Evidence for Consistent Intragenic and Intergenic Interactions between SNP Effects in the APOA1/C3/A4/A5 Gene Cluster

Objective: Evaluate the consistency of the contribution of interactions between single nucleotide polymorphism (SNP) genotype eff ects to variation in measures of lipid metabolism across ethnic strata within gender. Methods and Results: We considered 80 SNPs within the apolipoprotein (APO) A1/C3/A4/A5 gene cluster using an over-parameterized general linear model to identify SNPs whose genotype eff ects combine non-additively to infl uence plasma levels of high density lipoprotein cholesterol (HDL-C), total cholesterol (TC) and triglycerides (TG) in a consistent manner across ethnic strata. We analyzed population-based samples of unrelated 18 to 30 year old African-Americans (n = 1,858) and European-Americans (n = 1,973) ascertained without regard to health at four fi eld centers (Birmingham, Ala.; Chicago, Ill.; Minneapolis, Minn. and Oakland, Calif., USA) by the Coronary Artery Risk Development in Young Adults (CARDIA) study. To identify which SNP genotype eff ects combine non-additively we used a two-tier analysis strategy. We fi rst required that pairs of SNPs show statistically signifi cant non-additivity in both ethnic strata within a gender, where experiment-wise signifi cance was evaluated using a permutation test to deReceived: October 7, 2005 Accepted: March 14, 2006 Published online: May 19, 2006 Dr. Charles F. Sing University of Michigan, Department of Human Genetics 1241 E. Catherine St., 5928 Buhl Bldg. Ann Arbor, MI 48109–0618 (USA) Tel. +1 734 647 3151, Fax +1 734 763 5277, E-Mail [email protected] © 2006 S. Karger AG, Basel 0001–5652/06/0612–0087$23.50/0 Accessible online at: www.karger.com/hhe Hum Hered 2006;61:87–96 88 A4/A5 gene cluster (11q23–24) are involved in lipid metabolism. Apolipoprotein (apo) A-I comprises approximately 70% of the high-density lipoprotein (HDL) particle. It acts as a cofactor of lecithin-cholesterol acyltransferase [2, 3] in facilitating the transport of cholesterol from the peripheral tissues to the liver in a process known as reverse cholesterol transport. ApoC-III is a major component of very low density lipoproteins (VLDL) and chylomicrons. It is thought to play a role in the hepatic uptake of TG-rich particles and their remnants [4] . ApoA-IV has been shown to have a role in lipid absorption, transport and metabolism, as a constituent of HDL and TG-rich lipoprotein particles [5] . Comparisons of human and mouse DNA sequence data have identifi ed the APOA5 gene as a new member of the APOA1/C3/A4 gene cluster [6] . ApoA-V is implicated in regulating lipoprotein lipasemediated VLDL-TG hydrolysis [7] . Th e statistical associations between variation in plasma levels of HDL-C, TC and TG and single-site and haplotype variations in the APOA1/C3/A4/A5 gene cluster have clearly established the infl uence of these genes in determining phenotypic variability [8–14] . It is widely acknowledged that gene-gene and gene-environment interaction eff ects also play an important role in the determining levels of these plasma measures of lipid metabolism [15–17] . Furthermore, the coordinated roles of the genes in this cluster in regulating lipoprotein structure and metabolism suggest that interactions between sites within the gene cluster may make a major contribution to predicting interindividual variation in HDL-C, TC and TG. To investigate this possibility we evaluated the consistency of the infl uence of interactions between pairs of single nucleotide polymorphisms (SNPs) within the APOA1/ C3/A4/A5 gene region on interindividual variation in plasma HDL-C, TC and TG levels in population-based samples of unrelated African-American and EuropeanAmerican males and females. To identify which SNPs are interacting to infl uence trait variability we used a two-tier analysis strategy. We fi rst required that pairs of SNPs show statistically signifi cant non-additivity of SNP genotype eff ects in both ethnic strata within a gender. Experiment-wise signifi cance was evaluated using a permutation test to determine the probability of observing the number of tests signifi cant in both ethnic strata by chance alone. We chose to consider gender specifi c consistency because of the well-documented gender diff erences in the natural history of the risk of developing CVD [18] and evidence for the gender specifi c genetic architecture of the quantitative CVD risk factors such as blood pressure, obesity and lipid levels [19] . Second, we required that there was no signifi cant evidence of heterogeneity of the phenotype-genotype relationships across ethnic strata and across fi eld centers within each ethnic group. Th e results from these analyses support three conclusions: (1) variations within the APOA1/C3/ A4/A5 gene cluster interact to infl uence interindividual variation in plasma TC levels; (2) the observed pairwise eff ects are not a consequence of linkage disequilibrium (LD) between the SNPs, and (3) ignoring interactions between SNP genotype eff ects when modeling multi-SNP genotype-phenotype relationships may result in underestimating the contribution of genetic variation to quantitative variation in measures of CVD risk.