Sequence variation in the CD36 gene and its relationship with plasma HDL cholesterol levels

Heart disease (HD) is a primary public health concern, with HD being one of the leading causes of death every year in the United States. Many risk factors influence HD, including lipid levels, and studies have shown that higher levels of plasma high density lipoprotein (HDL) cholesterol have a protective effect against HD. Recent genome-wide linkage scans have associated a locus on chromosome 7, harboring CD36, as being involved in components of the metabolic syndrome, including HDL-C levels. Therefore, identifying variation in this gene affecting HDL-C levels is of great public health importance. The "common variant-common disease" hypothesis has been tested by a limited number of studies through common SNP genotyping with inconsistent results. To date, no studies to our knowledge have evaluated CD36 using the "rare variant-common disease" hypothesis. The aim of this study was to further evaluate the role of common and rare variation in CD36 by sequencing individuals having extremely low and high HDL-cholesterol levels in two populations, U.S. Non-Hispanic Whites (NHWs), and African Blacks. In our initial sequence analysis, 343 variants were identified in CD36, 168 of which were previously unreported in the SeattleSNPs database. According to preliminary analysis of the sequencing data, our findings support the associations of three SNPs with HDL-C levels reported in the literature. No striking difference was noticed between the distribution of rare variants between high and low HDL-C groups. We identified four common variants (MAF ≥ 5%) in our sequencing data from our small sample that displayed statistically significant differences in MAF between the low and high HDL-C groups but have not been confirmed yet by genotyping in the entire NHW and Black populations while thirteen common variants had p-values between 5-10%, which may be statistically significant due to the small sample size. To date, screening data was compiled for the entire NHWs and Black samples for a total of nineteen common variants. None of these variants displayed a significant p-value in our entire NHW and Black samples. Additional variants identified in sequencing remain to be screened in the entire NHW and Black samples