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Abstract
Lipoprotein(a), Lp(a), is a modified low-density lipoprotein particle that contains apolipoprotein(a), encoded by LPA, and is a highly heritable, causal risk factor for cardiovascular diseases that varies in concentrations across ancestries. Here, we use deep-coverage whole genome sequencing in 8392 individuals of European and African ancestry to discover and interpret both single-nucleotide variants and copy number (CN) variation associated with Lp(a). We observe that genetic determinants between Europeans and Africans have several unique determinants. The common variant rs12740374 associated with Lp(a) cholesterol is an eQTL for SORT1 and independent of LDL cholesterol. Observed associations of aggregates of rare non-coding variants are largely explained by LPA structural variation, namely the LPA kringle IV 2 (KIV2)-CN. Finally, we find that LPA risk genotypes confer greater relative risk for incident atherosclerotic cardiovascular diseases compared to directly measured Lp(a), and are significantly associated with measures of subclinical atherosclerosis in African Americans.
Circulating lipoprotein(a) is an important risk factor for cardiovascular disease and shows variability between different ethnic groups. Here, Zekavat et al. perform whole-genome sequencing in individuals of European and African ancestries and find ancestry-specific genetic determinants for lipoprotein(a) levels.
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1 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); Yale School of Medicine, New Haven, USA (GRID:grid.47100.32) (ISNI:0000000419368710); Yale University, Department of Computational Biology & Bioinformatics, New Haven, USA (GRID:grid.47100.32) (ISNI:0000000419368710)
2 University of Helsinki, Institute for Molecular Medicine, Helsinki, Finland (GRID:grid.7737.4) (ISNI:0000 0004 0410 2071)
3 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, USA (GRID:grid.66859.34); Harvard Medical School, Department of Genetics, Boston, USA (GRID:grid.38142.3c) (ISNI:000000041936754X)
4 University of Tartu, Department of Biotechnology, Institute of Molecular and Cell Biology, Tartu, Estonia (GRID:grid.10939.32) (ISNI:0000 0001 0943 7661); Estonian Genome Center, Tallinn, Estonia (GRID:grid.10939.32)
5 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); Analytic and Translational Genetics Unit, Boston, USA (GRID:grid.32224.35) (ISNI:0000 0004 0386 9924)
6 University of California, Los Angeles, Department of Biological Chemistry, Los Angeles, USA (GRID:grid.19006.3e) (ISNI:0000 0000 9632 6718)
7 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34)
8 Boston University School of Public Health, Department of Biostatistics, Boston, USA (GRID:grid.189504.1) (ISNI:0000 0004 1936 7558)
9 University of Virginia, Center for Public Health Genomics, Charlottesville, USA (GRID:grid.27755.32) (ISNI:0000 0000 9136 933X)
10 University of Maryland School of Medicine, Program in Personalized and Genomic Medicine, Division of Endocrinology, Diabetes & Nutrition, Department of Medicine, Baltimore, USA (GRID:grid.411024.2) (ISNI:0000 0001 2175 4264)
11 University of Washington, Department of Biostatistics, School of Public Health and Community Medicine, Seattle, USA (GRID:grid.34477.33) (ISNI:0000000122986657)
12 University of Minnesota, Department of Laboratory Medicine and Pathology, Minneapolis, USA (GRID:grid.17635.36) (ISNI:0000000419368657)
