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Breeze CE, Lin BM, Winkler CA, Franceschini N. African ancestry-derived APOL1 risk genotypes show proximal epigenetic associations. BMC Genomics 2024; 25:452. [PMID: 38714935 PMCID: PMC11077761 DOI: 10.1186/s12864-024-10226-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/14/2024] [Indexed: 05/12/2024] Open
Abstract
Apolipoprotein L1 (APOL1) coding variants, termed G1 and G2, are established genetic risk factors for a growing spectrum of diseases, including kidney disease, in individuals of African ancestry. Evidence suggests that the risk variants, which show a recessive mode of inheritance, lead to toxic gain-of-function changes of the APOL1 protein. Disease occurrence and presentation vary, likely due to modifiers or second hits. To understand the role of the epigenetic landscape in relation to APOL1 risk variants, we performed methylation quantitative trait locus (meQTL) analysis to identify differentially methylated CpGs influenced by APOL1 risk variants in 611 African American individuals. We identified five CpGs that were significantly associated with APOL1 risk alleles in discovery and replication studies, and one CpG-APOL1 association was independent of other genomic variants. Our study highlights proximal DNA methylation alterations that may help explain the variable disease risk and clinical manifestation of APOL1 variants.
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Affiliation(s)
- Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Cheryl A Winkler
- Cancer Innovation Laboratory, National Cancer Institute, National Institutes of Health, Basic Research Program, Frederick National Laboratory, Frederick, MD, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.
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Scholz M, Horn K, Pott J, Wuttke M, Kühnapfel A, Nasr MK, Kirsten H, Li Y, Hoppmann A, Gorski M, Ghasemi S, Li M, Tin A, Chai JF, Cocca M, Wang J, Nutile T, Akiyama M, Åsvold BO, Bansal N, Biggs ML, Boutin T, Brenner H, Brumpton B, Burkhardt R, Cai J, Campbell A, Campbell H, Chalmers J, Chasman DI, Chee ML, Chee ML, Chen X, Cheng CY, Cifkova R, Daviglus M, Delgado G, Dittrich K, Edwards TL, Endlich K, Michael Gaziano J, Giri A, Giulianini F, Gordon SD, Gudbjartsson DF, Hallan S, Hamet P, Hartman CA, Hayward C, Heid IM, Hellwege JN, Holleczek B, Holm H, Hutri-Kähönen N, Hveem K, Isermann B, Jonas JB, Joshi PK, Kamatani Y, Kanai M, Kastarinen M, Khor CC, Kiess W, Kleber ME, Körner A, Kovacs P, Krajcoviechova A, Kramer H, Krämer BK, Kuokkanen M, Kähönen M, Lange LA, Lash JP, Lehtimäki T, Li H, Lin BM, Liu J, Loeffler M, Lyytikäinen LP, Magnusson PKE, Martin NG, Matsuda K, Milaneschi Y, Mishra PP, Mononen N, Montgomery GW, Mook-Kanamori DO, Mychaleckyj JC, März W, Nauck M, Nikus K, Nolte IM, Noordam R, Okada Y, Olafsson I, Oldehinkel AJ, Penninx BWJH, Perola M, Pirastu N, Polasek O, Porteous DJ, Poulain T, Psaty BM, Rabelink TJ, Raffield LM, Raitakari OT, Rasheed H, Reilly DF, Rice KM, Richmond A, Ridker PM, Rotter JI, Rudan I, Sabanayagam C, Salomaa V, Schneiderman N, Schöttker B, Sims M, Snieder H, Stark KJ, Stefansson K, Stocker H, Stumvoll M, Sulem P, Sveinbjornsson G, Svensson PO, Tai ES, Taylor KD, Tayo BO, Teren A, Tham YC, Thiery J, Thio CHL, Thomas LF, Tremblay J, Tönjes A, van der Most PJ, Vitart V, Völker U, Wang YX, Wang C, Wei WB, Whitfield JB, Wild SH, Wilson JF, Winkler TW, Wong TY, Woodward M, Sim X, Chu AY, Feitosa MF, Thorsteinsdottir U, Hung AM, Teumer A, Franceschini N, Parsa A, Köttgen A, Schlosser P, Pattaro C. X-chromosome and kidney function: evidence from a multi-trait genetic analysis of 908,697 individuals reveals sex-specific and sex-differential findings in genes regulated by androgen response elements. Nat Commun 2024; 15:586. [PMID: 38233393 PMCID: PMC10794254 DOI: 10.1038/s41467-024-44709-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/30/2023] [Indexed: 01/19/2024] Open
Abstract
X-chromosomal genetic variants are understudied but can yield valuable insights into sexually dimorphic human traits and diseases. We performed a sex-stratified cross-ancestry X-chromosome-wide association meta-analysis of seven kidney-related traits (n = 908,697), identifying 23 loci genome-wide significantly associated with two of the traits: 7 for uric acid and 16 for estimated glomerular filtration rate (eGFR), including four novel eGFR loci containing the functionally plausible prioritized genes ACSL4, CLDN2, TSPAN6 and the female-specific DRP2. Further, we identified five novel sex-interactions, comprising male-specific effects at FAM9B and AR/EDA2R, and three sex-differential findings with larger genetic effect sizes in males at DCAF12L1 and MST4 and larger effect sizes in females at HPRT1. All prioritized genes in loci showing significant sex-interactions were located next to androgen response elements (ARE). Five ARE genes showed sex-differential expressions. This study contributes new insights into sex-dimorphisms of kidney traits along with new prioritized gene targets for further molecular research.
