Abstract 11298: Absence of Rare Coding Sequence Variants of Large Effect in GWAS Loci for High-Density Lipoprotein Cholesterol
Background: Common non-coding DNA sequence variants at 47 genomic regions have been associated with plasma high-density lipoprotein cholesterol (HDL-C) in a recently published genome-wide association study (GWAS). Here, we test the hypothesis that rare coding sequence variants at these loci confer a large effect on plasma HDL-C.
Methods: We performed targeted sequencing of 4,118 exons from 407 genes within 300 kilobases of 47 loci recently mapped for HDL-C. We selected exons using customized hybrid capture (Agilent) and used next-generation sequencing technology (Illumina). We sequenced exons in participants with extremely high HDL-C (n=385, mean 101.8 mg/dL) or extremely low HDL-C (n=334, mean 31.6 mg/dL). To replicate identified variants, we genotyped using the Exome Array (Illumina HumanExome BeadChip) in independent participants with extremely high (n=514) and low HDL-C (n=580). In the discovery and replication samples, we tested whether rare coding sequence variants, individually or aggregated within a gene, were associated with plasma HDL-C.
Results: Across the discovery sequencing, we identified 8,714 missense, nonsense, or splice site DNA sequence variants. Of these, 8,138 were rare (defined as minor allele frequency < 5%). The rare, nonsense variant with the strongest association evidence was in the PPP1R15A gene (0.4% frequency, OR for high HDL-C of 9.81, P= 0.04). The rare, missense or splice-site variant with the strongest association evidence was in the CETP gene (3.3% frequency, OR for high HDL-C of 0.23, P=1.0 x 10-5). Across discovery and replication, 3 variants associated with HDL-C after accounting for the 33 variants tested (threshold P<1.5 x 10-3). Of these, none were novel. In analyses where all rare variants within each gene are collapsed, only CETP (P=2.0 x 10-6) had a significant association signal after accounting for the number of genes tested (threshold P<1.2 x 10-4).
Conclusions: After sequencing genes from GWAS loci in participants with very extreme HDL-C, we did not identify any new rare coding sequence variants with a strong effect on HDL-C. These results provide insight regarding the design of similar sequencing studies for cardiovascular traits with respect to sample size, follow-up, and analysis methodology.
- © 2013 by American Heart Association, Inc.