13 Los Angeles Biomedical Research Institute, Division of Cardiology, Harbor-UCLA Medical Center, Los Angeles, USA (GRID:grid.19006.3e) (ISNI:0000 0000 9632 6718)
14 NHLBI Framingham Heart Study, Framingham, USA (GRID:grid.19006.3e); Boston university Schools of Medicine and Public health, Sections of Preventive medicine and Epidemiology, and cardiovascular medicine, Departments of Medicine and Epidemiology, Boston, USA (GRID:grid.189504.1) (ISNI:0000 0004 1936 7558)
15 Boston University School of Public Health, Department of Biostatistics, Boston, USA (GRID:grid.189504.1) (ISNI:0000 0004 1936 7558); NHLBI Framingham Heart Study, Framingham, USA (GRID:grid.189504.1)
16 Harbor-UCLA Medical Center, Departments of Pediatrics and Medicine, The Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, USA (GRID:grid.239844.0) (ISNI:0000 0001 0157 6501)
17 Johns Hopkins University School of Medicine, Division of Cardiology, Department of Medicine, Baltimore, USA (GRID:grid.21107.35) (ISNI:0000 0001 2171 9311)
18 University of Maryland School of Medicine, Department of Medicine, Baltimore, USA (GRID:grid.411024.2) (ISNI:0000 0001 2175 4264)
19 University of Mississippi Medical Center, Department of Medicine, Jackson, USA (GRID:grid.410721.1) (ISNI:0000 0004 1937 0407)
20 Estonian Genome Center, Tallinn, Estonia (GRID:grid.410721.1)
21 National Institute for Health and Welfare, Helsinki, Finland (GRID:grid.14758.3f) (ISNI:0000 0001 1013 0499)
22 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Lab, Cambridge, USA (GRID:grid.116068.8) (ISNI:0000 0001 2341 2786)
23 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, USA (GRID:grid.66859.34); Analytic and Translational Genetics Unit, Boston, USA (GRID:grid.32224.35) (ISNI:0000 0004 0386 9924)
24 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); Estonian Genome Center, Tallinn, Estonia (GRID:grid.66859.34)
25 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); University of Helsinki, Institute for Molecular Medicine, Helsinki, Finland (GRID:grid.7737.4) (ISNI:0000 0004 0410 2071); University of Helsinki, Department of Public Health, Faculty of Medicine, Helsinki, Finland (GRID:grid.7737.4) (ISNI:0000 0004 0410 2071)
26 Broad Institute of MIT and Harvard, Program in Medical and Population Genetics, Cambridge, USA (GRID:grid.66859.34); Harvard Medical School, Department of Medicine, Boston, USA (GRID:grid.38142.3c) (ISNI:000000041936754X); Massachusetts General Hospital, Center for Genomic Medicine, Boston, USA (GRID:grid.32224.35) (ISNI:0000 0004 0386 9924); Massachusetts General Hospital, Cardiovascular Research Center, Boston, USA (GRID:grid.32224.35) (ISNI:0000 0004 0386 9924)
27 New York Genome Center, New York, USA (GRID:grid.429884.b)
28 University of Michigan, Ann Arbor, USA (GRID:grid.214458.e) (ISNI:0000000086837370)
29 Massachusetts General Hospital, Boston, USA (GRID:grid.32224.35) (ISNI:0000 0004 0386 9924)
30 Wake Forest Baptist Health, Winston-Salem, USA (GRID:grid.412860.9) (ISNI:0000 0004 0459 1231)
31 University of Pennsylvania, Children’s Hospital of Philadelphia, Philadelphia, USA (GRID:grid.25879.31) (ISNI:0000 0004 1936 8972); University of Pennsylvania, Philadelphia, USA (GRID:grid.25879.31) (ISNI:0000 0004 1936 8972)
32 Emory University, Atlanta, USA (GRID:grid.189967.8) (ISNI:0000 0001 0941 6502)
33 University of Maryland, Baltimore, USA (GRID:grid.411024.2) (ISNI:0000 0001 2175 4264)