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Affiliation(s)
- Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Janne Pott
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Andreas Kühnapfel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - M Kamal Nasr
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Mathias Gorski
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Man Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Adrienne Tin
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, USA
- Division of Nephrology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Massimiliano Cocca
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Judy Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Teresa Nutile
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso'-CNR, Naples, Italy
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Bjørn Olav Åsvold
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Thibaud Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Ben Brumpton
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Clinic of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ralph Burkhardt
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Jianwen Cai
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - John Chalmers
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Miao Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Miao Li Chee
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Renata Cifkova
- Center for Cardiovascular Prevention, Charles University in Prague, First Faculty of Medicine and Thomayer University Hospital, Prague, Czech Republic
- Department of Medicine II, Charles University in Prague, First Faculty of Medicine, Prague, Czech Republic
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Graciela Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Katalin Dittrich
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
| | - Todd L Edwards
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Iceland School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Stein Hallan
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Nephrology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Pavel Hamet
- Montreal University Hospital Research Center, CHUM, Montréal, QC, Canada
- Medpharmgene, Montreal, QC, Canada
| | - Catharina A Hartman
- Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Jacklyn N Hellwege
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bernd Holleczek
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hilma Holm
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kristian Hveem
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Berend Isermann
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Laboratory Medicine, University of Leipzig, Leipzig, Germany
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
- Beijing Institute of Ophthalmology, Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
- Privatpraxis Prof Jonas und Dr Panda-Jonas, Heidelberg, Germany
| | - Peter K Joshi
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Masahiro Kanai
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Wieland Kiess
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Antje Körner
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Alena Krajcoviechova
- Center for Cardiovascular Prevention, Charles University in Prague, First Faculty of Medicine and Thomayer University Hospital, Prague, Czech Republic
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
- Division of Nephrology and Hypertension, Loyola University Chicago, Chicago, IL, USA
| | - Bernhard K Krämer
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Mikko Kuokkanen
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, USA
| | - James P Lash
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Hengtong Li
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | | | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, and The Wellbeing Services County of Pirkanmaa, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Charlottesville, VA, USA
| | - Winfried März
- Vth Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University Graz, Graz, Austria
- Synlab Academy, Synlab Holding Deutschland GmbH, Augsburg, Germany
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Yukinori Okada
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | - Albertine J Oldehinkel
- Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC/Vrije Universiteit and GGZ inGeest, Amsterdam, the Netherlands
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nicola Pirastu
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
- Biostatistics Unit - Population and Medical Genomics Programme, Genomics Research Centre, Human Technopole Palazzo Italia, Viale Rita Levi‑Montalcini, 1, 20157, Milan, Italy
| | | | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Tanja Poulain
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- University Hospital for Children and Adolescents, Pediatric Research Unit, Medical Faculty, University Medical Center, University of Leipzig, Leipzig, Germany
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Ton J Rabelink
- Department of Internal Medicine, Section of Nephrology, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory of Experimental Vascular Research, Leiden University Medical Center, Leiden, the Netherlands
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Humaira Rasheed
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Medicine and Laboratory Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Anne Richmond
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Neil Schneiderman
- Department of Psychology, University of Miami, Coral Gables, FL, USA
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | - Mario Sims
- Department of Social Medicine, Population and Public Health, University of California at Riverside School of Medicine, Riverside, CA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaus J Stark
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Hannah Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research, Heidelberg University, Heidelberg, Germany
| | | | | | | | - Per O Svensson
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Department of Cardiology, Södersjukhuset, Stockholm, Sweden
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
| | - Andrej Teren
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Cardiology and Intensive Care Medicine, University Hospital OWL of Bielefeld University, Campus Klinikum Bielefeld, Teutoburger Straße 50, 33604, Bielefeld, Germany
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Joachim Thiery
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute for Laboratory Medicine, University of Leipzig, Leipzig, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laurent F Thomas
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- BioCore - Bioinformatics Core Facility, Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Laboratory Medicine, St.Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Johanne Tremblay
- Montreal University Hospital Research Center, CHUM, Montréal, QC, Canada
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Chaolong Wang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen Bin Wei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sarah H Wild
- Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Tsinghua Medicine, Tsinghua University, Beijing, China
| | - Mark Woodward
- The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
- The George Institute for Global Health, School of Public Health, Imperial College London, London, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | | | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Adriana M Hung
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Medical Center, Division of Nephrology & Hypertension, Nashville, TN, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- Department of Population Medicine and Lifestyle Diseases Prevention, Medical University of Bialystok, Bialystok, Poland
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Afshin Parsa
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Pascal Schlosser
- Institute of Genetic Epidemiology, Department of Data Driven Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated with the University of Lübeck), Bolzano, Italy
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3
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Hughes O, Bentley AR, Breeze CE, Aguet F, Xu X, Nadkarni G, Sun Q, Lin BM, Gilliland T, Meyer MC, Du J, Raffield LM, Kramer H, Morton RW, Gouveia MH, Atkinson EG, Valladares-Salgado A, Wacher-Rodarte N, Dueker ND, Guo X, Hai Y, Adeyemo A, Best LG, Cai J, Chen G, Chong M, Doumatey A, Eales J, Goodarzi MO, Ipp E, Irvin MR, Jiang M, Jones AC, Kooperberg C, Krieger JE, Lange EM, Lanktree MB, Lash JP, Lotufo PA, Loos RJF, Ha My VT, Peralta-Romero J, Qi L, Raffel LJ, Rich SS, Rodriquez EJ, Tarazona-Santos E, Taylor KD, Umans JG, Wen J, Young BA, Yu Z, Zhang Y, Ida Chen YD, Rundek T, Rotter JI, Cruz M, Fornage M, Lima-Costa MF, Pereira AC, Paré G, Natarajan P, Cole SA, Carson AP, Lange LA, Li Y, Perez-Stable EJ, Do R, Charchar FJ, Tomaszewski M, Mychaleckyj JC, Rotimi C, Morris AP, Franceschini N. Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. Cell Genom 2024; 4:100468. [PMID: 38190104 PMCID: PMC10794846 DOI: 10.1016/j.xgen.2023.100468] [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] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p < 5 × 10-8), of which two have not been previously reported in any ancestry group. We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. We demonstrate the varying but increased predictive power offered by a multi-ancestry polygenic score for eGFR and highlight the importance of population diversity in GWASs and multi-omics resources to enhance opportunities for clinical translation for all.
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Affiliation(s)
- Odessica Hughes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA; UCL Cancer Institute, University College London, London, UK
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Girish Nadkarni
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Gilliland
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mariah C Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jiawen Du
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly Kramer
- Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, IL, USA
| | - Robert W Morton
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 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, 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, Mexico
| | - Nicole D Dueker
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lyle G Best
- Missouri Breaks Industries Research Inc., Eagle Butte, SD, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Chong
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Eli Ipp
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marguerite Ryan Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Minzhi Jiang
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alana C Jones
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jose E Krieger
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew B Lanktree
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - James P Lash
- Division of Nephrology, Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Paulo A Lotufo
- Center for Clinical and Epidemiological Research, Hospital Universitário, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vy Thi Ha My
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesús Peralta-Romero
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Lihong Qi
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Erik J Rodriquez
- Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Jason G Umans
- MedStar Health Research Institute, Hyattsville MD and Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bessie A Young
- University of Washington School of Medicine, Seattle, WA, USA; Office of Healthcare Equity, UW Justice, Equity, Diversity, and Inclusion Center for Transformational Research (UW JEDI-CTR), University of Washington, Seattle, WA, USA; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Zhi Yu
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Ying Zhang
- Center for American Indian Health Research, Department of Biostatistics and Epidemiology, Hudson College of Public Health, The University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Tanja Rundek
- Department of Neurology, Epidemiology and Public Health, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | | | - Alexandre C Pereira
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Aging Division, Brigham Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guillaume Paré
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eliseo J Perez-Stable
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Ron Do
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fadi J Charchar
- School of Science, Psychology and Sport, Federation University, Ballarat, VIC, Australia; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK; Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Josyf C Mychaleckyj
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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4
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Sachar M, Lin BM, Wong V, Li W, Huang V, Harris J, Ezzedine K, Cho E, Qureshi AA. Association between acetaminophen use and vitiligo in US women and men. Australas J Dermatol 2023; 64:e348-e351. [PMID: 37688423 PMCID: PMC10840899 DOI: 10.1111/ajd.14152] [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: 08/18/2022] [Revised: 05/30/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND/OBJECTIVES Exposure to chemical phenols, which can act as tyrosine analogues and result in anti-melanocyte autoimmunity, has been associated with vitiligo. Acetaminophen (N-acetyl-p-aminophenol) is an over-the-counter analgesic of phenolic origin. The risk of vitiligo with systemic exposure to acetaminophen has not yet been evaluated. METHODS We examined the risk of vitiligo with regular use acetaminophen in women, the Nurses' Health Study (NHS) and in men, the Health Professionals Follow-up Study (HPFS). Regular acetaminophen use was asked biennially from 1990 in NHS and from 1986 in HPFS, and the year of clinician-diagnosed vitiligo was asked retrospectively in 2012 in the cohorts. RESULTS In NHS, a total of 161 vitiligo cases were identified during a follow-up of 571,724 person-years; in HPFS, a total of 183 vitiligo cases were identified during a follow-up of 680,313 person-years. Regular use of acetaminophen was associated with an increased vitiligo risk in NHS but not HPFS. The multivariable relative risk (RR) was 1.52 (95% confidence interval [CI] 1.03-2.25) in NHS and 1.09 (95% CI 0.76-1.55) in HPFS. The higher risk of vitiligo was similar by duration of acetaminophen use in women; the multivariable RRs were 1.47 (95% CI 0.98-2.21) for acetaminophen use under 5 years, and 1.78 (95% CI 1.11-2.84) for acetaminophen use over 5 years. CONCLUSIONS Acetaminophen may be associated with a higher risk of vitiligo in women.
