Fine mapping the CETP region reveals a common intronic insertion associated to HDL-C

Individuals with exceptional longevity and their offspring have significantly larger high-density lipoprotein concentrations (HDL-C) particle sizes due to the increased homozygosity for the I405V variant in the cholesteryl ester transfer protein (CETP) gene. In this study, we investigate the association of CETP and HDL-C further to identify novel, independent CETP variants associated with HDL-C in humans. We performed a meta-analysis of HDL-C within the CETP region using 59,432 individuals imputed with 1000 Genomes data. We performed replication in an independent sample of 47,866 individuals and validation was done by Sanger sequencing. The meta-analysis of HDL-C within the CETP region identified five independent variants, including an exonic variant and a common intronic insertion. We replicated these 5 variants significantly in an independent sample of 47,866 individuals. Sanger sequencing of the insertion within a single family confirmed segregation of this variant. The strongest reported association between HDL-C and CETP variants, was rs3764261; however, after conditioning on the five novel variants we identified the support for rs3764261 was highly reduced (βunadjusted=3.179 mg/dl (P value=5.25×10−509), βadjusted=0.859 mg/dl (P value=9.51×10−25)), and this finding suggests that these five novel variants may partly explain the association of CETP with HDL-C. Indeed, three of the five novel variants (rs34065661, rs5817082, rs7499892) are independent of rs3764261. The causal variants in CETP that account for the association with HDL-C remain unknown. We used studies imputed to the 1000 Genomes reference panel for fine mapping of the CETP region. We identified and validated five variants within this region that may partly account for the association of the known variant (rs3764261), as well as other sources of genetic contribution to HDL-C. Newly discovered variants of the cholesteryl ester transfer protein (CETP) gene are associated with levels of “good” cholesterol. One version of the CETP gene is known to lead to higher concentrations of high-density lipoprotein (HDL) cholesterol, the type that helps protect against heart disease. However, other beneficial variants remain undiscovered. An international research team led by Cornelia van Duijn from Erasmus Medical Center in Rotterdam, The Netherlands, conducted a meta-analysis of previous studies that collectively compiled data from close to 60,000 people. They identified five novel variants linking CETP with HDL levels. Four of these were single letter differences and one was an insertion of a chunk of DNA. The researchers validated the findings in an independent cohort of around 48,000 people. People who carry these genetic variants may live longer and experience healthier aging.