hereditary component for diabetic nephropathy. However, only a few genes have been associated with diabetic nephropathy or ESRD in diabetic patients. Our aim was to detect novel genetic variants associated with diabetic nephropathy and ESRD. METHODS We exploited a novel algorithm, 'Bag of Naive Bayes', whose marker selection strategy is complementary to that of conventional genome-wide association models based on univariate association tests. The analysis was performed on a genome-wide association study of 3,464 patients with type 1 diabetes from the Finnish Diabetic Nephropathy (FinnDiane) Study and subsequently replicated with 4,263 type 1 diabetes patients from the Steno Diabetes Centre, the All Ireland-Warren 3-Genetics of Kidneys in Diabetes UK collection (UK-Republic of Ireland) and the Genetics of Kidneys in Diabetes US Study (GoKinD US). RESULTS Five genetic loci (WNT4/ZBTB40-rs12137135, RGMA/MCTP2-rs17709344, MAPRE1P2-rs1670754, SEMA6D/SLC24A5-rs12917114 and SIK1-rs2838302) were associated with ESRD in the FinnDiane study. An association between ESRD and rs17709344, tagging the previously identified rs12437854 and located between the RGMA and MCTP2 genes, was replicated in independent case-control cohorts. rs12917114 near SEMA6D was associated with ESRD in the replication cohorts under the genotypic model (p < 0.05), and rs12137135 upstream of WNT4 was associated with ESRD in Steno. CONCLUSIONS/INTERPRETATION This study supports the previously identified findings on the RGMA/MCTP2 region and suggests novel susceptibility loci for ESRD. This highlights the importance of applying complementary statistical methods to detect novel genetic variants in diabetic nephropathy and, in general, in complex diseases.
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Affiliation(s)
- Francesco Sambo
- Department of Information Engineering, University of Padova, Padova, Italy
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38
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Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T, Chan Y, Salem RM, Lek M, Flannick J, Sim X, Manning A, Ladenvall C, Bumpstead S, Hämäläinen E, Aalto K, Maksimow M, Salmi M, Blankenberg S, Ardissino D, Shah S, Horne B, McPherson R, Hovingh GK, Reilly MP, Watkins H, Goel A, Farrall M, Girelli D, Reiner AP, Stitziel NO, Kathiresan S, Gabriel S, Barrett JC, Lehtimäki T, Laakso M, Groop L, Kaprio J, Perola M, McCarthy MI, Boehnke M, Altshuler DM, Lindgren CM, Hirschhorn JN, Metspalu A, Freimer NB, Zeller T, Jalkanen S, Koskinen S, Raitakari O, Durbin R, MacArthur DG, Salomaa V, Ripatti S, Daly MJ, Palotie A. Distribution and medical impact of loss-of-function variants in the Finnish founder population. PLoS Genet 2014; 10:e1004494. [PMID: 25078778 PMCID: PMC4117444 DOI: 10.1371/journal.pgen.1004494] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/14/2014] [Indexed: 01/19/2023] Open
Abstract
Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10⁻⁸) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P = 1.5×10⁻¹¹⁷). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10⁻⁴), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers.
