Members of the apolipoprotein gene cluster (APOA1/C3/A4/A5) on human chromosome 11q23 play an important role in lipid metabolism. Polymorphisms in both APOA5 and APOC3 are strongly associated with plasma triglyceride concentrations. The close genomic locations of these two genes as well as their functional similarity have hindered efforts to define whether each gene independently influences human triglyceride concentrations. In this study, we examined the linkage disequilibrium and haplotype structure of 49 SNPs in a 150-kb region spanning the gene cluster. We identified a total of five common APOA5 haplotypes with a frequency of greater than 8% in samples of northern European origin. The APOA5 haplotype block did not extend past the 7 SNPs in the gene and was separated from the other apolipoprotein gene in the cluster by a region of significantly increased recombination. Furthermore, one previously identified triglyceride risk haplotype of APOA5 (APOA5*3) showed no association with three APOC3 SNPs previously associated with triglyceride concentrations, in contrast to the other risk haplotype (APOA5*2), which was associated with all three minor APOC3 SNP alleles. These results highlight the complex genetic relationship between APOA5 and APOC3 and support the notion that APOA5 represents an independent risk gene affecting plasma triglyceride concentrations in humans.
KeywordsSingle nucleotide polymorphism; Apolipoprotein A5; Haplotype; Linkage disequilibrium; Recombination; Four-gamete testThe apolipoprotein gene cluster on human chromosome 11q23 contains four apolipoprotein genes (APOA1/C3/A4/A5) in a genomic interval of approximately 60 kb [1]. Three of these genes (APOA1/C3/A4) have been well described, and each plays an important role in lipid metabolism in humans and mice. For example, mice lacking apoA1 have significantly reduced plasma high-density lipoprotein (HDL) cholesterol levels [2]. In contrast, mice lacking apoC3 show lower concentration of plasma triglycerides compared to control littermates [3].In humans, analyses of genetic sequence variants around these three genes have revealed polymorphisms associated with plasma lipid levels (for a review, see [4] in APOA1 primarily affect HDL-cholesterol cocentrations, while variation in APOC3 is primarily associated with altered plasma triglyceride concentrations. In APOC3, two rare alleles in the promoter region (−482C →T and −455T →C) and a minor allele in the 3′UTR (SstI polymorphism, 3238G →C) have repeatedly been associated with elevated plasma triglyceride concentrations in several human populations [5][6][7][8][9][10][11][12][13][14][15]. However, the lack of strong functional data at least for the SstI polymorphism raises questions whether the association seen in humans is due to these sequence variants in APOC3 directly or due to other functional variants in APOC3 or possibly in one of the neighboring apolipoprotein genes.Recently, we identified a fourth member (APOA5) of the chromosome 11 apolipoprotein gene cluster, located approximatel...