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Pankratz N, Wei P, Brody JA, Chen MH, de Vries PS, Huffman JE, Stimson MR, Auer PL, Boerwinkle E, Cushman M, de Maat MPM, Folsom AR, Franco OH, Gibbs RA, Haagenson KK, Hofman A, Johnsen JM, Kovar CL, Kraaij R, McKnight B, Metcalf GA, Muzny D, Psaty BM, Tang W, Uitterlinden AG, van Rooij JGJ, Dehghan A, O'Donnell CJ, Reiner AP, Morrison AC, Smith NL. Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors. Hum Mol Genet 2022; 31:3120-3132. [PMID: 35552711 PMCID: PMC9476613 DOI: 10.1093/hmg/ddac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/10/2021] [Revised: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 11/12/2022] Open
Abstract
Plasma levels of fibrinogen, coagulation factors VII and VIII and von Willebrand factor (vWF) are four intermediate phenotypes that are heritable and have been associated with the risk of clinical thrombotic events. To identify rare and low-frequency variants associated with these hemostatic factors, we conducted whole-exome sequencing in 10 860 individuals of European ancestry (EA) and 3529 African Americans (AAs) from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium and the National Heart, Lung and Blood Institute's Exome Sequencing Project. Gene-based tests demonstrated significant associations with rare variation (minor allele frequency < 5%) in fibrinogen gamma chain (FGG) (with fibrinogen, P = 9.1 × 10-13), coagulation factor VII (F7) (with factor VII, P = 1.3 × 10-72; seven novel variants) and VWF (with factor VIII and vWF; P = 3.2 × 10-14; one novel variant). These eight novel rare variant associations were independent of the known common variants at these loci and tended to have much larger effect sizes. In addition, one of the rare novel variants in F7 was significantly associated with an increased risk of venous thromboembolism in AAs (Ile200Ser; rs141219108; P = 4.2 × 10-5). After restricting gene-based analyses to only loss-of-function variants, a novel significant association was detected and replicated between factor VIII levels and a stop-gain mutation exclusive to AAs (rs3211938) in CD36 molecule (CD36). This variant has previously been linked to dyslipidemia but not with the levels of a hemostatic factor. These efforts represent the largest integration of whole-exome sequence data from two national projects to identify genetic variation associated with plasma hemostatic factors.
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Affiliation(s)
- Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Peng Wei
- 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
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, Framingham, MA, 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
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jennifer E Huffman
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Center for Population Genomics, MAVERIC, VA Boston Healthcare System, Boston, MA, USA
| | - Mary Rachel Stimson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 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
| | - Mary Cushman
- Departments of Medicine and Pathology, University of Vermont, Colchester, VT, USA
| | - Moniek P M de Maat
- Department of Hematology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Aaron R Folsom
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kelly K Haagenson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jill M Johnsen
- Research Institute Bloodworks, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 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
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Christopher J O'Donnell
- Framingham Heart Study, National Heart, Lung and Blood Institute, Framingham, MA, USA
- Cardiology Section, Department of Medicine, Boston Veterans Administration Healthcare, Harvard Medical School, Boston, MA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, 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
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle WA, USA
- Seattle Epidemiologic Research and Information Center, Veterans Administration Office of Research and Development, Seattle, WA, USA
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Tang W, Stimson MR, Basu S, Heckbert SR, Cushman M, Pankow JS, Folsom AR, Pankratz N. Burden of rare exome sequence variants in PROC gene is associated with venous thromboembolism: a population-based study. J Thromb Haemost 2020; 18:445-453. [PMID: 31680443 PMCID: PMC7787541 DOI: 10.1111/jth.14676] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 06/20/2019] [Revised: 10/13/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Rare coding mutations underlying deficiencies of antithrombin and proteins C and S contribute to familial venous thromboembolism (VTE). It is uncertain whether rare variants play a role in the etiology of VTE in the general population. OBJECTIVES We conducted a deep whole-exome sequencing (WES) study to investigate the associations between rare coding variants and the risk of VTE in two population-based prospective cohorts. PATIENTS/METHODS Whole-exome sequencing was performed in the Longitudinal Investigation of Thromboembolism Etiology (LITE), which combines the Atherosclerosis Risk in Communities (ARIC) study (316 incident VTE events among 3159 African Americans [AAs] and 458 incident VTEs among 7772 European Americans [EAs]) and the Cardiovascular Healthy Study (CHS; 60 incident VTEs among 1751 EAs). We performed gene-based tests of rare variants (allele frequency < 1%, exome-wide significance P < 1.47 × 10-6 ) separately in each study and ancestry group, and meta-analyzed the results for the EAs in ARIC and CHS. RESULTS In the meta-analysis of EAs, we identified one gene, PROC, in which the burden of rare, coding variants was significantly associated with increased risk of VTE (HR = 5.42 [3.11, 9.42] for carriers versus non-carriers, P = 2.27 × 10-9 ). In ARIC EAs, carriers of the PROC rare variants had on average 0.75 standard deviation (SD) lower concentrations of plasma protein C and 0.28 SD higher D-dimer (P < .05) than non-carriers. Adjustment for low protein C status did not eliminate the association of PROC burden with VTE. In AAs, rare coding PROC variants were not associated with VTE. CONCLUSIONS Rare coding variants in PROC contribute to increased VTE risk in EAs in this general population sample.
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Affiliation(s)
- Weihong Tang
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Mary Rachel Stimson
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, Washington, United States
| | - Mary Cushman
- Department of Pathology, University of Vermont, Burlington, Vermont, United States
| | - James S. Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Aaron R. Folsom
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
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