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Affiliation(s)
- Elaine T. Lim
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Würtz
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Computational Medicine, Institute of Health Sciences, University of Oulu, Oulu, Finland
| | - Aki S. Havulinna
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Priit Palta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karola Rehnström
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Michael Inouye
- Medical Systems Biology, Department of Pathology and Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Tuuli Lappalainen
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Stanford Center for Computational, Evolutionary and Human Genomics, Stanford, California, United States of America
| | - Yingleong Chan
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Rany M. Salem
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jason Flannick
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xueling Sim
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alisa Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Claes Ladenvall
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Eija Hämäläinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | | | - Marko Salmi
- Department of Medical Microbiology and Immunology, University of Turku and National Institute for Health and Welfare, Turku, Finland
| | - Stefan Blankenberg
- University Heart Centre Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Svati Shah
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Benjamin Horne
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, Utah, United States of America
| | - Ruth McPherson
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Gerald K. Hovingh
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Muredach P. Reilly
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Domenico Girelli
- University of Verona School of Medicine, Department of Medicine, Verona, Italy
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Nathan O. Stitziel
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, Tampere, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Leif Groop
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- University of Helsinki, Hjelt Institute, Dept of Public Health, Helsinki, Finland
- National Institute for Health and Welfare, Dept of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Markus Perola
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David M. Altshuler
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cecilia M. Lindgren
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Children's Hospital Boston, Boston, Massachusetts, United States of America
| | | | - Nelson B. Freimer
- University of California Los Angeles Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tanja Zeller
- University Heart Centre Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Sirpa Jalkanen
- Department of Medical Microbiology and Immunology, University of Turku and National Institute for Health and Welfare, Turku, Finland
| | - Seppo Koskinen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, Helsinki, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Daniel G. MacArthur
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- University of Helsinki, Hjelt Institute, Dept of Public Health, Helsinki, Finland
- Department of Biometry, Hjelt Institute, University of Helsinki, Helsinki, Finland
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MJD); (AP)
| | - Aarno Palotie
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MJD); (AP)
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39
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Chan Y, Lim E, Sandholm N, Wang S, McKnight A, Ripke S, Daly M, Neale B, Salem R, Hirschhorn J, Daly MJ, Neale BM, Salem RM, Hirschhorn JN. An excess of risk-increasing low-frequency variants can be a signal of polygenic inheritance in complex diseases. Am J Hum Genet 2014; 94:437-52. [PMID: 24607388 DOI: 10.1016/j.ajhg.2014.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/12/2014] [Indexed: 02/05/2023] Open
Abstract
In most complex diseases, much of the heritability remains unaccounted for by common variants. It has been postulated that lower-frequency variants contribute to the remaining heritability. Here, we describe a method to test for polygenic inheritance from lower-frequency variants by using GWAS summary association statistics. We explored scenarios with many causal low-frequency variants and showed that there is more power to detect risk variants than to detect protective variants, resulting in an increase in the ratio of detected risk to protective variants (R/P ratio). Such an excess can also occur if risk variants are present and kept at lower frequencies because of negative selection. The R/P ratio can be falsely elevated because of reasons unrelated to polygenic inheritance, such as uneven sample sizes or asymmetric population stratification, so precautions to correct for these confounders are essential. We tested our method on published GWAS results and observed a strong signal in some diseases (schizophrenia and type 2 diabetes) but not others. We also explored the shared genetic component in overlapping phenotypes related to inflammatory bowel disease (Crohn disease [CD] and ulcerative colitis [UC]) and diabetic nephropathy (macroalbuminuria and end-stage renal disease [ESRD]). Although the signal was still present when both CD and UC were jointly analyzed, the signal was lost when macroalbuminuria and ESRD were jointly analyzed, suggesting that these phenotypes should best be studied separately. Thus, our method may also help guide the design of future genetic studies of various traits and diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Mark J Daly
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, MA 02114, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, MA 02114, USA
| | - Rany M Salem
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joel N Hirschhorn
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA.
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40
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Sandholm N, McKnight AJ, Salem RM, Brennan EP, Forsblom C, Harjutsalo V, Mäkinen VP, McKay GJ, Sadlier DM, Williams WW, Martin F, Panduru NM, Tarnow L, Tuomilehto J, Tryggvason K, Zerbini G, Comeau ME, Langefeld CD, Godson C, Hirschhorn JN, Maxwell AP, Florez JC, Groop PH. Chromosome 2q31.1 associates with ESRD in women with type 1 diabetes. J Am Soc Nephrol 2013; 24:1537-43. [PMID: 24029427 DOI: 10.1681/asn.2012111122] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Sex and genetic variation influence the risk of developing diabetic nephropathy and ESRD in patients with type 1 diabetes. We performed a genome-wide association study in a cohort of 3652 patients from the Finnish Diabetic Nephropathy (FinnDiane) Study with type 1 diabetes to determine whether sex-specific genetic risk factors for ESRD exist. A common variant, rs4972593 on chromosome 2q31.1, was associated with ESRD in women (P<5×10(-8)) but not in men (P=0.77). This association was replicated in the meta-analysis of three independent type 1 diabetes cohorts (P=0.02) and remained significant for women (P<5×10(-8); odds ratio, 1.81 [95% confidence interval, 1.47 to 2.24]) upon combined meta-analysis of the discovery and replication cohorts. rs4972593 is located between the genes that code for the Sp3 transcription factor, which interacts directly with estrogen receptor α and regulates the expression of genes linked to glomerular function and the pathogenesis of nephropathy, and the CDCA7 transcription factor, which regulates cell proliferation. Further examination revealed potential transcription factor-binding sites within rs4972593 and predicted eight estrogen-responsive elements within 5 kb of this locus. Moreover, we found sex-specific differences in the glomerular expression levels of SP3 (P=0.004). Overall, these results suggest that rs4972593 is a sex-specific genetic variant associated with ESRD in patients with type 1 diabetes and may underlie the sex-specific protection against ESRD.
