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Morris AP, Le TH, Wu H, Akbarov A, van der Most PJ, Hemani G, Smith GD, Mahajan A, Gaulton KJ, Nadkarni GN, Valladares-Salgado A, Wacher-Rodarte N, Mychaleckyj JC, Dueker ND, Guo X, Hai Y, Haessler J, Kamatani Y, Stilp AM, Zhu G, Cook JP, Ärnlöv J, Blanton SH, de Borst MH, Bottinger EP, Buchanan TA, Cechova S, Charchar FJ, Chu PL, Damman J, Eales J, Gharavi AG, Giedraitis V, Heath AC, Ipp E, Kiryluk K, Kramer HJ, Kubo M, Larsson A, Lindgren CM, Lu Y, Madden PAF, Montgomery GW, Papanicolaou GJ, Raffel LJ, Sacco RL, Sanchez E, Stark H, Sundstrom J, Taylor KD, Xiang AH, Zivkovic A, Lind L, Ingelsson E, Martin NG, Whitfield JB, Cai J, Laurie CC, Okada Y, Matsuda K, Kooperberg C, Chen YDI, Rundek T, Rich SS, Loos RJF, Parra EJ, Cruz M, Rotter JI, Snieder H, Tomaszewski M, Humphreys BD, Franceschini N. Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies. Nat Commun 2019; 10:29. [PMID: 30604766 PMCID: PMC6318312 DOI: 10.1038/s41467-018-07867-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/03/2018] [Indexed: 02/07/2023] Open
Abstract
Chronic kidney disease (CKD) affects ~10% of the global population, with considerable ethnic differences in prevalence and aetiology. We assemble genome-wide association studies of estimated glomerular filtration rate (eGFR), a measure of kidney function that defines CKD, in 312,468 individuals of diverse ancestry. We identify 127 distinct association signals with homogeneous effects on eGFR across ancestries and enrichment in genomic annotations including kidney-specific histone modifications. Fine-mapping reveals 40 high-confidence variants driving eGFR associations and highlights putative causal genes with cell-type specific expression in glomerulus, and in proximal and distal nephron. Mendelian randomisation supports causal effects of eGFR on overall and cause-specific CKD, kidney stone formation, diastolic blood pressure and hypertension. These results define novel molecular mechanisms and putative causal genes for eGFR, offering insight into clinical outcomes and routes to CKD treatment development. Estimated glomerular filtration rate (eGFR) is a measure of kidney function used to define chronic kidney disease. Here, Morris et al. perform trans-ethnic genome-wide meta-analyses for eGFR in 312,468 individuals and identify novel loci and downstream putative causal genes.
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Affiliation(s)
- Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK. .,Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
| | - Thu H Le
- Department of Medicine, Division of Nephrology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Haojia Wu
- Division of Nephrology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, Netherlands
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, BS8 1TH, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, BS8 1TH, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Kyle J Gaulton
- Department of Pediatrics, University of California, San Diego, San Diego, CA, 92161, USA
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Division of Nephrology and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, 06720, Mexico
| | - Niels Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiologia Clinica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, 06720, Mexico
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Nicole D Dueker
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33124, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Yang Hai
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Gu Zhu
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society, Division of Family Medicine and Primary Care, Karolinska Institutet, Huddinge, 141 83, Sweden.,School of Health and Social Studies, Dalarna University, Falun, 791 88, Sweden
| | - Susan H Blanton
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33124, USA.,Dr John T Macdonald Department of Human Genetics, University of Miami, Miami, FL, 33124, USA
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, Netherlands
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Thomas A Buchanan
- Department of Medicine, Division of Endocrinology and Diabetes, Keck School of Medicine of USC, Los Angeles, CA, 90033, USA
| | - Sylvia Cechova
- Department of Medicine, Division of Nephrology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Fadi J Charchar
- School of Health and Life Sciences, Federation University Australia, Ballarat, VIC, 3350, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, LE1 7RH, UK.,Department of Physiology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Pei-Lun Chu
- Department of Internal Medicine, Fu Jen Catholic University Hospital, School of Medicine, Fu Jen Catholic University, New Taipei City, 242, Taiwan
| | - Jeffrey Damman
- Department of Pathology, Erasmus Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, Netherlands
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Uppsala University, Uppsala, 751 85, Sweden
| | - Andrew C Heath
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Eli Ipp
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90024, USA.,Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, 90502, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Holly J Kramer
- Department of Medicine and Nephrology, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Anders Larsson
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, 751 85, Sweden
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Li Ka Shing Centre for Health Information and Discovery, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.,Broad Institute of Harvard and MIT, Boston, MA, 02142, USA
| | - Yingchang Lu
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Grant W Montgomery
- Brisbane Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia
| | - George J Papanicolaou
- Epidemiology Branch, Division of Cardiovascular Sciences, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Leslie J Raffel
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of California, Irvine Orange, CA, 92868, USA
| | - Ralph L Sacco
- Departments of Neurology and Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Evelyn F McKnight Brain Institute, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Jackson Memorial Hospital, University of Miami, Miami, FL, 33136-1096, USA
| | - Elena Sanchez
- Department of Medicine, Division of Nephrology, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Johan Sundstrom
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, 751 85, Sweden
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Anny H Xiang
- Department of Research and Education, Kaiser Permanente Southern California, Pasadena, CA, 91101, USA
| | - Aleksandra Zivkovic
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Lars Lind
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, 751 85, Sweden
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94309, USA.,Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94309, USA.,Stanford Diabetes Research Center, Stanford University, Stanford, CA, 94305, USA.,Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Nicholas G Martin
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - John B Whitfield
- Genetic Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Jianwen Cai
- Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7420, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Suita, 565-0871, Japan
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Tatjana Rundek
- Departments of Neurology and Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Evelyn F McKnight Brain Institute, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, 06720, Mexico
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB, Groningen, Netherlands
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK.,Division of Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Benjamin D Humphreys
- Division of Nephrology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27516-8050, USA.
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