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Yin X, Chan LS, Bose D, Jackson AU, VandeHaar P, Locke AE, Fuchsberger C, Stringham HM, Welch R, Yu K, Fernandes Silva L, Service SK, Zhang D, Hector EC, Young E, Ganel L, Das I, Abel H, Erdos MR, Bonnycastle LL, Kuusisto J, Stitziel NO, Hall IM, Wagner GR, Kang J, Morrison J, Burant CF, Collins FS, Ripatti S, Palotie A, Freimer NB, Mohlke KL, Scott LJ, Wen X, Fauman EB, Laakso M, Boehnke M. Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci. Nat Commun 2022; 13:1644. [PMID: 35347128 PMCID: PMC8960770 DOI: 10.1038/s41467-022-29143-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [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: 08/13/2021] [Accepted: 02/23/2022] [Indexed: 01/13/2023] Open
Abstract
Few studies have explored the impact of rare variants (minor allele frequency < 1%) on highly heritable plasma metabolites identified in metabolomic screens. The Finnish population provides an ideal opportunity for such explorations, given the multiple bottlenecks and expansions that have shaped its history, and the enrichment for many otherwise rare alleles that has resulted. Here, we report genetic associations for 1391 plasma metabolites in 6136 men from the late-settlement region of Finland. We identify 303 novel association signals, more than one third at variants rare or enriched in Finns. Many of these signals identify genes not previously implicated in metabolite genome-wide association studies and suggest mechanisms for diseases and disease-related traits.
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Affiliation(s)
- Xianyong Yin
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Lap Sum Chan
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Debraj Bose
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Anne U. Jackson
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Peter VandeHaar
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Adam E. Locke
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108 USA
| | - Christian Fuchsberger
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA ,grid.511439.bInstitute for Biomedicine, Eurac Research, Bolzano, 39100 Italy
| | - Heather M. Stringham
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Ryan Welch
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Ketian Yu
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Lilian Fernandes Silva
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70210 Finland
| | - Susan K. Service
- grid.19006.3e0000 0000 9632 6718Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90024 USA
| | - Daiwei Zhang
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA ,grid.25879.310000 0004 1936 8972Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Emily C. Hector
- grid.40803.3f0000 0001 2173 6074Department of Statistics, North Carolina State University, Raleigh, NC 27695 USA
| | - Erica Young
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108 USA ,grid.4367.60000 0001 2355 7002Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110 USA
| | - Liron Ganel
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108 USA
| | - Indraniel Das
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108 USA
| | - Haley Abel
- grid.4367.60000 0001 2355 7002Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Michael R. Erdos
- grid.94365.3d0000 0001 2297 5165Molecular Genetics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Lori L. Bonnycastle
- grid.94365.3d0000 0001 2297 5165Molecular Genetics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Johanna Kuusisto
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70210 Finland ,grid.410705.70000 0004 0628 207XCenter for Medicine and Clinical Research, Kuopio University Hospital, Kuopio, 70210 Finland
| | - Nathan O. Stitziel
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO 63108 USA ,grid.4367.60000 0001 2355 7002Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Department of Genetics, Washington University School of Medicine, St Louis, MO 63110 USA
| | - Ira M. Hall
- grid.47100.320000000419368710Center for Genomic Health, Department of Genetics, Yale University, New Haven, CT 06510 USA
| | - Gregory R. Wagner
- grid.429438.00000 0004 0402 1933Metabolon, Inc., Morrisville, NC 27560 USA
| | | | - Jian Kang
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Jean Morrison
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Charles F. Burant
- grid.214458.e0000000086837370Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Francis S. Collins
- grid.94365.3d0000 0001 2297 5165Molecular Genetics Section, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Samuli Ripatti
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Public Health, University of Helsinki, Helsinki, 00014 Finland ,grid.66859.340000 0004 0546 1623Broad Institute of MIT & Harvard, Cambridge, MA 02142 USA
| | - Aarno Palotie
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00290 Finland ,grid.7737.40000 0004 0410 2071Department of Public Health, University of Helsinki, Helsinki, 00014 Finland ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology, and Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Nelson B. Freimer
- grid.19006.3e0000 0000 9632 6718Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90024 USA
| | - Karen L. Mohlke
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Laura J. Scott
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Xiaoquan Wen
- grid.214458.e0000000086837370Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
| | - Eric B. Fauman
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139 USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, 70210, Finland.
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA.