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Affiliation(s)
- Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
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41
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Friese RS, Altshuler AE, Zhang K, Miramontes-Gonzalez JP, Hightower CM, Jirout ML, Salem RM, Gayen JR, Mahapatra NR, Biswas N, Cale M, Vaingankar SM, Kim HS, Courel M, Taupenot L, Ziegler MG, Schork NJ, Pravenec M, Mahata SK, Schmid-Schönbein GW, O'Connor DT. MicroRNA-22 and promoter motif polymorphisms at the Chga locus in genetic hypertension: functional and therapeutic implications for gene expression and the pathogenesis of hypertension. Hum Mol Genet 2013; 22:3624-40. [PMID: 23674521 DOI: 10.1093/hmg/ddt213] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Hypertension is a common hereditary syndrome with unclear pathogenesis. Chromogranin A (Chga), which catalyzes formation and cargo storage of regulated secretory granules in neuroendocrine cells, contributes to blood pressure homeostasis centrally and peripherally. Elevated Chga occurs in spontaneously hypertensive rat (SHR) adrenal glands and plasma, but central expression is unexplored. In this report, we measured SHR and Wistar-Kyoto rat (control) Chga expression in central and peripheral nervous systems, and found Chga protein to be decreased in the SHR brainstem, yet increased in the adrenal and the plasma. By re-sequencing, we systematically identified five promoter, two coding and one 3'-untranslated region (3'-UTR) polymorphism at the SHR (versus WKY or BN) Chga locus. Using HXB/BXH recombinant inbred (RI) strain linkage and correlations, we demonstrated genetic determination of Chga expression in SHR, including a cis-quantitative trait loci (QTLs) (i.e. at the Chga locus), and such expression influenced biochemical determinants of blood pressure, including a cascade of catecholamine biosynthetic enzymes, catecholamines themselves and steroids. Luciferase reporter assays demonstrated that the 3'-UTR polymorphism (which disrupts a microRNA miR-22 motif) and promoter polymorphisms altered gene expression consistent with the decline in SHR central Chga expression. Coding region polymorphisms did not account for changes in Chga expression or function. Thus, we hypothesized that the 3'-UTR and promoter mutations lead to dysregulation (diminution) of Chga in brainstem cardiovascular control nuclei, ultimately contributing to the pathogenesis of hypertension in SHR. Accordingly, we demonstrated that in vivo administration of miR-22 antagomir to SHR causes substantial (∼18 mmHg) reductions in blood pressure, opening a novel therapeutic avenue for hypertension.