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Affiliation(s)
- M Sachar
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - B M Lin
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Massachusetts Eye and Ear Infirmary, Department of Otolaryngology, Boston, Massachusetts, USA
| | - V Wong
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - W Li
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing, China
| | - V Huang
- Department of Dermatology, University of California, Davis, California, USA
| | - J Harris
- Department of Dermatology, University of Massachusetts, Worcester, Massachusetts, USA
| | - K Ezzedine
- Department of Dermatology, Mondor Hospital (AP-HP), Paris Est Créteil University, Créteil, France
| | - E Cho
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Epidemiology, Brown University School of Public Health, Providence, Rhode Island, USA
| | - A A Qureshi
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Epidemiology, Brown University School of Public Health, Providence, Rhode Island, USA
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5
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Cho H, Qu Y, Liu C, Tang B, Lyu R, Lin BM, Roach J, Azcarate-Peril MA, Aguiar Ribeiro A, Love MI, Divaris K, Wu D. Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data. Brief Bioinform 2023; 24:bbad279. [PMID: 37738402 PMCID: PMC10516371 DOI: 10.1093/bib/bbad279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/07/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 09/24/2023] Open
Abstract
Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.
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Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Yixiang Qu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Chuwen Liu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Boyang Tang
- Department of Statistics, University of Connecticut, Storrs, CT, United States
| | - Ruiqi Lyu
- School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - M Andrea Azcarate-Peril
- Department of Medicine and Nutrition, University of North Carolina, Chapel Hill, NC, United States
| | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, University of North Carolina, Chapel Hill, NC, United States
| | - Michael I Love
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States
| | - Kimon Divaris
- Division of Pediatric and Public Health, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, United States
- Division of Oral and Craniofacial Health Sciences, Adam School of Dentistry, University of North Carolina, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
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6
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Reynolds KM, Horimoto ARVR, Lin BM, Zhang Y, Kurniansyah N, Yu B, Boerwinkle E, Qi Q, Kaplan R, Daviglus M, Hou L, Zhou LY, Cai J, Shaikh SR, Sofer T, Browning SR, Franceschini N. Ancestry-driven metabolite variation provides insights into disease states in admixed populations. Genome Med 2023; 15:52. [PMID: 37461045 PMCID: PMC10351197 DOI: 10.1186/s13073-023-01209-z] [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: 11/22/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Metabolic pathways are related to physiological functions and disease states and are influenced by genetic variation and environmental factors. Hispanics/Latino individuals have ancestry-derived genomic regions (local ancestry) from their recent admixture that have been less characterized for associations with metabolite abundance and disease risk. METHODS We performed admixture mapping of 640 circulating metabolites in 3887 Hispanic/Latino individuals from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Metabolites were quantified in fasting serum through non-targeted mass spectrometry (MS) analysis using ultra-performance liquid chromatography-MS/MS. Replication was performed in 1856 nonoverlapping HCHS/SOL participants with metabolomic data. RESULTS By leveraging local ancestry, this study identified significant ancestry-enriched associations for 78 circulating metabolites at 484 independent regions, including 116 novel metabolite-genomic region associations that replicated in an independent sample. Among the main findings, we identified Native American enriched genomic regions at chromosomes 11 and 15, mapping to FADS1/FADS2 and LIPC, respectively, associated with reduced long-chain polyunsaturated fatty acid metabolites implicated in metabolic and inflammatory pathways. An African-derived genomic region at chromosome 2 was associated with N-acetylated amino acid metabolites. This region, mapped to ALMS1, is associated with chronic kidney disease, a disease that disproportionately burdens individuals of African descent. CONCLUSIONS Our findings provide important insights into differences in metabolite quantities related to ancestry in admixed populations including metabolites related to regulation of lipid polyunsaturated fatty acids and N-acetylated amino acids, which may have implications for common diseases in populations.
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Affiliation(s)
- Kaylia M Reynolds
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina, 123 W Franklin St, Suite 401, NC, NC 27516, Chapel Hill, USA
| | | | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Ying Zhang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Nuzulul Kurniansyah
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Bing Yu
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Laura Y Zhou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Saame Raza Shaikh
- Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Departments of Medicine and Biostatistics, Harvard University, Boston, MA, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, 123 W Franklin St, Suite 401, NC, NC 27516, Chapel Hill, USA.
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7
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Cho H, Ren Z, Divaris K, Roach J, Lin BM, Liu C, Azcarate-Peril MA, Simancas-Pallares MA, Shrestha P, Orlenko A, Ginnis J, North KE, Zandona AGF, Ribeiro AA, Wu D, Koo H. Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries. Nat Commun 2023; 14:2919. [PMID: 37217495 PMCID: PMC10202936 DOI: 10.1038/s41467-023-38346-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 06/11/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.
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Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Ren
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffrey Roach
- UNC Information Technology Services and Research Computing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chuwen Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miguel A Simancas-Pallares
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Poojan Shrestha
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Orlenko
- Artificial Intelligence Innovation Lab, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeannie Ginnis
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hyun Koo
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Lin BM, Cho H, Liu C, Roach J, Ribeiro AA, Divaris K, Wu D. BZINB Model-Based Pathway Analysis and Module Identification Facilitates Integration of Microbiome and Metabolome Data. Microorganisms 2023; 11:766. [PMID: 36985339 PMCID: PMC10056694 DOI: 10.3390/microorganisms11030766] [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: 01/31/2023] [Revised: 03/04/2023] [Accepted: 03/12/2023] [Indexed: 03/19/2023] Open
Abstract
Integration of multi-omics data is a challenging but necessary step to advance our understanding of the biology underlying human health and disease processes. To date, investigations seeking to integrate multi-omics (e.g., microbiome and metabolome) employ simple correlation-based network analyses; however, these methods are not always well-suited for microbiome analyses because they do not accommodate the excess zeros typically present in these data. In this paper, we introduce a bivariate zero-inflated negative binomial (BZINB) model-based network and module analysis method that addresses this limitation and improves microbiome-metabolome correlation-based model fitting by accommodating excess zeros. We use real and simulated data based on a multi-omics study of childhood oral health (ZOE 2.0; investigating early childhood dental caries, ECC) and find that the accuracy of the BZINB model-based correlation method is superior compared to Spearman's rank and Pearson correlations in terms of approximating the underlying relationships between microbial taxa and metabolites. The new method, BZINB-iMMPath, facilitates the construction of metabolite-species and species-species correlation networks using BZINB and identifies modules of (i.e., correlated) species by combining BZINB and similarity-based clustering. Perturbations in correlation networks and modules can be efficiently tested between groups (i.e., healthy and diseased study participants). Upon application of the new method in the ZOE 2.0 study microbiome-metabolome data, we identify that several biologically-relevant correlations of ECC-associated microbial taxa with carbohydrate metabolites differ between healthy and dental caries-affected participants. In sum, we find that the BZINB model is a useful alternative to Spearman or Pearson correlations for estimating the underlying correlation of zero-inflated bivariate count data and thus is suitable for integrative analyses of multi-omics data such as those encountered in microbiome and metabolome studies.
