Genetics
Resequencing the entire CETP gene uncovers rare variants that independently affect HDL cholesterol in both whites and African blacks (Metabolism 2016)
Original title: Resequencing of the CETP gene in American whites and African blacks: Association of rare and common variants with HDL-cholesterol levels
This study resequenced the entire CETP gene, whose common variants are well documented for their effects on lipid levels and CETP mass/activity, to identify uncommon and rare variants and test their effects on plasma lipid traits, since these effects remained undefined. The gene and flanking regions were resequenced in 190 individuals (95 non-Hispanic whites, 95 African blacks) with extreme HDL-cholesterol levels, identifying 279 sequence variants, 25 of them novel. Selected variants were genotyped in 623 non-Hispanic whites and 788 African blacks, with 184 quality-controlled variants tested via gene-based, single-site, haplotype, and rare-variant (SKAT-O) association analyses. Two novel independent associations, rs1968905 and rs289740, were identified with HDL-cholesterol in African blacks, and rare variants (minor allele frequency below 0.01) were associated with HDL-cholesterol in both non-Hispanic whites (P=0.024) and African blacks (P=0.009).
Original abstract
Background: Cholesteryl ester transfer protein (CETP) plays a crucial role in lipid metabolism. Associations of common CETP variants with variation in plasma lipid levels, and/or CETP mass/activity have been extensively studied and well-documented; however, the effects of uncommon/rare CETP variants on plasma lipid profile remain undefined. Hence, resequencing of the gene in extreme phenotypes and follow-up rare-variant association analyses are essential to fill this gap.
Objective: To identify common and uncommon/rare variants in the CETP gene by resequencing the entire gene and test the effects of both common and uncommon/rare CETP variants on plasma lipid traits in two genetically distinct populations.
Methods And Results: The entire CETP gene plus flanking regions were resequenced in 190 individuals comprising 95 non-Hispanic whites (NHWs) and 95 African blacks with extreme HDL-C levels. A total of 279 sequence variants were identified, of which 25 were novel. Selected variants were genotyped in the entire samples of 623 NHWs and 788 African blacks and 184 QC-passed variants were tested in relation to plasma lipid traits by using gene-based, single-site, haplotype and rare variant association analyses (SKAT-O). Two novel and independent associations of rs1968905 and rs289740 with HDL-C were identified in African blacks. Using SKAT-O analysis, we also identified rare variants with minor allele frequency <0.01 to be associated with HDL-C in both NHWs (P=0.024) and African blacks (P=0.009).
Conclusions: Our results point out that in addition to the common CETP variants, rare genetic variants in the CETP gene also contribute to the phenotypic variation of HDL-C in the general population.
Summary written by cetpinhibition.org from the published abstract; figures as published. Page updated 19 August 2026. Methods.