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Affiliation(s)
- Ryan S Friese
- Department of Bioengineering, VA San Diego Healthcare System, University of California at San Diego, CA 92093, USA
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42
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Williams WW, Salem RM, McKnight AJ, Sandholm N, Forsblom C, Taylor A, Guiducci C, McAteer JB, McKay GJ, Isakova T, Brennan EP, Sadlier DM, Palmer C, Söderlund J, Fagerholm E, Harjutsalo V, Lithovius R, Gordin D, Hietala K, Kytö J, Parkkonen M, Rosengård-Bärlund M, Thorn L, Syreeni A, Tolonen N, Saraheimo M, Wadén J, Pitkäniemi J, Sarti C, Tuomilehto J, Tryggvason K, Österholm AM, He B, Bain S, Martin F, Godson C, Hirschhorn JN, Maxwell AP, Groop PH, Florez JC. Association testing of previously reported variants in a large case-control meta-analysis of diabetic nephropathy. Diabetes 2012; 61:2187-94. [PMID: 22721967 PMCID: PMC3402313 DOI: 10.2337/db11-0751] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We formed the GEnetics of Nephropathy-an International Effort (GENIE) consortium to examine previously reported genetic associations with diabetic nephropathy (DN) in type 1 diabetes. GENIE consists of 6,366 similarly ascertained participants of European ancestry with type 1 diabetes, with and without DN, from the All Ireland-Warren 3-Genetics of Kidneys in Diabetes U.K. and Republic of Ireland (U.K.-R.O.I.) collection and the Finnish Diabetic Nephropathy Study (FinnDiane), combined with reanalyzed data from the Genetics of Kidneys in Diabetes U.S. Study (U.S. GoKinD). We found little evidence for the association of the EPO promoter polymorphism, rs161740, with the combined phenotype of proliferative retinopathy and end-stage renal disease in U.K.-R.O.I. (odds ratio [OR] 1.14, P = 0.19) or FinnDiane (OR 1.06, P = 0.60). However, a fixed-effects meta-analysis that included the previously reported cohorts retained a genome-wide significant association with that phenotype (OR 1.31, P = 2 × 10(-9)). An expanded investigation of the ELMO1 locus and genetic regions reported to be associated with DN in the U.S. GoKinD yielded only nominal statistical significance for these loci. Finally, top candidates identified in a recent meta-analysis failed to reach genome-wide significance. In conclusion, we were unable to replicate most of the previously reported genetic associations for DN, and significance for the EPO promoter association was attenuated.
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Affiliation(s)
- Winfred W. Williams
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rany M. Salem
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Endocrine Research Unit, Department of Endocrinology, Children’s Hospital, Boston, Massachusetts
| | - Amy Jayne McKnight
- Nephrology Research, Centre for Public Health, Queen’s University of Belfast, Belfast, U.K
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Department of Biomedical Engineering and Computational Science, Aalto University, Helsinki, Finland
| | - Carol Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Andrew Taylor
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Candace Guiducci
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Jarred B. McAteer
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Gareth J. McKay
- Nephrology Research, Centre for Public Health, Queen’s University of Belfast, Belfast, U.K
| | - Tamara Isakova
- Division of Nephrology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Eoin P. Brennan
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Denise M. Sadlier
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
- Mater University Hospital, Dublin, Ireland
| | - Cameron Palmer
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Endocrine Research Unit, Department of Endocrinology, Children’s Hospital, Boston, Massachusetts
| | - Jenny Söderlund
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Emma Fagerholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Valma Harjutsalo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Department of Chronic Disease Prevention, Welfare and Health Promotion Division, National Institute for Health and Welfare, Helsinki, Finland
| | - Raija Lithovius
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Daniel Gordin
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Kustaa Hietala
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
| | - Janne Kytö
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
| | - Maija Parkkonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Milla Rosengård-Bärlund
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Lena Thorn
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Anna Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Nina Tolonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Markku Saraheimo
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Johan Wadén
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Janne Pitkäniemi
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Cinzia Sarti