34 University of Washington, Seattle, USA (GRID:grid.34477.33) (ISNI:0000000122986657)
35 University of Mississippi, Jackson, USA (GRID:grid.251313.7) (ISNI:0000 0001 2169 2489)
36 National Institutes of Health, Bethesda, USA (GRID:grid.94365.3d) (ISNI:0000 0001 2297 5165)
37 Johns Hopkins University, Baltimore, USA (GRID:grid.21107.35) (ISNI:0000 0001 2171 9311)
38 University of Kentucky, Lexington, USA (GRID:grid.266539.d) (ISNI:0000 0004 1936 8438)
39 Duke University, Durham, USA (GRID:grid.26009.3d) (ISNI:0000 0004 1936 7961)
40 University of Alabama, Birmingham, USA (GRID:grid.265892.2) (ISNI:0000000106344187)
41 Stanford University, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956)
42 University of Wisconsin Milwaukee, Milwaukee, USA (GRID:grid.267468.9) (ISNI:0000 0001 0695 7223)
43 Cleveland Clinic, Cleveland, USA (GRID:grid.239578.2) (ISNI:0000 0001 0675 4725)
44 University of Colorado, Denver, USA (GRID:grid.241116.1) (ISNI:0000000107903411)
45 Columbia University, New York, USA (GRID:grid.21729.3f) (ISNI:0000000419368729)
46 Boston University, Boston, USA (GRID:grid.189504.1) (ISNI:0000 0004 1936 7558); Massachusetts General Hospital, Boston, USA (GRID:grid.32224.35) (ISNI:0000 0004 0386 9924)
47 Fundação de Hematologia e Hemoterapia de Pernambuco - Hemope, Recife, Brazil (GRID:grid.32224.35)
48 University of Texas Rio Grande Valley School of Medicine, Brownsville, USA (GRID:grid.449717.8) (ISNI:0000 0004 5374 269X)
49 University of Texas Health, Houston, USA (GRID:grid.267308.8) (ISNI:0000 0000 9206 2401)
50 National Jewish Health, Denver, USA (GRID:grid.240341.0) (ISNI:0000 0004 0396 0728)
51 Medical College of Wisconsin, Milwaukee, USA (GRID:grid.30760.32) (ISNI:0000 0001 2111 8460)
52 University of California, San Francisco, San Francisco, USA (GRID:grid.266102.1) (ISNI:0000 0001 2297 6811)
53 Women’s Health Initiative, Seattle, USA (GRID:grid.453840.e)
54 University of California, Los Angeles, Los Angeles, USA (GRID:grid.19006.3e) (ISNI:0000 0000 9632 6718)
55 Brigham & Women’s Hospital, Boston, USA (GRID:grid.62560.37) (ISNI:0000 0004 0378 8294)
56 University of Virginia, Charlottesville, USA (GRID:grid.27755.32) (ISNI:0000 0000 9136 933X)
57 Los Angeles Biomedical Research Institute, Los Angeles, USA (GRID:grid.19006.3e) (ISNI:0000 0000 9632 6718)
58 The Broad Institute, Cambridge, USA (GRID:grid.66859.34)
59 National Taiwan University, Taipei, Taiwan (GRID:grid.19188.39) (ISNI:0000 0004 0546 0241)
60 University of Vermont, Burlington, USA (GRID:grid.59062.38) (ISNI:0000 0004 1936 7689)
61 Blood Systems Research Institute UCSF, San Francisco, USA (GRID:grid.280902.1) (ISNI:0000 0004 0395 6091)
62 University of Illinois at Chicago, Chicago, USA (GRID:grid.185648.6) (ISNI:0000 0001 2175 0319)
63 Mayo Clinic, Rochester, USA (GRID:grid.66875.3a) (ISNI:0000 0004 0459 167X)
64 Vanderbilt University, Nashville, USA (GRID:grid.152326.1) (ISNI:0000 0001 2264 7217)
65 University of Cincinnati, Cincinnati, USA (GRID:grid.24827.3b) (ISNI:0000 0001 2179 9593)
66 Icahn School of Medicine at Mount Sinai, New York, USA (GRID:grid.59734.3c) (ISNI:0000 0001 0670 2351)
67 University of North Carolina, Chapel Hill, USA (GRID:grid.410711.2) (ISNI:0000 0001 1034 1720)
68 University of Texas Rio Grande Valley School of Medicine, Edinburg, USA (GRID:grid.449717.8) (ISNI:0000 0004 5374 269X)
69 Washington University in St Louis, St Louis, USA (GRID:grid.4367.6) (ISNI:0000 0001 2355 7002)
