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Locke AE, Steinberg KM, Chiang CWK, Service SK, Havulinna AS, Stell L, Pirinen M, Abel HJ, Chiang CC, Fulton RS, Jackson AU, Kang CJ, Kanchi KL, Koboldt DC, Larson DE, Nelson J, Nicholas TJ, Pietilä A, Ramensky V, Ray D, Scott LJ, Stringham HM, Vangipurapu J, Welch R, Yajnik P, Yin X, Eriksson JG, Ala-Korpela M, Järvelin MR, Männikkö M, Laivuori H, Dutcher SK, Stitziel NO, Wilson RK, Hall IM, Sabatti C, Palotie A, Salomaa V, Laakso M, Ripatti S, Boehnke M, Freimer NB. Exome sequencing of Finnish isolates enhances rare-variant association power. Nature 2019; 572:323-328. [PMID: 31367044 PMCID: PMC6697530 DOI: 10.1038/s41586-019-1457-z] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 07/02/2019] [Indexed: 12/30/2022]
Abstract
Exome-sequencing studies have generally been underpowered to identify deleterious alleles with a large effect on complex traits as such alleles are mostly rare. Because the population of northern and eastern Finland has expanded considerably and in isolation following a series of bottlenecks, individuals of these populations have numerous deleterious alleles at a relatively high frequency. Here, using exome sequencing of nearly 20,000 individuals from these regions, we investigate the role of rare coding variants in clinically relevant quantitative cardiometabolic traits. Exome-wide association studies for 64 quantitative traits identified 26 newly associated deleterious alleles. Of these 26 alleles, 19 are either unique to or more than 20 times more frequent in Finnish individuals than in other Europeans and show geographical clustering comparable to Mendelian disease mutations that are characteristic of the Finnish population. We estimate that sequencing studies of populations without this unique history would require hundreds of thousands to millions of participants to achieve comparable association power.
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Affiliation(s)
- Adam E Locke
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Karyn Meltz Steinberg
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Charleston W K Chiang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Susan K Service
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Laurel Stell
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Helsinki Institute for Information Technology HIIT and Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Haley J Abel
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Colby C Chiang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Krishna L Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel C Koboldt
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Joanne Nelson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas J Nicholas
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- USTAR Center for Genetic Discovery and Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Arto Pietilä
- National Institute for Health and Welfare, Helsinki, Finland
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
- Federal State Institution "National Medical Research Center for Preventive Medicine" of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Debashree Ray
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Departments of Epidemiology and Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Ryan Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pranav Yajnik
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Johan G Eriksson
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mika Ala-Korpela
- Systems Epidemiology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, The Alfred Hospital, Monash University, Melbourne, Victoria, Australia
| | - Marjo-Riitta Järvelin
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Northern Finland Birth Cohorts, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital and University of Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Susan K Dutcher
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ira M Hall
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Analytical and Translational Genetics Unit (ATGU), Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
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Tsai EA, Gilbert MA, Grochowski CM, Underkoffler LA, Meng H, Zhang X, Wang MM, Shitaye H, Hankenson KD, Piccoli D, Lin H, Kamath BM, Devoto M, Spinner NB, Loomes KM. THBS2 Is a Candidate Modifier of Liver Disease Severity in Alagille Syndrome. Cell Mol Gastroenterol Hepatol 2016; 2:663-675.e2. [PMID: 28090565 PMCID: PMC5042888 DOI: 10.1016/j.jcmgh.2016.05.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/17/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Alagille syndrome is an autosomal-dominant, multisystem disorder caused primarily by mutations in JAG1, resulting in bile duct paucity, cholestasis, cardiac disease, and other features. Liver disease severity in Alagille syndrome is highly variable, however, factors influencing the hepatic phenotype are unknown. We hypothesized that genetic modifiers may contribute to the variable expressivity of this disorder. METHODS We performed a genome-wide association study in a cohort of Caucasian subjects with known pathogenic JAG1 mutations, comparing patients with mild vs severe liver disease, followed by functional characterization of a candidate locus. RESULTS We identified a locus that reached suggestive genome-level significance upstream of the thrombospondin 2 (THBS2) gene. THBS2 codes for a secreted matricellular protein that regulates cell proliferation, apoptosis, and angiogenesis, and has been shown to affect Notch signaling. By using a reporter mouse line, we detected thrombospondin 2 expression in bile ducts and periportal regions of the mouse liver. Examination of Thbs2-null mouse livers showed increased microvessels in the portal regions of adult mice. We also showed that thrombospondin 2 interacts with NOTCH1 and NOTCH2 and can inhibit JAG1-NOTCH2 interactions. CONCLUSIONS Based on the genome-wide association study results, thrombospondin 2 localization within bile ducts, and demonstration of interactions of thrombospondin 2 with JAG1 and NOTCH2, we propose that changes in thrombospondin 2 expression may further perturb JAG1-NOTCH2 signaling in patients harboring a JAG1 mutation and lead to a more severe liver phenotype. These results implicate THBS2 as a plausible candidate genetic modifier of liver disease severity in Alagille syndrome.
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Key Words
- ALGS, Alagille syndrome
- BSA, bovine serum albumin
- CK19, cytokeratin 19
- ChiLDReN, Childhood Liver Disease Research Network
- Cholestasis
- GFP, green fluorescent protein
- GWAS, genome-wide association study
- Gene Modifier
- Genome-Wide Association Study
- JAG1
- NOTCH2
- PCR, polymerase chain reaction
- SNP, single-nucleotide polymorphism
- THBS2, thrombospondin 2
- cDNA, complementary DNA
- ddPCR, droplet digital polymerase chain reaction
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Affiliation(s)
- Ellen A Tsai
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania; Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Melissa A Gilbert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christopher M Grochowski
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lara A Underkoffler
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - He Meng
- Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Xiaojie Zhang
- Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Michael M Wang
- Department of Neurology, University of Michigan, Ann Arbor, Michigan; Department of Physiology, University of Michigan, Ann Arbor, Michigan; VA Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Hailu Shitaye
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan
| | - Kurt D Hankenson
- Department of Physiology, Department of Small Animal Clinical Sciences, Colleges of Natural Science, Osteopathic Medicine, and Veterinary Medicine, Michigan State University, East Lansing, Michigan; Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Piccoli
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Henry Lin
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Binita M Kamath
- Division of Gastroenterology, Hepatology, and Nutrition, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Marcella Devoto
- Division of Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Nancy B Spinner
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathleen M Loomes
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
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