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Chronic Disease Prevention, Welfare and Health Promotion Division, National Institute for Health and Welfare, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- South Ostrobothnia Central Hospital, Seinäjoki, Finland
| | - Karl Tryggvason
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anne-May Österholm
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bing He
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Steve Bain
- Institute of Life Sciences, Swansea University, Swansea, U.K
| | - Finian Martin
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Catherine Godson
- UCD Diabetes Research Centre, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Endocrine Research Unit, Department of Endocrinology, Children’s Hospital, Boston, Massachusetts
| | - Alexander P. Maxwell
- Nephrology Research, Centre for Public Health, Queen’s University of Belfast, Belfast, U.K
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
- Division of Nephrology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
| | - Jose C. Florez
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Corresponding author: Jose C. Florez,
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Bradfield JP, Taal HR, Timpson NJ, Scherag A, Lecoeur C, Warrington NM, Hypponen E, Holst C, Valcarcel B, Thiering E, Salem RM, Schumacher FR, Cousminer DL, Sleiman PMA, Zhao J, Berkowitz RI, Vimaleswaran KS, Jarick I, Pennell CE, Evans DM, St Pourcain B, Berry DJ, Mook-Kanamori DO, Hofman A, Rivadeneira F, Uitterlinden AG, van Duijn CM, van der Valk RJP, de Jongste JC, Postma DS, Boomsma DI, Gauderman WJ, Hassanein MT, Lindgren CM, Mägi R, Boreham CAG, Neville CE, Moreno LA, Elliott P, Pouta A, Hartikainen AL, Li M, Raitakari O, Lehtimäki T, Eriksson JG, Palotie A, Dallongeville J, Das S, Deloukas P, McMahon G, Ring SM, Kemp JP, Buxton JL, Blakemore AIF, Bustamante M, Guxens M, Hirschhorn JN, Gillman MW, Kreiner-Møller E, Bisgaard H, Gilliland FD, Heinrich J, Wheeler E, Barroso I, O'Rahilly S, Meirhaeghe A, Sørensen TIA, Power C, Palmer LJ, Hinney A, Widen E, Farooqi IS, McCarthy MI, Froguel P, Meyre D, Hebebrand J, Jarvelin MR, Jaddoe VWV, Smith GD, Hakonarson H, Grant SFA. A genome-wide association meta-analysis identifies new childhood obesity loci. Nat Genet 2012; 44:526-31. [PMID: 22484627 PMCID: PMC3370100 DOI: 10.1038/ng.2247] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 03/14/2012] [Indexed: 12/19/2022]
Abstract
Multiple genetic variants have been associated with adult obesity and a few with severe obesity in childhood; however, less progress has been made in establishing genetic influences on common early-onset obesity. We performed a North American, Australian and European collaborative meta-analysis of 14 studies consisting of 5,530 cases (≥95th percentile of body mass index (BMI)) and 8,318 controls (<50th percentile of BMI) of European ancestry. Taking forward the eight newly discovered signals yielding association with P < 5 × 10(-6) in nine independent data sets (2,818 cases and 4,083 controls), we observed two loci that yielded genome-wide significant combined P values near OLFM4 at 13q14 (rs9568856; P = 1.82 × 10(-9); odds ratio (OR) = 1.22) and within HOXB5 at 17q21 (rs9299; P = 3.54 × 10(-9); OR = 1.14). Both loci continued to show association when two extreme childhood obesity cohorts were included (2,214 cases and 2,674 controls). These two loci also yielded directionally consistent associations in a previous meta-analysis of adult BMI(1).
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Affiliation(s)
- Jonathan P Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Salem RM, Pandey B, Richard E, Fung MM, Garcia EP, Brophy VH, Schork NJ, O'Connor DT, Bhatnagar V. The VA Hypertension Primary Care Longitudinal Cohort: Electronic medical records in the post-genomic era. Health Informatics J 2012; 16:274-86. [PMID: 21216807 DOI: 10.1177/1460458210380527] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Veterans Affairs Hypertension Primary Care Longitudinal Cohort (VAHC) was initiated in 2003 as a pilot study designed to link the VA electronic medical record system with individual genetic data. Between June 2003 and December 2004, 1,527 hypertensive participants were recruited. Protected health information (PHI) was extracted from the regional VA data warehouse. Differences between the clinic and mail recruits suggested that clinic recruitment resulted in an over-sampling of African Americans. A review of medical records in a random sample of study participants confirmed that the data warehouse accurately captured most selected diagnoses. Genomic DNA was acquired non-invasively from buccal cells in mouthwash; ~ 96.5 per cent of samples contained DNA suitable for genotyping, with an average DNA yield of 5.02 ± 0.12 micrograms, enough for several thousand genotypes. The coupling of detailed medical databases with genetic information has the potential to facilitate the genetic study of hypertension and other complex diseases.
