Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks

Gina M. Peloso, Paul L. Auer, Joshua C. Bis, Arend Voorman, Alanna C. Morrison, Nathan O. Stitziel, Jennifer A. Brody, Sumeet A. Khetarpal, Jacy R. Crosby, Myriam Fornage, Aaron Isaacs, Johanna Jakobsdottir, Mary F. Feitosa, Gail Davies, Jennifer E. Huffman, Ani Manichaikul, Brian Davis, Kurt Lohman, Aron Y. Joon, Albert V. SmithMegan L. Grove, Paolo Zanoni, Valeska Redon, Serkalem Demissie, Kim Lawson, Ulrike Peters, Christopher Carlson, Rebecca D. Jackson, Kelli K. Ryckman, Rachel H. MacKey, Jennifer G. Robinson, David S. Siscovick, Pamela J. Schreiner, Josyf C. Mychaleckyj, James S. Pankow, Albert Hofman, Andre G. Uitterlinden, Tamara B. Harris, Kent D. Taylor, Jeanette M. Stafford, Lindsay M. Reynolds, Riccardo E. Marioni, Abbas Dehghan, Oscar H. Franco, Aniruddh P. Patel, Yingchang Lu, George Hindy, Omri Gottesman, Erwin P. Bottinger, Olle Melander, Marju Orho-Melander, Ruth J F Loos, Stefano Duga, Piera Angelica Merlini, Martin Farrall, Anuj Goel, Rosanna Asselta, Domenico Girelli, Nicola Martinelli, Svati H. Shah, William E. Kraus, Mingyao Li, Daniel J. Rader, Muredach P. Reilly, Ruth McPherson, Hugh Watkins, Diego Ardissino, Qunyuan Zhang, Judy Wang, Michael Y. Tsai, Herman A. Taylor, Adolfo Correa, Michael E. Griswold, Leslie A. Lange, John M. Starr, Igor Rudan, Gudny Eiriksdottir, Lenore J. Launer, Jose M. Ordovas, Daniel Levy, Y. D Ida Chen, Alexander P. Reiner, Caroline Hayward, Ozren Polasek, Ian J. Deary, Ingrid B. Borecki, Yongmei Liu, Vilmundur Gudnason, James G. Wilson, Cornelia M. Van Duijn, Charles Kooperberg, Stephen S. Rich, Bruce M. Psaty, Jerome I. Rotter, Christopher J. O'Donnell, Kenneth Rice, Eric Boerwinkle, Sekar Kathiresan, L. Adrienne Cupples

Research output: Contribution to journalArticlepeer-review

254 Scopus citations


Low-frequency coding DNA sequence variants in the proprotein convertase subtilisin/kexin type 9 gene (PCSK9) lower plasma low-density lipoprotein cholesterol (LDL-C), protect against risk of coronary heart disease (CHD), and have prompted the development of a new class of therapeutics. It is uncertain whether the PCSK9 example represents a paradigm or an isolated exception. We used the "Exome Array" to genotype >200,000 low-frequency and rare coding sequence variants across the genome in 56,538 individuals (42,208 European ancestry [EA] and 14,330 African ancestry [AA]) and tested these variants for association with LDL-C, high-density lipoprotein cholesterol (HDL-C), and triglycerides. Although we did not identify new genes associated with LDL-C, we did identify four low-frequency (frequencies between 0.1% and 2%) variants (ANGPTL8 rs145464906 [c.361C>T; p.Gln121-], PAFAH1B2 rs186808413 [c.482C>T; p.Ser161Leu], COL18A1 rs114139997 [c.331G>A; p.Gly111Arg], and PCSK7 rs142953140 [c.1511G>A; p.Arg504His]) with large effects on HDL-C and/or triglycerides. None of these four variants was associated with risk for CHD, suggesting that examples of low-frequency coding variants with robust effects on both lipids and CHD will be limited.

Original languageEnglish (US)
Pages (from-to)223-232
Number of pages10
JournalAmerican Journal of Human Genetics
Issue number2
StatePublished - Feb 6 2014

Bibliographical note

Funding Information:
The authors wish to acknowledge the support of the National Heart, Lung, and Blood Institute (NHLBI) and the contributions of the research institutions, study investigators, field staff, and study participants in creating this resource for biomedical research. Funding for GO ESP was provided by NHLBI grants RC2 HL-103010 (HeartGO), RC2 HL-102923 (LungGO), and RC2 HL-102924 (WHISP). The exome sequencing was performed through NHLBI grants RC2 HL-102925 (BroadGO) and RC2 HL-102926 (SeattleGO). Infrastructure for the CHARGE Consortium is supported, in part, by the National Heart, Lung, and Blood Institute (grant HL105756). G.M.P. is supported by award number T32HL007208 from the NHLBI. S.K. is supported by a Research Scholar award from the Massachusetts General Hospital (MGH), the Howard Goodman Fellowship from MGH, the Donovan Family Foundation, R01HL107816, and a grant from Fondation Leducq. Exome Array genotyping in case-control studies of coronary heart disease was supported by NIH RC2 HL-102925 and an investigator-initiated research grant from Merck to S.K. N.O.S. is supported, in part, by a career development award from the NIH/NHLBI K08-HL114642. A.D. is supported by NWO grant (veni, 916.12.154) and the EUR Fellowship. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NHLBI or NIH. A full listing of acknowledgements is provided in Supplemental Data .


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