Loss-of-Function Mutations in APOC 3 , Triglycerides , and Coronary Disease

Background—Plasma triglyceride levels are heritable and are correlated with the risk of coronary heart disease. Sequencing of the protein-coding regions of the human genome (the exome) has the potential to identify rare mutations that have a large effect on phenotype. Methods—We sequenced the protein-coding regions of 18,666 genes in each of 3734 participants of European or African ancestry in the Exome Sequencing Project. We conducted tests to determine whether rare mutations in coding sequence, individually or in aggregate within a gene, were associated with plasma triglyceride levels. For mutations associated with triglyceride levels, we subsequently evaluated their association with the risk of coronary heart disease in 110,970 persons. Results—An aggregate of rare mutations in the gene encoding apolipoprotein C3 (APOC3) was associated with lower plasma triglyceride levels. Among the four mutations that drove this result, three were loss-of-function mutations: a nonsense mutation (R19X) and two splice-site mutations (IVS2+1G→A and IVS3+1G→T). The fourth was a missense mutation (A43T). Approximately 1 in 150 persons in the study was a heterozygous carrier of at least one of these four mutations. Triglyceride levels in the carriers were 39% lower than levels in noncarriers (P<1×10−20), and circulating levels of APOC3 in carriers were 46% lower than levels in noncarriers (P = 8×10−10). The risk of coronary heart disease among 498 carriers of any rare APOC3 mutation was 40% lower than the risk among 110,472 noncarriers (odds ratio, 0.60; 95% confidence interval, 0.47 to 0.75; P = 4×10−6). Conclusions—Rare mutations that disrupt APOC3 function were associated with lower levels of plasma triglycerides and APOC3. Carriers of these mutations were found to have a reduced risk of coronary heart disease. (Funded by the National Heart, Lung, and Blood Institute and others.) In observational studies, plasma triglyceride levels are associated with the risk of coronary heart disease.1,2 Heritability accounts for more than 50% of the individual variation in Copyright © 2014 Massachusetts Medical Society. Address reprint requests to: Dr. Sekar Kathiresan at the Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St., CPZN 5.252, Boston, MA 02114, or at skathiresan@partners.org. *The authors and members of the Triglycerides and High-Density Lipoprotein (TG and HDL) Working Group and their affiliations are listed in the Appendix. Ms. Jacy Crosby and Drs. Gina Peloso, Paul L. Auer, Alex P. Reiner, Eric Boerwinkle, and Sekar Kathiresan contributed equally to this article and assume responsibility for its content and integrity. The views expressed in this article are solely those of the authors and do not necessarily represent the official views of the National Heart, Lung, and Blood Institute (NHLBI) or the National Institutes of Health (NIH). Disclosure forms provided by the authors are available with the full text of this article at NEJM.org. NIH Public Access Author Manuscript N Engl J Med. Author manuscript; available in PMC 2015 January 03. Published in final edited form as: N Engl J Med. 2014 July 3; 371(1): 22–31. doi:10.1056/NEJMoa1307095. N IH -P A A uhor M anscript N IH -P A A uhor M anscript N IH -P A A uhor M anscript triglyceride levels.3 Genomewide association studies have identified common DNA sequence variants at more than 150 genetic loci that are related to plasma lipids4,5 and have suggested that plasma triglyceride-rich lipoproteins directly influence the risk of coronary heart disease.6 These findings lead to two unanswered questions: first, to what extent do rare DNA sequence variants, particularly those in protein-coding sequences, contribute to individual variation in plasma triglyceride levels and the risk of coronary heart disease at the population level, and second, are there specific genetic variants that might lower triglyceride levels and reduce the risk of coronary heart disease? Recent advances in DNA sequencing technology allow comprehensive detection of rare DNA sequence variants. When sequencing is performed in large populations, a sufficient number of mutation carriers can be identified to evaluate the correlation of genotype with phenotype. In particular, it is advantageous to focus sequencing on exons, the elements of the genome that code for proteins (collectively called the exome),7,8 since mutations in protein-coding sequences (e.g., missense, nonsense, or splice-site mutations) are most readily interpreted. To address the two questions posed above, we sequenced the exomes of 3734 persons in the United States, identified mutations, and tested the mutations for association with plasma triglyceride levels. We subsequently investigated whether the same mutations were related to the risk of clinical coronary heart disease.