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Affiliation(s)
- Bridget M. Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chuwen Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeff Roach
- Research Computing, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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9
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Reynolds KM, Lin BM, Armstrong ND, Ottosson F, Zhang Y, Williams AS, Yu B, Boerwinkle E, Thygarajan B, Daviglus ML, Muoio D, Qi Q, Kaplan R, Melander O, Lash JP, Cai J, Irvin MR, Newgard CB, Sofer T, Franceschini N. Circulating Metabolites Associated with Albuminuria in a Hispanic/Latino Population. Clin J Am Soc Nephrol 2023; 18:204-212. [PMID: 36517247 PMCID: PMC10103280 DOI: 10.2215/cjn.09070822] [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: 08/04/2022] [Revised: 11/22/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Albuminuria is associated with metabolic abnormalities, but these relationships are not well understood. We studied the association of metabolites with albuminuria in Hispanic/Latino people, a population with high risk for metabolic disease. METHODS We used data from 3736 participants from the Hispanic Community Health Study/Study of Latinos, of which 16% had diabetes and 9% had an increased urine albumin-to-creatinine ratio (UACR). Metabolites were quantified in fasting serum through nontargeted mass spectrometry (MS) analysis using ultra-performance liquid chromatography-MS/MS. Spot UACR was inverse normally transformed and tested for the association with each metabolite or combined, correlated metabolites, in covariate-adjusted models that accounted for the study design. In total, 132 metabolites were available for replication in the Hypertension Genetic Epidemiology Network study ( n =300), and 29 metabolites were available for replication in the Malmö Offspring Study ( n =999). RESULTS Among 640 named metabolites, we identified 148 metabolites significantly associated with UACR, including 18 novel associations that replicated in independent samples. These metabolites showed enrichment for D-glutamine and D-glutamate metabolism and arginine biosynthesis, pathways previously reported for diabetes and insulin resistance. In correlated metabolite analyses, we identified two modules significantly associated with UACR, including a module composed of lipid metabolites related to the biosynthesis of unsaturated fatty acids and alpha linolenic acid and linoleic acid metabolism. CONCLUSIONS Our study identified associations of albuminuria with metabolites involved in glucose dysregulation, and essential fatty acids and precursors of arachidonic acid in Hispanic/Latino population. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/CJASN/2023_02_08_CJN09070822.mp3.
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Affiliation(s)
- Kaylia M. Reynolds
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Bridget M. Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Nicole D. Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Filip Ottosson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ying Zhang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Bing Yu
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas
| | - Bharat Thygarajan
- Division of Molecular Pathology and Genomics, University of Minnesota, Minneapolis, Minnesota
| | - Martha L. Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Deborah Muoio
- Duke University Medical Center, Durham, North Carolina
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - James P. Lash
- Division of Nephrology, Department of Medicine, University of Illinois, Chicago, Illinois
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, Massachusetts
- Departments of Medicine and Biostatistics, Harvard University, Boston, Massachusetts
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
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10
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Young KL, Fisher V, Deng X, Brody JA, Graff M, Lim E, Lin BM, Xu H, Amin N, An P, Aslibekyan S, Fohner AE, Hidalgo B, Lenzini P, Kraaij R, Medina-Gomez C, Prokić I, Rivadeneira F, Sitlani C, Tao R, van Rooij J, Zhang D, Broome JG, Buth EJ, Heavner BD, Jain D, Smith AV, Barnes K, Boorgula MP, Chavan S, Darbar D, De Andrade M, Guo X, Haessler J, Irvin MR, Kalyani RR, Kardia SLR, Kooperberg C, Kim W, Mathias RA, McDonald ML, Mitchell BD, Peyser PA, Regan EA, Redline S, Reiner AP, Rich SS, Rotter JI, Smith JA, Weiss S, Wiggins KL, Yanek LR, Arnett D, Heard-Costa NL, Leal S, Lin D, McKnight B, Province M, van Duijn CM, North KE, Cupples LA, Liu CT. Whole-exome sequence analysis of anthropometric traits illustrates challenges in identifying effects of rare genetic variants. HGG Adv 2023; 4:100163. [PMID: 36568030 PMCID: PMC9772568 DOI: 10.1016/j.xhgg.2022.100163] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Anthropometric traits, measuring body size and shape, are highly heritable and significant clinical risk factors for cardiometabolic disorders. These traits have been extensively studied in genome-wide association studies (GWASs), with hundreds of genome-wide significant loci identified. We performed a whole-exome sequence analysis of the genetics of height, body mass index (BMI) and waist/hip ratio (WHR). We meta-analyzed single-variant and gene-based associations of whole-exome sequence variation with height, BMI, and WHR in up to 22,004 individuals, and we assessed replication of our findings in up to 16,418 individuals from 10 independent cohorts from Trans-Omics for Precision Medicine (TOPMed). We identified four trait associations with single-nucleotide variants (SNVs; two for height and two for BMI) and replicated the LECT2 gene association with height. Our expression quantitative trait locus (eQTL) analysis within previously reported GWAS loci implicated CEP63 and RFT1 as potential functional genes for known height loci. We further assessed enrichment of SNVs, which were monogenic or syndromic variants within loci associated with our three traits. This led to the significant enrichment results for height, whereas we observed no Bonferroni-corrected significance for all SNVs. With a sample size of ∼20,000 whole-exome sequences in our discovery dataset, our findings demonstrate the importance of genomic sequencing in genetic association studies, yet they also illustrate the challenges in identifying effects of rare genetic variants.
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Affiliation(s)
- Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Virginia Fisher
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Xuan Deng
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Misa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Elise Lim
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Hanfei Xu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ping An
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Institute for Public Health Genetics, University of Washington, Seattle, WA 98101, USA
| | - Bertha Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Petra Lenzini
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Ivana Prokić
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Colleen Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam 3015CN, the Netherlands
| | - Di Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jai G Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Erin J Buth
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Benjamin D Heavner
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.,Tempus Labs, Chicago, IL 60654, USA
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Dawood Darbar
- Division of Cardiology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariza De Andrade
- Health Quantitative Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rita R Kalyani
- Division of Endocrinology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Merry-Lynn McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Susan Redline
- Department of Medicine, Brigham & Women's Hospital, Boston, MA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Scott Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donna Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | | | - Suzanne Leal
- Department of Neurology, Columbia University, New York City, NY, USA
| | - Danyu Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA 98105, USA
| | - Michael Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
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11
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Li Z, Li X, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, Quick C, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Auer PL, Bielak LF, Bis JC, Blackwell TW, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Conomos MP, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Franceschini N, Freedman BI, Göring HHH, Guo X, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Lin BM, Manichaikul A, Manning AK, Martin LW, Mathias RA, Meigs JB, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Smith JA, Taylor KD, Taub MA, Vasan RS, Weeks DE, Wilson JG, Yanek LR, Zhao W, Rotter JI, Willer CJ, Natarajan P, Peloso GM, Lin X. A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nat Methods 2022; 19:1599-1611. [PMID: 36303018 PMCID: PMC10008172 DOI: 10.1038/s41592-022-01640-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 09/06/2022] [Indexed: 02/07/2023]
Abstract
Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.
