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Liu H, Abedini A, Ha E, Ma Z, Sheng X, Dumoulin B, Qiu C, Aranyi T, Li S, Dittrich N, Chen HC, Tao R, Tarng DC, Hsieh FJ, Chen SA, Yang SF, Lee MY, Kwok PY, Wu JY, Chen CH, Khan A, Limdi NA, Wei WQ, Walunas TL, Karlson EW, Kenny EE, Luo Y, Kottyan L, Connolly JJ, Jarvik GP, Weng C, Shang N, Cole JB, Mercader JM, Mandla R, Majarian TD, Florez JC, Haas ME, Lotta LA, Drivas TG, Vy HMT, Nadkarni GN, Wiley LK, Wilson MP, Gignoux CR, Rasheed H, Thomas LF, Åsvold BO, Brumpton BM, Hallan SI, Hveem K, Zheng J, Hellwege JN, Zawistowski M, Zöllner S, Franceschini N, Hu H, Zhou J, Kiryluk K, Ritchie MD, Palmer M, Edwards TL, Voight BF, Hung AM, Susztak K. Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants. Science 2025; 387:eadp4753. [PMID: 39913582 DOI: 10.1126/science.adp4753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 11/20/2024] [Indexed: 02/17/2025]
Abstract
Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and identified 1026 (97 previously unknown) independent loci. Ancestry-specific analysis indicated an attenuation of newly identified signals on common variants in European ancestry populations and the power of population diversity for further discoveries. We defined genotype effects on allele-specific gene expression and regulatory circuitries in more than 700 human kidneys and 237,000 cells. We found 1363 coding variants disrupting 782 genes, with 601 genes also targeted by regulatory variants and convergence in 161 genes. Integrating 32 types of genetic information, we present the "Kidney Disease Genetic Scorecard" for prioritizing potentially causal genes, cell types, and druggable targets for kidney disease.
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Affiliation(s)
- Hongbo Liu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Amin Abedini
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Eunji Ha
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ziyuan Ma
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Xin Sheng
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, Zhejiang, China
- Department of Nephrology, Children' Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Bernhard Dumoulin
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Chengxiang Qiu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Tamas Aranyi
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Molecular Life Sciences, HUN-REN Research Center for Natural Sciences, Budapest, Hungary
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Shen Li
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole Dittrich
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Hua-Chang Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Der-Cherng Tarng
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Feng-Jen Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Shih-Ann Chen
- Cardiovascular Center, Taichung Veterans General Hospital, Taichung, Taiwan, ROC
- National Chung Hsing University, Taichung, Taiwan, ROC
- Heart Rhythm Center, Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Department of Internal Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan, ROC
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan, ROC
| | - Mei-Yueh Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
- Department of Internal Medicine, Kaohsiung Medical University Gangshan Hospital, Kaohsiung, Taiwan, ROC
| | - Pui-Yan Kwok
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Theresa L Walunas
- Department of Medicine, Division of General Internal Medicine and Center for Health Information Partnerships, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Leah Kottyan
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Josep M Mercader
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ravi Mandla
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine and Cardiovascular Research Institute, Cardiology Division, University of California, San Francisco, CA, USA
- Graduate Program in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy D Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mary E Haas
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Luca A Lotta
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Theodore G Drivas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Ha My T Vy
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish N Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Hasso Plattner Institute of Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura K Wiley
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Melissa P Wilson
- Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Humaira Rasheed
- KGJebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Laurent F Thomas
- KGJebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bjørn Olav Åsvold
- KGJebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ben M Brumpton
- KGJebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Clinic of Thoracic and Occupational Medicine, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Stein I Hallan
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Kristian Hveem
- KGJebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jie Zheng
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Shanghai Digital Medicine Innovation Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jacklyn N Hellwege
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Hailong Hu
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jianfu Zhou
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Palmer
- Pathology and Laboratory Medicine at the Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Benjamin F Voight
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Adriana M Hung
- Division of Nephrology and Hypertension, Vanderbilt Center for Kidney Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- VA Tennessee Valley Healthcare System, Clinical Sciences Research and Development, Nashville, TN, USA
| | - Katalin Susztak
- Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Kidney Innovation Center, University of Pennsylvania, Philadelphia, PA, USA
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