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Fung MM, Salem RM, Lipkowitz MS, Bhatnagar V, Pandey B, Schork NJ, O'Connor DT. Methylenetetrahydrofolate reductase (MTHFR) polymorphism A1298C (Glu429Ala) predicts decline in renal function over time in the African-American Study of Kidney Disease and Hypertension (AASK) Trial and Veterans Affairs Hypertension Cohort (VAHC). Nephrol Dial Transplant 2011; 27:197-205. [PMID: 21613384 DOI: 10.1093/ndt/gfr257] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Hyperhomocysteinemia is associated with increased venous thrombosis and cardiovascular disease (CVD). Mutations in the human methylenetetrahydrofolate reductase (MTHFR) gene have been associated with increased homocysteine levels and risks of CVD in various populations including those with kidney disease. Here, we evaluated the influence of MTHFR variants on progressive loss of kidney function. METHODS We analyzed 821 subjects with hypertensive nephrosclerosis from the longitudinal National Institute of Diabetes and Digestive and Kidney Diseases African-American Study of Kidney Disease and Hypertension (AASK) Trial to determine whether decline in glomerular filtration rate (GFR) over ∼4.2 years was predicted by common genetic variation within MTHFR at non-synonymous positions C677T (Ala222Val) and A1298C (Glu429Ala) or by MTHFR haplotypes. The effect on GFR decline was then supported by a study of 1333 subjects from the San Diego Veterans Affairs Hypertension Cohort (VAHC), followed over ∼4.5 years. Linear effect models were utilized to determine both genotype [single-nucleotide polymorphism (SNP)] and genotype (SNP)-by-time interactions. RESULTS In AASK, the polymorphism at A1298C predicted the rate of GFR decline: A1298/A1298 major allele homozygosity resulted in a less pronounced decline of GFR, with a significant SNP-by-time interaction. An independent follow-up study in the San Diego VAHC subjects supports that A1298/A1298 homozygotes have the greatest estimated GFR throughout the study. Haplotype analysis with C677T yielded concurring results. CONCLUSION We conclude that the MTHFR-coding polymorphism at A1298C is associated with renal decline in African-Americans with hypertensive nephrosclerosis and is supported by a veteran cohort with a primary care diagnosis of hypertension. Further investigation is needed to confirm such findings and to determine what molecular mechanism may contribute to this association.
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Affiliation(s)
- Maple M Fung
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Fung MM, Salem RM, Naqshbandi D, O'Connor DT. 96 Clinical and ACE Genetic Predictors of Incident Chronic Kidney Disease in Non-Diabetic Hypertensive Veterans. Am J Kidney Dis 2011. [DOI: 10.1053/j.ajkd.2011.02.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Fung MM, Salem RM, Mehtani P, Thomas B, Lu CF, Perez B, Rao F, Stridsberg M, Ziegler MG, Mahata SK, O'Connor DT. Direct vasoactive effects of the chromogranin A (CHGA) peptide catestatin in humans in vivo. Clin Exp Hypertens 2010; 32:278-87. [PMID: 20662728 DOI: 10.3109/10641960903265246] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Catestatin is a bioactive peptide of chromogranin A (CHGA) that is co-released with catecholamines from secretory vesicles. Catestatin may function as a vasodilator and is diminished in hypertension. To evaluate this potential vasodilator in vivo without systemic counterregulation, we infused catestatin to target concentrations of approximately 50, approximately 500, approximately 5000 nM into dorsal hand veins of 18 normotensive men and women, after pharmacologic venoconstriction with phenylephrine. Pancreastatin, another CHGA peptide, was infused as a negative control. After preconstriction to approximately 69%, increasing concentrations of catestatin resulted in dose-dependent vasodilation (P = 0.019), in female subjects (to approximately 44%) predominantly. The EC(50) (approximately 30 nM) for vasodilation induced by catestatin was the same order of magnitude to circulating endogenous catestatin (4.4 nM). No vasodilation occurred during the control infusion with pancreastatin. Plasma CHGA, catestatin, and CHGA-to-catestatin processing were then determined in 622 healthy subjects without hypertension. Female subjects had higher plasma catestatin levels than males (P = 0.001), yet lower CHGA precursor concentrations (P = 0.006), reflecting increased processing of CHGA-to-catestatin (P < 0.001). Our results demonstrate that catestatin dilates human blood vessels in vivo, especially in females. Catestatin may contribute to sex differences in endogenous vascular tone, thereby influencing the complex predisposition to hypertension.