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Grants
- R01 DK078616 NIDDK NIH HHS
- U01 HG007417 NHGRI NIH HHS
- KL2 TR001100 NCATS NIH HHS
- R01 HL112064 NHLBI NIH HHS
- N01-HC-95160 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R35 HG010692 NHGRI NIH HHS
- U01-HL054472 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-HL142711 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-DK071891 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- F30 HL149180 NHLBI NIH HHS
- R01 NR019628 NINR NIH HHS
- R01 HL113323 NHLBI NIH HHS
- N01-HC-95166 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1RR033176 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- R01 HL132947 NHLBI NIH HHS
- P30 DK040561 NIDDK NIH HHS
- U01 HL137183 NHLBI NIH HHS
- R01-HL127564 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P30 CA016672 NCI NIH HHS
- R01-HL071051 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL104135 NHLBI NIH HHS
- T32 HL144442 NHLBI NIH HHS
- R35 CA197449 NCI NIH HHS
- P30 ES010126 NIEHS NIH HHS
- DP5 OD029586 NIH HHS
- R01-NS058700 U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)
- R01 HL123915 NHLBI NIH HHS
- R01 HL120393 NHLBI NIH HHS
- R01HL071259 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL046380 NHLBI NIH HHS
- R01HL071251, R01HL071258, R01HL071259 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U54 HG003067 NHGRI NIH HHS
- 75N92020D00003 NHLBI NIH HHS
- K01 AG059898 NIA NIH HHS
- U01 DK085524 NIDDK NIH HHS
- KL2 TR002542 NCATS NIH HHS
- R01-HL055673-18S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R03 HL141439 NHLBI NIH HHS
- HHSN268201500001I NHLBI NIH HHS
- R01-MH078143, R01-MH078111, R01-MH083824 U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)
- U01 DK062413 NIDDK NIH HHS
- R01 HL109946 NHLBI NIH HHS
- U01-HL054495 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K01 HL136700 NHLBI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- U01 HL080295 NHLBI NIH HHS
- NO1-HC-25195 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HG006703 NHGRI NIH HHS
- UL1-TR-001420 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- U01 HG012064 NHGRI NIH HHS
- R35-CA197449 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
- P30 ES005605 NIEHS NIH HHS
- R01 AR042742 NIAMS NIH HHS
- R21 HL140385 NHLBI NIH HHS
- HHSN268201800015I NHLBI NIH HHS
- U01 HL130114 NHLBI NIH HHS
- R01 HL117191 NHLBI NIH HHS
- R01 HG009974 NHGRI NIH HHS
- U01-HL054473 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 DK113003 NIDDK NIH HHS
- UL1RR033176 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL059367 NHLBI NIH HHS
- R24 AG047115 NIA NIH HHS
- U01-HL137181 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL107202 NHLBI NIH HHS
- NR0224103 U.S. Department of Health & Human Services | NIH | National Institute of Nursing Research (NINR)
- P50 HL118006 NHLBI NIH HHS
- U01-HL72518, HL087698, HL49762, HL59684, HL58625, HL071025, HL112064 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01 HL120393 NHLBI NIH HHS
- R01 DK117445 NIDDK NIH HHS
- R01-AG058921 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- R03-HL154284 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1-TR-000040, UL1-TR-001079, UL1-TR-001420, UL1-TR-001881 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R01 AG058921 NIA NIH HHS
- R01 HL129132 NHLBI NIH HHS
- R01 HL113338 NHLBI NIH HHS
- HHSN268201800012I NHLBI NIH HHS
- R01 HL153805 NHLBI NIH HHS
- R01 DK072193 NIDDK NIH HHS
- R01 HL137922 NHLBI NIH HHS
- R01 AI079139 NIAID NIH HHS
- N01-HC-95164 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-DK085524 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- U19 AI111224 NIAID NIH HHS
- R35 HL135824 NHLBI NIH HHS
- 75N92019D00031 NHLBI NIH HHS
- R01 DK110113 NIDDK NIH HHS
- N01-HC-95159, N01-HC-95160, N01-HC-95161, N01-HC-95162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- N01-HC-95165 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL138737 NHLBI NIH HHS
- P30 DK079626 NIDDK NIH HHS
- R01 NS058700 NINDS NIH HHS
- R01 HL127564 NHLBI NIH HHS
- T32 HG000040 NHGRI NIH HHS
- DK063491 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 HL141845 NHLBI NIH HHS
- R01 DK075787 NIDDK NIH HHS
- R01 AR072199 NIAMS NIH HHS
- R01 HL120854 NHLBI NIH HHS
- R01 HL163560 NHLBI NIH HHS
- R01HL071258 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-HG009088 U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)
- R01 HL163972 NHLBI NIH HHS
- K23 HL123778 NHLBI NIH HHS
- U01 HL137181 NHLBI NIH HHS
- R01 MH078111 NIMH NIH HHS
- HHSN268201700005I NHLBI NIH HHS
- N01-HC-95159 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01-HL113323 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL141944 NHLBI NIH HHS
- R01 HL119443 NHLBI NIH HHS
- R01-HL071051, R01-HL071205, R01HL071250 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P60-AG10484 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- 75N92020D00007 NHLBI NIH HHS
- UM1 AI068634 NIAID NIH HHS
- HHSN268201500003I NHLBI NIH HHS
- HHSN268201700004I NHLBI NIH HHS
- N01-HC-95163 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01-HL071205 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- F30 HL107066 NHLBI NIH HHS
- R01-HL153805 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL105756 NHLBI NIH HHS
- K01 HL125751 NHLBI NIH HHS
- R01 HL067348 NHLBI NIH HHS
- T32 HL007208 NHLBI NIH HHS
- R01 HL142711 NHLBI NIH HHS
- R35 HL135818 NHLBI NIH HHS
- R01-HL92301 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- T32 GM074897 NIGMS NIH HHS
- I01 BX005295 BLRD VA
- 75N92020D00001 NHLBI NIH HHS
- R01 HL113326 NHLBI NIH HHS
- R00 HL129045 NHLBI NIH HHS
- UL1-TR-000040 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- UL1-TR-001079 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- U01 HL072524 NHLBI NIH HHS
- R35-HL135818 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K08 HL140203 NHLBI NIH HHS
- N01-HC-95162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- K08 HL141601 NHLBI NIH HHS
- 75N92020D00005 NHLBI NIH HHS
- R01-DK117445 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01-AR48797 U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- R56 AG058543 NIA NIH HHS
- U19 AI077439 NIAID NIH HHS
- R01 HL142028 NHLBI NIH HHS
- 75N92020D00004 NHLBI NIH HHS
- HHSN268201800011I NHLBI NIH HHS
- R35 GM127131 NIGMS NIH HHS
- U01 HL137880 NHLBI NIH HHS
- R01 HG010869 NHGRI NIH HHS
- R01-HL133040 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201700003I NHLBI NIH HHS
- R01HL071250 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- N01-HC-95168 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL148239 NHLBI NIH HHS
- U01-HL137162 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 AI132476 NIAID NIH HHS
- T32 GM007205 NIGMS NIH HHS
- HHSN268201800010I NHLBI NIH HHS
- R01-HL092577-06S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UL1-TR-001881 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R01-HL104135-04S1 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL132320 NHLBI NIH HHS
- U01 DK078616 NIDDK NIH HHS
- HHSN268201700001I NHLBI NIH HHS
- R01-HL141944 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01 HL137162 NHLBI NIH HHS
- R01 HG005701 NHGRI NIH HHS
- 75N92020D00001, 75N92020D00002, 75N92020D00003, 75N92020D00004 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01 HL143221 NHLBI NIH HHS
- R01 HL142992 NHLBI NIH HHS
- K01 HL129039 NHLBI NIH HHS
- R01 HL133870 NHLBI NIH HHS
- R01 DA037904 NIDA NIH HHS
- R21 HL123677 NHLBI NIH HHS
- R01 DK071891 NIDDK NIH HHS
- HHSN268201800001I U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- 75N92020D00002 NHLBI NIH HHS
- K01 HL130609 NHLBI NIH HHS
- N01-HC-95167 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- T32 HL007374 NHLBI NIH HHS
- N01-HC-95169 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U01-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 AR063611 NIAMS NIH HHS
- KL2TR002490 U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)
- R03 HL154284 NHLBI NIH HHS
- M01-RR000052 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- 75N92020D00006 NHLBI NIH HHS
- S10 OD020069 NIH HHS
- R01 MD012765 NIMHD NIH HHS
- N01-HC-95161 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- HHSN268201700002I NHLBI NIH HHS
- R01 HL151855 NHLBI NIH HHS
- K23 HL138461 NHLBI NIH HHS
- U01 CA182913 NCI NIH HHS
- UG3 HL151865 NHLBI NIH HHS
- F32 HL150992 NHLBI NIH HHS
- R01-MD012765 U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)
- 75N92020D00005, 75N92020D00006, 75N92020D00007 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01 MH101244 NIMH NIH HHS
- U01 HG009088 NHGRI NIH HHS
- N01-HC-95163, N01-HC-95164, N01-HC-95165, N01-HC-95166 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P42 ES016454 NIEHS NIH HHS
- UM1 DK078616 NIDDK NIH HHS
- U01-HL054509 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R35-HL135824 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- M01-RR07122 U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)
- U01 DK105561 NIDDK NIH HHS
- U01-HL072524 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P20 GM121334 NIGMS NIH HHS
- N01-HC-95167, N01-HC-95168, N01-HC-95169 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL131565 NHLBI NIH HHS
- R01HL071251 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R13 CA124365 NCI NIH HHS
