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Edmondson, A.C.* ; Braund, P.S.* ; Stylianou, I.M.* ; Khera, A.V.* ; Nelson, C.P.* ; Wolfe, M.L.* ; Derohannessian, S.L.* ; Keating, B.J.* ; Qu, L.* ; He, J.* ; Tobin, M.D.* ; Tomaszewski, M.* ; Baumert, J.J. ; Klopp, N. ; Döring, A. ; Thorand, B. ; Li, M.* ; Reilly, M.P.* ; Koenig, W.* ; Samani, N.J.* ; Rader, D.J.*

Dense genotyping of candidate gene loci identifies variants associated with high-density lipoprotein cholesterol.

Circ. Cardiovasc. Genet. 4, 145-155 (2011)

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BACKGROUND: Plasma levels of high-density lipoprotein cholesterol (HDL-C) are known to be heritable, but only a fraction of the heritability is explained. We used a high-density genotyping array containing single-nucleotide polymorphisms (SNPs) from HDL-C candidate genes selected on known biology of HDL-C metabolism, mouse genetic studies, and human genetic association studies. SNP selection was based on tagging SNPs and included low-frequency nonsynonymous SNPs. METHODS AND RESULTS: Association analysis in a cohort containing extremes of HDL-C (case-control, n=1733) provided a discovery phase, with replication in 3 additional populations for a total meta-analysis in 7857 individuals. We replicated the majority of loci identified through genome-wide association studies and present on the array (including ABCA1, APOA1/C3/A4/A5, APOB, APOE/C1/C2, CETP, CTCF-PRMT8, FADS1/2/3, GALNT2, LCAT, LILRA3, LIPC, LIPG, LPL, LRP4, SCARB1, TRIB1, ZNF664) and provide evidence that suggests an association in several previously unreported candidate gene loci (including ABCG1, GPR109A/B/81, NFKB1, PON1/2/3/4). There was evidence for multiple, independent association signals in 5 loci, including association with low-frequency nonsynonymous variants. CONCLUSIONS: Genetic loci associated with HDL-C are likely to harbor multiple, independent causative variants, frequently with opposite effects on the HDL-C phenotype. Cohorts comprising subjects at the extremes of the HDL-C distribution may be efficiently used in a case-control discovery of quantitative traits.

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