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Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP. Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. Nat Commun 2022; 13:7592. [PMID: 36481753 PMCID: PMC9732337 DOI: 10.1038/s41467-022-35354-7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.
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Affiliation(s)
- Marsha M. Wheeler
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98105 USA
| | - Adrienne M. Stilp
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Shuquan Rao
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA ,grid.506261.60000 0001 0706 7839State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020 China
| | - Bjarni V. Halldórsson
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.9580.40000 0004 0643 5232School of Technology, Reykjavik University, Reykjavík, Iceland
| | - Doruk Beyter
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Jia Wen
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Anna V. Mihkaylova
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Caitlin P. McHugh
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - John Lane
- grid.17635.360000000419368657Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Min-Zhi Jiang
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Laura M. Raffield
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Goo Jun
- grid.267308.80000 0000 9206 2401Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Fritz J. Sedlazeck
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Ginger Metcalf
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Yao Yao
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Joshua B. Bis
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Nathalie Chami
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Paul S. de Vries
- grid.267308.80000 0000 9206 2401Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA ,grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Pinkal Desai
- grid.5386.8000000041936877XDivision of Hematology and Oncology, Weill Cornell Medical College, New York, NY 10065 USA
| | - James S. Floyd
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Yan Gao
- grid.251313.70000 0001 2169 2489Jackson Heart Study, Department of Medicine, University of Mississippi, Jackson, MS 39216 USA
| | - Kai Kammers
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Wonji Kim
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 2115 USA
| | - Jee-Young Moon
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Aakrosh Ratan
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Lisa R. Yanek
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Laura Almasy
- grid.25879.310000 0004 1936 8972Children’s Hospital of Philadelphia and University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
| | - Lewis C. Becker
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - John Blangero
- grid.449717.80000 0004 5374 269XDepartment of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Michael H. Cho
- grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 2115 USA
| | - Joanne E. Curran
- grid.449717.80000 0004 5374 269XDepartment of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520 USA
| | - Myriam Fornage
- grid.267308.80000 0000 9206 2401Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Robert C. Kaplan
- grid.251993.50000000121791997Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Joshua P. Lewis
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ruth J. F. Loos
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,grid.59734.3c0000 0001 0670 2351Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Braxton D. Mitchell
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD USA
| | - Alanna C. Morrison
- grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Michael Preuss
- grid.59734.3c0000 0001 0670 2351The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Bruce M. Psaty
- grid.34477.330000000122986657Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101 USA
| | - Stephen S. Rich
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA 22908 USA
| | - Jerome I. Rotter
- grid.513199.6The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Hua Tang
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Russell P. Tracy
- grid.59062.380000 0004 1936 7689Departments of Pathology & Laboratory Medicine and Biochemistry, Larner College of Medicine at the University of Vermont, Colchester, VT 5446 USA
| | - Eric Boerwinkle
- grid.267308.80000 0000 9206 2401Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Goncalo R. Abecasis
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Thomas W. Blackwell
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Albert V. Smith
- grid.214458.e0000000086837370TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109 USA
| | - Andrew D. Johnson
- grid.279885.90000 0001 2293 4638Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA 1702 USA
| | - Rasika A. Mathias
- grid.21107.350000 0001 2171 9311GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Deborah A. Nickerson
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98105 USA
| | - Matthew P. Conomos
- grid.34477.330000000122986657Department of Biostatistics, University of Washington, Seattle, WA 98105 USA
| | - Yun Li
- grid.10698.360000000122483208Departments of Biostatistics, Genetics, Computer Science, Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Unnur Þorsteinsdóttir
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Magnús K. Magnússon
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Kari Stefansson
- grid.421812.c0000 0004 0618 6889deCODE genetics/Amgen Inc., Reykjavik, Iceland ,grid.14013.370000 0004 0640 0021Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Nathan D. Pankratz
- grid.17635.360000000419368657Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455 USA
| | - Daniel E. Bauer
- grid.2515.30000 0004 0378 8438Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115 USA ,grid.511171.2Harvard Stem Cell Institute, Boston, MA 02138 USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 USA
| | - Paul L. Auer
- grid.30760.320000 0001 2111 8460Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226 USA
| | - Alex P. Reiner
- grid.34477.330000000122986657Department of Epidemiology, University of Washington, Seattle, WA 98105 USA
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