- R01-HL045522 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P01 HL132825 NHLBI NIH HHS
- R01 HL118267 NHLBI NIH HHS
- HHSN268201800013I NIMHD NIH HHS
- R01-HL67348 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U54 GM115428 NIGMS NIH HHS
- R01 HL055673 NHLBI NIH HHS
- HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UM1-DK078616 U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- R01 HL149683 NHLBI NIH HHS
- R01 HL092301 NHLBI NIH HHS
- P30 DK020595 NIDDK NIH HHS
- R01 HL149836 NHLBI NIH HHS
- K08 HL145095 NHLBI NIH HHS
- K01 HL135405 NHLBI NIH HHS
- R03 OD030608 NIH HHS
- HHSN268201800014I NHLBI NIH HHS
- R01-HL113338 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- F32-HL085989 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- UM1 AI068636 NIAID NIH HHS
- R01 AG057381 NIA NIH HHS
- U19-CA203654 U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
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Affiliation(s)
- Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Margaret Sunitha Selvaraj
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Theodore Arapoglou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Corbin Quick
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yaowu Liu
- School of Statistics, Southwestern University of Finance and Economics, Chengdu, China
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rounak Dey
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Donna K Arnett
- Dean's Office, University of Kentucky, College of Public Health, Lexington, KY, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Barry I Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Harald H H Göring
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Rita R Kalyani
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa W Martin
- Division in Cardiology, George Washington School of Medicine and Health Sciences, Washington, DC, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore VA Medical Center, Baltimore, MD, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Departments of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Daniel E Weeks
- Department of Human Genetics and Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - James G Wilson
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Cristen J Willer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Statistics, Harvard University, Cambridge, MA, USA.
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12
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Vy HMT, Lin BM, Gulamali FF, Kooperberg C, Graff M, Wong J, Campbell KN, Matise TC, Coresh J, Thomas F, Reiner AP, Nassir R, Schnatz PF, Johns T, Buyske S, Haiman C, Cooper R, Loos RJ, Horowitz CR, Gutierrez OM, Do R, Franceschini N, Nadkarni GN. Genome-Wide Epistatic Interaction between DEF1B and APOL1 High-Risk Genotypes for Chronic Kidney Disease. Clin J Am Soc Nephrol 2022; 17:1522-1525. [PMID: 35948364 PMCID: PMC9528279 DOI: 10.2215/cjn.03610322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ha My T. Vy
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bridget M. Lin
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Faris F. Gulamali
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Jenny Wong
- Barbara T. Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kirk N. Campbell
- Barbara T. Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tara C. Matise
- Department of Genetics, Rutgers University, New Brunswick, New Jersey
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Fridtjof Thomas
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Rami Nassir
- Department of Pathology, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Peter F. Schnatz
- Department of Obstetrics and Gynecology, The Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Tanya Johns
- Division of Nephrology, Albert Einstein College of Medicine, Bronx, New York
| | - Steven Buyske
- Department of Genetics, Rutgers University, New Brunswick, New Jersey
| | - Christopher Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Richard Cooper
- Department of Public Health Sciences, Loyola University School of Public Health, Chicago, Illinois
| | - Ruth J.F. Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carol R. Horowitz
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Orlando M. Gutierrez
- Division of Nephrology, University of Alabama Heersink School of Medicine, Birmingham, Alabama
| | - Ron Do
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nora Franceschini
- Barbara T. Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish N. Nadkarni
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Division of Data Driven and Digital Medicine (D3M), Icahn School of Medicine at Mount Sinai, New York, New York
- The Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, New York
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13
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Highland HM, Wojcik GL, Graff M, Nishimura KK, Hodonsky CJ, Baldassari AR, Cote AC, Cheng I, Gignoux CR, Tao R, Li Y, Boerwinkle E, Fornage M, Haessler J, Hindorff LA, Hu Y, Justice AE, Lin BM, Lin D, Stram DO, Haiman CA, Kooperberg C, Le Marchand L, Matise TC, Kenny EE, Carlson CS, Stahl EA, Avery CL, North KE, Ambite JL, Buyske S, Loos RJ, Peters U, Young KL, Bien SA, Huckins LM. Predicted gene expression in ancestrally diverse populations leads to discovery of susceptibility loci for lifestyle and cardiometabolic traits. Am J Hum Genet 2022; 109:669-679. [PMID: 35263625 PMCID: PMC9069067 DOI: 10.1016/j.ajhg.2022.02.013] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/15/2022] [Indexed: 02/06/2023] Open
Abstract
One mechanism by which genetic factors influence complex traits and diseases is altering gene expression. Direct measurement of gene expression in relevant tissues is rarely tenable; however, genetically regulated gene expression (GReX) can be estimated using prediction models derived from large multi-omic datasets. These approaches have led to the discovery of many gene-trait associations, but whether models derived from predominantly European ancestry (EA) reference panels can map novel associations in ancestrally diverse populations remains unclear. We applied PrediXcan to impute GReX in 51,520 ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) participants (35% African American, 45% Hispanic/Latino, 10% Asian, and 7% Hawaiian) across 25 key cardiometabolic traits and relevant tissues to identify 102 novel associations. We then compared associations in PAGE to those in a random subset of 50,000 White British participants from UK Biobank (UKBB50k) for height and body mass index (BMI). We identified 517 associations across 47 tissues in PAGE but not UKBB50k, demonstrating the importance of diverse samples in identifying trait-associated GReX. We observed that variants used in PrediXcan models were either more or less differentiated across continental-level populations than matched-control variants depending on the specific population reflecting sampling bias. Additionally, variants from identified genes specific to either PAGE or UKBB50k analyses were more ancestrally differentiated than those in genes detected in both analyses, underlining the value of population-specific discoveries. This suggests that while EA-derived transcriptome imputation models can identify new associations in non-EA populations, models derived from closely matched reference panels may yield further insights. Our findings call for more diversity in reference datasets of tissue-specific gene expression.
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Affiliation(s)
- Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Katherine K Nishimura
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Antoine R Baldassari
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Alanna C Cote
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yuqing Li
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA; Brown Foundation Institute for Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jeffrey Haessler
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, NIH National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Yao Hu
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger Health System, Danville, PA 17822, USA
| | - Bridget M Lin
- Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Danyu Lin
- Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Daniel O Stram
- Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Christopher A Haiman
- Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | | | - Tara C Matise
- Genetics, Rutgers University, New Brunswick, NJ 08901-8554, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher S Carlson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eli A Stahl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jose Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA 90292, USA
| | - Steven Buyske
- Statistics, Rutgers University, New Brunswick, NJ 08901-8554, USA
| | - Ruth J Loos
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ulrike Peters
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Stephanie A Bien
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laura M Huckins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education and Clinical Centers, James J. Peters Department of Veterans Affairs Medical Center, Bronx, NY 14068, USA.
