Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction

Abstract

Myocardial infarction (MI), a leading cause of death around the world, displays a complex pattern of inheritance. When MI occurs early in life, genetic inheritance is a major component to risk. Previously, rare mutations in low-density lipoprotein (LDL) genes have been shown to contribute to MI risk in individual families, whereas common variants at more than 45 loci have been associated with MI risk in the population. Here we evaluate how rare mutations contribute to early-onset MI risk in the population. We sequenced the protein-coding regions of 9,793 genomes from patients with MI at an early age (≤50 years in males and ≤60 years in females) along with MI-free controls. We identified two genes in which rare coding-sequence mutations were more frequent in MI cases versus controls at exome-wide significance. At low-density lipoprotein receptor (LDLR), carriers of rare non-synonymous mutations were at 4.2-fold increased risk for MI; carriers of null alleles at LDLR were at even higher risk (13-fold difference). Approximately 2% of early MI cases harbour a rare, damaging mutation in LDLR; this estimate is similar to one made more than 40 years ago using an analysis of total cholesterol. Among controls, about 1 in 217 carried an LDLR coding-sequence mutation and had plasma LDL cholesterol > 190 mg dl(-1). At apolipoprotein A-V (APOA5), carriers of rare non-synonymous mutations were at 2.2-fold increased risk for MI. When compared with non-carriers, LDLR mutation carriers had higher plasma LDL cholesterol, whereas APOA5 mutation carriers had higher plasma triglycerides. Recent evidence has connected MI risk with coding-sequence mutations at two genes functionally related to APOA5, namely lipoprotein lipase and apolipoprotein C-III (refs 18, 19). Combined, these observations suggest that, as well as LDL cholesterol, disordered metabolism of triglyceride-rich lipoproteins contributes to MI risk.

Figure 1. Overall design for the Early-Onset Myocardial Infarction Study within the U.S. National Heart, Lung, and Blood Institute’s Exome Sequencing Project

Whole exome sequencing was performed in 1,973 individuals from the phenotypic extremes. To test the hypothesis that low-frequency variants confer risk for myocardial infarction (MI), we performed follow-up statistical imputation and array-based genotyping of single nucleotide variants. To test the hypothesis that a burden of rare mutations in a gene confers risk for MI, we performed targeted re-sequencing and additional exome sequencing.

Figure 2. Apolipoprotein A-V (APOA5) mutations discovered after sequencing of 13,432 individuals

Individual mutations (non-synonymous, indel frameshift and splice-site variants with minor allele frequency less than 1%) are depicted according to genomic position along the length of the APOA5 gene starting at the 5′ end (top). The number of circles on the left and right represents the number of times that mutation is observed in cases or controls, respectively. Dashed lines across the gene connect the same mutation seen in cases and controls. Mutations are shaded in red, blue, or yellow if observed in cases only, controls only, or both cases and controls, respectively.

Figure 3. Low-density lipoprotein receptor (LDLR) mutations discovered after sequencing 9,793 individuals

A. Individual disruptive mutations (nonsense, indel frameshift, and splice-site variants with minor allele frequency less than 1%) are depicted according to genomic position along the length of the LDLR gene starting at the 5′ end (top). The number of circles on the left and right represents the number of times that mutation is observed in cases or controls, respectively. Mutations are shaded in red or blue, if observed in cases only or controls only, respectively. B. Low-density lipoprotein cholesterol level as a function of LDLR gene mutation annotation. Mean (height of bar) and 95 % confidence intervals (error bars) are shown. Each individual is categorized based on mutation annotation as follows. Non-Carriers: carriers without a missense or disruptive mutation; “Deleterious (PolyPhen)” as defined by nonsense, splice-site, indel frameshift, and missense annotated as “possibly damaging” or “probably damaging” by PolyPhen-2 HumDiv software; “Deleterious (Broad)” as defined by nonsense, splice-site, indel frameshift, and missense annotated as deleterious by at least one of five protein prediction algorithms (LRT score, MutationTaster, PolyPhen-2 HumDiv, PolyPhen-2 HumVar and SIFT); “Deleterious (Strict)” as defined by nonsense, splice-site, indel frameshift, and missense annotated as deleterious by all five of the above protein prediction algorithms; Disruptive: carriers of mutations that are nonsense, indel frameshift, or splice-site.