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Ganel L, Chen L, Christ R, Vangipurapu J, Young E, Das I, Kanchi K, Larson D, Regier A, Abel H, Kang CJ, Scott A, Havulinna A, Chiang CWK, Service S, Freimer N, Palotie A, Ripatti S, Kuusisto J, Boehnke M, Laakso M, Locke A, Stitziel NO, Hall IM. Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences. Hum Genomics 2021; 15:34. [PMID: 34099068 PMCID: PMC8185936 DOI: 10.1186/s40246-021-00335-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 03/23/2021] [Accepted: 05/26/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a combination of the number of mitochondria per cell and cell-type composition. Here, we studied MT-CN variation in blood-derived DNA from 19184 Finnish individuals using a combination of genome (N = 4163) and exome sequencing (N = 19034) data as well as imputed genotypes (N = 17718). RESULTS We identified two loci significantly associated with MT-CN variation: a common variant at the MYB-HBS1L locus (P = 1.6 × 10-8), which has previously been associated with numerous hematological parameters; and a burden of rare variants in the TMBIM1 gene (P = 3.0 × 10-8), which has been reported to protect against non-alcoholic fatty liver disease. We also found that MT-CN is strongly associated with insulin levels (P = 2.0 × 10-21) and other metabolic syndrome (metS)-related traits. Using a Mendelian randomization framework, we show evidence that MT-CN measured in blood is causally related to insulin levels. We then applied an MT-CN polygenic risk score (PRS) derived from Finnish data to the UK Biobank, where the association between the PRS and metS traits was replicated. Adjusting for cell counts largely eliminated these signals, suggesting that MT-CN affects metS via cell-type composition. CONCLUSION These results suggest that measurements of MT-CN in blood-derived DNA partially reflect differences in cell-type composition and that these differences are causally linked to insulin and related traits.
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Affiliation(s)
- Liron Ganel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lei Chen
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryan Christ
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jagadish Vangipurapu
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Erica Young
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Indraniel Das
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Krishna Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - David 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
| | - Allison Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Haley Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandra Scott
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Aki Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Charleston W K Chiang
- 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 Service
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, 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
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Adam Locke
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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3
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Chen L, Abel HJ, Das I, Larson DE, Ganel L, Kanchi KL, Regier AA, Young EP, Kang CJ, Scott AJ, Chiang C, Wang X, Lu S, Christ R, Service SK, Chiang CWK, Havulinna AS, Kuusisto J, Boehnke M, Laakso M, Palotie A, Ripatti S, Freimer NB, Locke AE, Stitziel NO, Hall IM. Association of structural variation with cardiometabolic traits in Finns. Am J Hum Genet 2021; 108:583-596. [PMID: 33798444 PMCID: PMC8059371 DOI: 10.1016/j.ajhg.2021.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/03/2021] [Indexed: 02/08/2023] Open
Abstract
The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10-54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10-21) and alanine (p = 6.14 × 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.
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Affiliation(s)
- Lei Chen
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Haley J Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Indraniel Das
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - David E Larson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liron Ganel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Krishna L Kanchi
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erica P Young
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Alexandra J Scott
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Colby Chiang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xinxin Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ryan Christ
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, 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 90095, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Finnish Institute for Health and Welfare (THL), Helsinki 00271, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland; Department of Medicine, Kuopio University Hospital, Kuopio 70210, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland; Department of Medicine, Kuopio University Hospital, Kuopio 70210, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Analytical and Translational Genetics Unit (ATGU), Psychiatric & Neurodevelopmental Genetics Unit, Departments of Psychiatry and Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - 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 90095, USA
| | - Adam E Locke
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathan O Stitziel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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4
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Abstract
Summary Here we present SVScore, a tool for in silico structural variation (SV) impact prediction. SVScore aggregates per-base single nucleotide polymorphism (SNP) pathogenicity scores across relevant genomic intervals for each SV in a manner that considers variant type, gene features and positional uncertainty. We show that the allele frequency spectrum of high-scoring SVs is strongly skewed toward lower frequencies, suggesting that they are under purifying selection, and that SVScore identifies deleterious variants more effectively than alternative methods. Notably, our results also suggest that duplications are under surprisingly strong selection relative to deletions, and that there are a similar number of strongly pathogenic SVs and SNPs in the human population. Availability and Implementation SVScore is implemented in Perl and available freely at {{ http://www.github.com/lganel/SVScore }} for use under the MIT license. Contact ihall@wustl.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Liron Ganel
- McDonnell Genome Institute.,Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - Ira M Hall
- McDonnell Genome Institute.,Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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5
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Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L, Montgomery SB, Battle A, Conrad DF, Hall IM. The impact of structural variation on human gene expression. Nat Genet 2017; 49:692-699. [PMID: 28369037 PMCID: PMC5406250 DOI: 10.1038/ng.3834] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 03/13/2017] [Indexed: 12/31/2022]
Abstract
Structural variants (SVs) are an important source of human genetic diversity, but their contribution to traits, disease and gene regulation remains unclear. We mapped cis expression quantitative trait loci (eQTLs) in 13 tissues via joint analysis of SVs, single-nucleotide variants (SNVs) and short insertion/deletion (indel) variants from deep whole-genome sequencing (WGS). We estimated that SVs are causal at 3.5-6.8% of eQTLs-a substantially higher fraction than prior estimates-and that expression-altering SVs have larger effect sizes than do SNVs and indels. We identified 789 putative causal SVs predicted to directly alter gene expression: most (88.3%) were noncoding variants enriched at enhancers and other regulatory elements, and 52 were linked to genome-wide association study loci. We observed a notable abundance of rare high-impact SVs associated with aberrant expression of nearby genes. These results suggest that comprehensive WGS-based SV analyses will increase the power of common- and rare-variant association studies.
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Affiliation(s)
- Colby Chiang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandra J. Scott
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joe R. Davis
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily K. Tsang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Xin Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yungil Kim
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Tarik Hadzic
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Farhan N. Damani
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Liron Ganel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Stephen B. Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Donald F. Conrad
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ira M. Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
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