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Affiliation(s)
- Maple M Fung
- Department of Medicine, University of California at San Diego and Veterans Affairs, San Diego Healthcare System, La Jolla, California, USA
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Chen Y, Salem RM, Rao F, Fung MM, Bhatnagar V, Pandey B, Mahata M, Waalen J, Nievergelt CM, Lipkowitz MS, Hamilton BA, Mahata SK, O'Connor DT. Common charge-shift mutation Glu65Lys in K+ channel β₁-Subunit KCNMB1: pleiotropic consequences for glomerular filtration rate and progressive renal disease. Am J Nephrol 2010; 32:414-24. [PMID: 20861615 DOI: 10.1159/000320131] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 08/09/2010] [Indexed: 01/13/2023]
Abstract
BACKGROUND Glomerular filtration rate (GFR) is a heritable trait, and hyperfiltration (GFR increment in remnant nephrons) may accelerate renal functional decline in chronic kidney disease (CKD). Mesangial and vascular smooth myocytes control GFR by contraction, dependent on voltage-gated Ca(2+) influx, which is controlled by the regulatory β₁-subunit (KCNMB1) of large-conductance heteromeric K+ ('BK') channels. KCNMB1 gain-of-function variant Glu65Lys results in generalized vasorelaxation and thus protection against systemic hypertension. Here we asked whether the Glu65Lys variant influences GFR, in the basal state or during progressive renal decline. METHODS We explored Glu65Lys effects on GFR in three populations spanning two ethnicities and two diseases (hypertension and nephrosclerosis). GFR was either estimated (eGFR from serum creatinine) or directly measured (iothalamate clearance). RESULTS The 65Lys variant was relatively common, occurring on ∼5-10% of chromosomes in different biogeographic ancestry groups, and 65Lys carriers exhibited higher eGFR in two primary care populations: extreme BP values in Kaiser clinics (p = 0.029, accounting for ∼0.2% of trait variance), or treated hypertensives in VA clinics (p = 0.017, accounting for ∼0.9% of trait variance). In blacks with progressive renal disease (NIDDK AASK), 65Lys carriers displayed a steeper slope in GFR chronic decline (p = 0.030, accounting for ∼0.4% of trait variance), and Glu65Lys genotype also predicted time of onset of renal failure (log rank p = 0.019). CONCLUSIONS Common KCNMB1 gain-of-function variant Glu65Lys influences GFR, and 65Lys carriers exhibit not only elevated baseline GFR, but also more rapid GFR decline (and consequent development of renal failure) in CKD. The results suggest that profiling patients at Glu65Lys can assist in gauging renal prognosis as well as selection of rational therapy in hypertension with progressive renal disease.
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Affiliation(s)
- Yuqing Chen
- Department of Medicine, University of California at San Diego, Calif., USA.