70 Brown University, Providence, USA (GRID:grid.40263.33) (ISNI:0000 0004 1936 9094)
71 Fred Hutchinson Cancer Research Center, Seattle, USA (GRID:grid.270240.3) (ISNI:0000 0001 2180 1622)
72 University of Pittsburgh, Pittsburgh, USA (GRID:grid.21925.3d) (ISNI:0000 0004 1936 9000)
73 Yale University, New Haven, USA (GRID:grid.47100.32) (ISNI:0000000419368710)
74 University of Texas Rio Grande Valley School of Medicine, San Antonio, USA (GRID:grid.215352.2) (ISNI:0000000121845633)
75 Fred Hutchinson Cancer Research Center, Seattle, USA (GRID:grid.270240.3) (ISNI:0000 0001 2180 1622); Women’s Health Initiative, Seattle, USA (GRID:grid.453840.e)
76 Tulane University, New Orleans, USA (GRID:grid.265219.b) (ISNI:0000 0001 2217 8588)
77 University of Iowa, Iowa City, USA (GRID:grid.214572.7) (ISNI:0000 0004 1936 8294)
78 National Health Research Institute Taiwan, Zhunan Township, Taiwan (GRID:grid.59784.37) (ISNI:0000000406229172)
79 Blood Works Northwest, Seattle, USA (GRID:grid.59784.37)
80 Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan (GRID:grid.410764.0) (ISNI:0000 0004 0573 0731)
81 Ohio State University Wexner Medical Center, Columbus, USA (GRID:grid.412332.5) (ISNI:0000 0001 1545 0811)
82 Blood Works Northwest, Seattle, USA (GRID:grid.214458.e); University of Washington, Seattle, USA (GRID:grid.34477.33) (ISNI:0000000122986657)
83 NIH National Heart, Lung, and Blood Institute, Bethesda, USA (GRID:grid.279885.9) (ISNI:0000 0001 2293 4638)
84 Albert Einstein College of Medicine, New York, USA (GRID:grid.251993.5) (ISNI:0000000121791997)
85 Blood Works Northwest, Seattle, USA (GRID:grid.241116.1)
86 Loyola University, Maywood, USA (GRID:grid.164971.c) (ISNI:0000 0001 1089 6558)
87 Harvard School of Public Health, Boston, USA (GRID:grid.38142.3c) (ISNI:000000041936754X)
88 Boston University, Boston, USA (GRID:grid.189504.1) (ISNI:0000 0004 1936 7558)
89 Brown University, Providence, USA (GRID:grid.40263.33) (ISNI:0000 0004 1936 9094); Women’s Health Initiative, Seattle, USA (GRID:grid.453840.e)
90 George Washington University, Washington, USA (GRID:grid.253615.6) (ISNI:0000 0004 1936 9510)
91 Harvard University, Cambridge, USA (GRID:grid.38142.3c) (ISNI:000000041936754X)
92 University of Arizona, Tucson, USA (GRID:grid.134563.6) (ISNI:0000 0001 2168 186X)
93 Howard University, Washington, USA (GRID:grid.257127.4) (ISNI:0000 0001 0547 4545)
94 University at Buffalo, Buffalo, USA (GRID:grid.273335.3) (ISNI:0000 0004 1936 9887)
95 University of Minnesota, Minneapolis, USA (GRID:grid.17635.36) (ISNI:0000000419368657)
96 Fred Hutchinson Cancer Research Center, Seattle, USA (GRID:grid.270240.3) (ISNI:0000 0001 2180 1622); University of Washington, Seattle, USA (GRID:grid.34477.33) (ISNI:0000000122986657)
97 Northwestern University, Chicago, USA (GRID:grid.16753.36) (ISNI:0000 0001 2299 3507)
98 Harvard Medical School, Boston, USA (GRID:grid.38142.3c) (ISNI:000000041936754X)
99 Baylor College of Medicine, Houston, USA (GRID:grid.39382.33) (ISNI:0000 0001 2160 926X)
100 UMass Memorial Medical Center, Worcester, USA (GRID:grid.416999.a) (ISNI:0000 0004 0591 6261)
101 Baylor College of Medicine, Ann Arbor, USA (GRID:grid.39382.33) (ISNI:0000 0001 2160 926X)
102 University of Minnesota, Minneapolis, USA (GRID:grid.17635.36) (ISNI:0000000419368657); University of Colorado at Boulder, Boulder, USA (GRID:grid.266190.a) (ISNI:0000000096214564)
103 Henry Ford Health System, Detroit, USA (GRID:grid.239864.2) (ISNI:0000 0000 8523 7701)