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14
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Lin BM, Zhang Y, Yu B, Boerwinkle E, Thygarajan B, Yunes M, Daviglus ML, Qi Q, Kaplan R, Lash J, Cai J, Sofer T, Franceschini N. Metabolome-wide association study of estimated glomerular filtration rates in Hispanics. Kidney Int 2022; 101:144-151. [PMID: 34774559 PMCID: PMC8741745 DOI: 10.1016/j.kint.2021.09.032] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 01/03/2023]
Abstract
Circulating metabolites are by-products of endogenous metabolism or exogenous sources and may inform disease states. Our study aimed to identify the source of variability in the association of metabolites with estimated glomerular filtration rate (eGFR) in Hispanics/Latinos with low chronic kidney disease prevalence by testing the association of 640 metabolites in 3,906 participants of the Hispanic Community Health Study/Study of Latinos. Metabolites were quantified in fasting serum through non-targeted mass spectrometry analysis. eGFR was regressed on inverse normally transformed metabolites in models accounting for study design and covariates. To identify the source of variation on eGFR associations, we tested the interaction of metabolites with lifestyle and clinical risk factors, and results were integrated with genotypes to identify metabolite genetic regulation. The mean age was 46 years, 43% were men, 22% were current smokers, 47% had a Caribbean Hispanic background, 19% had diabetes and the mean cohort eGFR was 96.4 ml/min/1.73 m2. We identified 404 eGFR-metabolite associations (False Discovery Rate under 0.05). Of these, 69 were previously reported, and 79 were novel associations with eGFR replicated in one or more published studies. There were significant interactions with lifestyle and clinical risk factors, with larger differences in eGFR-metabolite associations within strata of age, urine albumin to creatinine ratio, diabetes and Hispanic/Latino background. Several newly identified metabolites were genetically regulated, and variants were located at genomic regions previously associated with eGFR. Thus, our results suggest complex mechanisms contribute to the association of eGFR with metabolites and provide new insights into these associations.
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Affiliation(s)
- Bridget M. Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Ying Zhang
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, 02115
| | - Bing Yu
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030
| | - Bharat Thygarajan
- Division of Molecular Pathology and Genomics, University of Minnesota, Minneapolis, MN
| | - Milagros Yunes
- Department of Medicine, Division of Nephrology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago College of Medicine, Chicago, IL
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle WA
| | - James Lash
- Division of Nephrology, Department of Medicine, University of Illinois, Chicago, IL
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, 02115,Departments of Medicine and Biostatistics, Harvard University, Boston, MA, 02115
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
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15
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Xie J, Cho H, Lin BM, Pillai M, Heimisdottir LH, Bandyopadhyay D, Zou F, Roach J, Divaris K, Wu D. Improved Metabolite Prediction Using Microbiome Data-Based Elastic Net Models. Front Cell Infect Microbiol 2021; 11:734416. [PMID: 34760716 PMCID: PMC8573316 DOI: 10.3389/fcimb.2021.734416] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
Microbiome data are becoming increasingly available in large health cohorts, yet metabolomics data are still scant. While many studies generate microbiome data, they lack matched metabolomics data or have considerable missing proportions of metabolites. Since metabolomics is key to understanding microbial and general biological activities, the possibility of imputing individual metabolites or inferring metabolomics pathways from microbial taxonomy or metagenomics is intriguing. Importantly, current metabolomics profiling methods such as the HMP Unified Metabolic Analysis Network (HUMAnN) have unknown accuracy and are limited in their ability to predict individual metabolites. To address this gap, we developed a novel metabolite prediction method, and we present its application and evaluation in an oral microbiome study. The new method for predicting metabolites using microbiome data (ENVIM) is based on the elastic net model (ENM). ENVIM introduces an extra step to ENM to consider variable importance (VI) scores, and thus, achieves better prediction power. We investigate the metabolite prediction performance of ENVIM using metagenomic and metatranscriptomic data in a supragingival biofilm multi-omics dataset of 289 children ages 3-5 who were participants of a community-based study of early childhood oral health (ZOE 2.0) in North Carolina, United States. We further validate ENVIM in two additional publicly available multi-omics datasets generated from studies of gut health. We select gene family sets based on variable importance scores and modify the existing ENM strategy used in the MelonnPan prediction software to accommodate the unique features of microbiome and metabolome data. We evaluate metagenomic and metatranscriptomic predictors and compare the prediction performance of ENVIM to the standard ENM employed in MelonnPan. The newly developed ENVIM method showed superior metabolite predictive accuracy than MelonnPan when trained with metatranscriptomics data only, metagenomics data only, or both. Better metabolite prediction is achieved in the gut microbiome compared with the oral microbiome setting. We report the best-predictable compounds in all these three datasets from two different body sites. For example, the metabolites trehalose, maltose, stachyose, and ribose are all well predicted by the supragingival microbiome.
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Affiliation(s)
- Jialiu Xie
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Bridget M. Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Malvika Pillai
- Carolina Health Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lara H. Heimisdottir
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Dipankar Bandyopadhyay
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Fei Zou
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, United States
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Division of Oral and Craniofacial Health Research, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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16
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Heimisdottir LH, Lin BM, Cho H, Orlenko A, Ribeiro AA, Simon-Soro A, Roach J, Shungin D, Ginnis J, Simancas-Pallares MA, Spangler HD, Zandoná AGF, Wright JT, Ramamoorthy P, Moore JH, Koo H, Wu D, Divaris K. Metabolomics Insights in Early Childhood Caries. J Dent Res 2021; 100:615-622. [PMID: 33423574 DOI: 10.1177/0022034520982963] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dental caries is characterized by a dysbiotic shift at the biofilm-tooth surface interface, yet comprehensive biochemical characterizations of the biofilm are scant. We used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence and severity. The study's analytical sample comprised 289 children ages 3 to 5 (51% with ECC) who attended public preschools in North Carolina and were enrolled in a community-based cross-sectional study of early childhood oral health. Clinical examinations were conducted by calibrated examiners in community locations using International Caries Detection and Classification System (ICDAS) criteria. Supragingival plaque collected from the facial/buccal surfaces of all primary teeth in the upper-left quadrant was analyzed using ultra-performance liquid chromatography-tandem mass spectrometry. Associations between individual metabolites and 18 clinical traits (based on different ECC definitions and sets of tooth surfaces) were quantified using Brownian distance correlations (dCor) and linear regression modeling of log2-transformed values, applying a false discovery rate multiple testing correction. A tree-based pipeline optimization tool (TPOT)-machine learning process was used to identify the best-fitting ECC classification metabolite model. There were 503 named metabolites identified, including microbial, host, and exogenous biochemicals. Most significant ECC-metabolite associations were positive (i.e., upregulations/enrichments). The localized ECC case definition (ICDAS ≥1 caries experience within the surfaces from which plaque was collected) had the strongest correlation with the metabolome (dCor P = 8 × 10-3). Sixteen metabolites were significantly associated with ECC after multiple testing correction, including fucose (P = 3.0 × 10-6) and N-acetylneuraminate (p = 6.8 × 10-6) with higher ECC prevalence, as well as catechin (P = 4.7 × 10-6) and epicatechin (P = 2.9 × 10-6) with lower. Catechin, epicatechin, imidazole propionate, fucose, 9,10-DiHOME, and N-acetylneuraminate were among the top 15 metabolites in terms of ECC classification importance in the automated TPOT model. These supragingival biofilm metabolite findings provide novel insights in ECC biology and can serve as the basis for the development of measures of disease activity or risk assessment.