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Smith EN, Chen W, Kähönen M, Kettunen J, Lehtimäki T, Peltonen L, Raitakari OT, Salem RM, Schork NJ, Shaw M, Srinivasan SR, Topol EJ, Viikari JS, Berenson GS, Murray SS. Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study. PLoS Genet 2010; 6:e1001094. [PMID: 20838585 PMCID: PMC2936521 DOI: 10.1371/journal.pgen.1001094] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/27/2010] [Indexed: 01/11/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide. Recent genome-wide association (GWA) studies have pinpointed many loci associated with CVD risk factors in adults. It is unclear, however, if these loci predict trait levels at all ages, if they are associated with how a trait develops over time, or if they could be used to screen individuals who are pre-symptomatic to provide the opportunity for preventive measures before disease onset. We completed a genome-wide association study on participants in the longitudinal Bogalusa Heart Study (BHS) and have characterized the association between genetic factors and the development of CVD risk factors from childhood to adulthood. We report 7 genome-wide significant associations involving CVD risk factors, two of which have been previously reported. Top regions were tested for replication in the Young Finns Study (YF) and two associations strongly replicated: rs247616 in CETP with HDL levels (combined P = 9.7×10−24), and rs445925 at APOE with LDL levels (combined P = 8.7×10−19). We show that SNPs previously identified in adult cross-sectional studies tend to show age-independent effects in the BHS with effect sizes consistent with previous reports. Previously identified variants were associated with adult trait levels above and beyond those seen in childhood; however, variants with time-dependent effects were also promising predictors. This is the first GWA study to evaluate the role of common genetic variants in the development of CVD risk factors in children as they advance through adulthood and highlights the utility of using longitudinal studies to identify genetic predictors of adult traits in children. We have studied the association between genetic factors on a whole genome level and cardiovascular disease (CVD) risk factors in a population of individuals studied from childhood through adulthood. The longitudinal study design has enabled the investigation of genetic variation influencing trait values over time. We have identified DNA variants that are associated with CVD trait values consistently over time, and a second set of variants that are associated with CVD trait values in a time-dependent manner. We also show that variants previously identified in adult populations have consistent effects within our population and that these effects are usually similar across childhood through adulthood. The discovery of time-dependent variants that influence CVD trait values over time can potentially be used to screen young individuals who are pre-symptomatic and provide the opportunity for preventive measures decades before disease onset.
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Affiliation(s)
- Erin N. Smith
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Wei Chen
- Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Mika Kähönen
- Department of Clinical Physiology, University Hospital of Tampere and University of Tampere Medical School, Tampere, Finland
| | - Johannes Kettunen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- FIMM, Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University Hospital of Tampere and University of Tampere Medical School, Tampere, Finland
| | - Leena Peltonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- FIMM, Institute for Molecular Medicine Finland, Helsinki, Finland
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, United States of America
| | - Olli T. Raitakari
- Department of Clinical Physiology, Turku University Hospital and Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Rany M. Salem
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, United States of America
| | - Nicholas J. Schork
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Marian Shaw
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Sathanur R. Srinivasan
- Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Eric J. Topol
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Jorma S. Viikari
- Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Gerald S. Berenson
- Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Sarah S. Murray
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
- * E-mail:
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Salem RM, O'Connor DT, Schork NJ. Curve-based multivariate distance matrix regression analysis: application to genetic association analyses involving repeated measures. Physiol Genomics 2010; 42:236-47. [PMID: 20423962 PMCID: PMC3032281 DOI: 10.1152/physiolgenomics.00118.2009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 04/21/2010] [Indexed: 01/09/2023] Open
Abstract
Most, if not all, human phenotypes exhibit a temporal, dosage-dependent, or age effect. Despite this fact, it is rare that data are collected over time or in sequence in relevant studies of the determinants of these phenotypes. The costs and organizational sophistication necessary to collect repeated measurements or longitudinal data for a given phenotype are clearly impediments to this, but greater efforts in this area are needed if insights into human phenotypic expression are to be obtained. Appropriate data analysis methods for genetic association studies involving repeated or longitudinal measures are also needed. We consider the use of longitudinal profiles obtained from fitted functions on repeated data collections from a set of individuals whose similarities are contrasted between sets of individuals with different genotypes to test hypotheses about genetic influences on time-dependent phenotype expression. The proposed approach can accommodate uncertainty of the fitted functions, as well as weighting factors across the time points, and is easily extended to a wide variety of complex analysis settings. We showcase the proposed approach with data from a clinical study investigating human blood vessel response to tyramine. We also compare the proposed approach with standard analytic procedures and investigate its robustness and power via simulation studies. The proposed approach is found to be quite flexible and performs either as well or better than traditional statistical methods.
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