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Affiliation(s)
- L H Heimisdottir
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - B M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - H Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - A Orlenko
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - A A Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - A Simon-Soro
- Biofilm Research Labs, Center for Innovation and Precision Dentistry, School of Dental Medicine and School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.,Department of Orthodontics and Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Stomatology, School of Dentistry, University of Sevilla, Sevilla, Spain
| | - J Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - D Shungin
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Odontology, Umeå University, Umeå, Sweden
| | - J Ginnis
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - M A Simancas-Pallares
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - H D Spangler
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - A G Ferreira Zandoná
- Department of Comprehensive Care, School of Dental Medicine, Tufts University, Boston, MA, USA
| | - J T Wright
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | | | - J H Moore
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - H Koo
- Biofilm Research Labs, Center for Innovation and Precision Dentistry, School of Dental Medicine and School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.,Department of Orthodontics and Divisions of Pediatric Dentistry and Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - D Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Division of Oral & Craniofacial Health Sciences, School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - K Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA.,Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
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17
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Wojcik GL, Graff M, Nishimura KK, Tao R, Haessler J, Gignoux CR, Highland HM, Patel YM, Sorokin EP, Avery CL, Belbin GM, Bien SA, Cheng I, Cullina S, Hodonsky CJ, Hu Y, Huckins LM, Jeff J, Justice AE, Kocarnik JM, Lim U, Lin BM, Lu Y, Nelson SC, Park SSL, Poisner H, Preuss MH, Richard MA, Schurmann C, Setiawan VW, Sockell A, Vahi K, Verbanck M, Vishnu A, Walker RW, Young KL, Zubair N, Acuña-Alonso V, Ambite JL, Barnes KC, Boerwinkle E, Bottinger EP, Bustamante CD, Caberto C, Canizales-Quinteros S, Conomos MP, Deelman E, Do R, Doheny K, Fernández-Rhodes L, Fornage M, Hailu B, Heiss G, Henn BM, Hindorff LA, Jackson RD, Laurie CA, Laurie CC, Li Y, Lin DY, Moreno-Estrada A, Nadkarni G, Norman PJ, Pooler LC, Reiner AP, Romm J, Sabatti C, Sandoval K, Sheng X, Stahl EA, Stram DO, Thornton TA, Wassel CL, Wilkens LR, Winkler CA, Yoneyama S, Buyske S, Haiman CA, Kooperberg C, Le Marchand L, Loos RJF, Matise TC, North KE, Peters U, Kenny EE, Carlson CS. Genetic analyses of diverse populations improves discovery for complex traits. Nature 2019; 570:514-518. [PMID: 31217584 DOI: 10.1038/s41586-019-1310-4] [Citation(s) in RCA: 518] [Impact Index Per Article: 103.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1-3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4-10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States-where minority populations have a disproportionately higher burden of chronic conditions13-the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities.
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Affiliation(s)
- Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine K Nishimura
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey Haessler
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher R Gignoux
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.,Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yesha M Patel
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elena P Sorokin
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gillian M Belbin
- The Center for Genomic Health, 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
| | - Stephanie A Bien
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sinead Cullina
- The Center for Genomic Health, 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
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yao Hu
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Janina Jeff
- The Center for Genomic Health, 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
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan M Kocarnik
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Bridget M Lin
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yingchang Lu
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sung-Shim L Park
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hannah Poisner
- The Center for Genomic Health, 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
| | - Michael H Preuss
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa A Richard
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Hasso-Plattner-Institute for Digital Engineering, Digital Health Center, Potsdam, Germany.,Hasso-Plattner-Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Veronica W Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alexandra Sockell
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Karan Vahi
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Marie Verbanck
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abhishek Vishnu
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan W Walker
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Niha Zubair
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Jose Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Kathleen C Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Hasso-Plattner-Institute for Digital Engineering, Digital Health Center, Potsdam, Germany.,Hasso-Plattner-Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Christian Caberto
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ewa Deelman
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Ron Do
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimberly Doheny
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay Fernández-Rhodes
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Benyam Hailu
- NIH National Institute on Minority Health and Health Disparities, Bethesda, MD, USA
| | - Gerardo Heiss
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brenna M Henn
- Department of Anthropology, University of California Davis, Davis, CA, USA
| | | | - Rebecca D Jackson
- Center for Clinical and Translational Science, Ohio State Medical Center, Columbus, OH, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Yuqing Li
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Cancer Prevention Institute of California, Fremont, CA, USA
| | - Dan-Yu Lin
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Girish Nadkarni
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul J Norman
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Loreall C Pooler
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Jane Romm
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, MD, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), Irapuato, Mexico
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eli A Stahl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Cheryl A Winkler
- Basic Science Program, Frederick National Laboratory, Frederick, MD, USA
| | - Sachi Yoneyama
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steven Buyske
- Department of Statistics, Rutgers University, New Brunswick, NJ, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charles Kooperberg
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ulrike Peters
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eimear E Kenny
- The Center for Genomic Health, 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. .,Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Christopher S Carlson
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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18
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Lin BM, Nadkarni GN, Tao R, Graff M, Fornage M, Buyske S, Matise TC, Highland HM, Wilkens LR, Carlson CS, Park SL, Setiawan VW, Ambite JL, Heiss G, Boerwinkle E, Lin DY, Morris AP, Loos RJF, Kooperberg C, North KE, Wassel CL, Franceschini N. Genetics of Chronic Kidney Disease Stages Across Ancestries: The PAGE Study. Front Genet 2019; 10:494. [PMID: 31178898 PMCID: PMC6544117 DOI: 10.3389/fgene.2019.00494] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022] Open
Abstract
Background Chronic kidney disease (CKD) is common and disproportionally burdens United States ethnic minorities. Its genetic determinants may differ by disease severity and clinical stages. To uncover genetic factors associated CKD severity among high-risk ethnic groups, we performed genome-wide association studies (GWAS) in diverse populations within the Population Architecture using Genomics and Epidemiology (PAGE) study. Methods We assembled multi-ethnic genome-wide imputed data on CKD non-overlapping cases [4,150 mild to moderate CKD, 1,105 end-stage kidney disease (ESKD)] and non-CKD controls for up to 41,041 PAGE participants (African Americans, Hispanics/Latinos, East Asian, Native Hawaiian, and American Indians). We implemented a generalized estimating equation approach for GWAS using ancestry combined data while adjusting for age, sex, principal components, study, and ethnicity. Results The GWAS identified a novel genome-wide associated locus for mild to moderate CKD nearby NMT2 (rs10906850, p = 3.7 × 10-8) that replicated in the United Kingdom Biobank white British (p = 0.008). Several variants at the APOL1 locus were associated with ESKD including the APOL1 G1 rs73885319 (p = 1.2 × 10-9). There was no overlap among associated loci for CKD and ESKD traits, even at the previously reported APOL1 locus (p = 0.76 for CKD). Several additional loci were associated with CKD or ESKD at p-values below the genome-wide threshold. These loci were often driven by variants more common in non-European ancestry. Conclusion Our genetic study identified a novel association at NMT2 for CKD and showed for the first time strong associations of the APOL1 variants with ESKD across multi-ethnic populations. Our findings suggest differences in genetic effects across CKD severity and provide information for study design of genetic studies of CKD in diverse populations.
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Affiliation(s)
- Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Girish N Nadkarni
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, United States.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Myriam Fornage
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, United States
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, United States
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - S Lani Park
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - V Wendy Setiawan
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Jose Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, United States
| | - Gerardo Heiss
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Eric Boerwinkle
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Dan-Yu Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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19
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Chen YC, Tan GA, Lin BM, Khor C. Superior mesenteric arteriovenous fistula presenting 10 years after extensive small bowel resection. Aust N Z J Surg 2000; 70:822-3. [PMID: 11147448 DOI: 10.1046/j.1440-1622.2000.01960.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Y C Chen
- Department of Surgery, Changi General Hospital, Singapore
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