Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip

Abstract

Blood lipids are important cardiovascular disease (CVD) risk factors with both genetic and environmental determinants. The Whitehall II study (n=5592) was genotyped with the gene-centric HumanCVD BeadChip (Illumina). We identified 195 SNPs in 16 genes/regions associated with 3 major lipid fractions and 2 apolipoprotein components at p<10(-5), with the associations being broadly concordant with prior genome-wide analysis. SNPs associated with LDL cholesterol and apolipoprotein B were located in LDLR, PCSK9, APOB, CELSR2, HMGCR, CETP, the TOMM40-APOE-C1-C2-C4 cluster, and the APOA5-A4-C3-A1 cluster; SNPs associated with HDL cholesterol and apolipoprotein AI were in CETP, LPL, LIPC, APOA5-A4-C3-A1, and ABCA1; and SNPs associated with triglycerides in GCKR, BAZ1B, MLXIPL, LPL, and APOA5-A4-C3-A1. For 48 SNPs in previously unreported loci that were significant at p<10(-4) in Whitehall II, in silico analysis including the British Women's Heart and Health Study, BRIGHT, ASCOT, and NORDIL studies (total n>12,500) revealed previously unreported associations of SH2B3 (p<2.2x10(-6)), BMPR2 (p<2.3x10(-7)), BCL3/PVRL2 (flanking APOE; p<4.4x10(-8)), and SMARCA4 (flanking LDLR; p<2.5x10(-7)) with LDL cholesterol. Common alleles in these genes explained 6.1%-14.7% of the variance in the five lipid-related traits, and individuals at opposite tails of the additive allele score exhibited substantial differences in trait levels (e.g., >1 mmol/L in LDL cholesterol [approximately 1 SD of the trait distribution]). These data suggest that multiple common alleles of small effect can make important contributions to individual differences in blood lipids potentially relevant to the assessment of CVD risk. These genes provide further insights into lipid metabolism and the likely effects of modifying the encoded targets therapeutically.

Figure 1

Manhattan Plots Showing the Associations of 48,032 SNPs by Chromosome for the 5 Lipid and Apolipoprotein Phenotypes versus −log₁₀ p Value The horizontal line indicates a p value threshold of 10⁻⁵. The Quantile/Quantile plots for the test statistics of the observed association p values plotted as a function of the expected SNP; association p values are inset for each trait. ^∗SNPs with MAF < 0.001 but with p < 10⁻⁵.

Figure 2

Forest Plots for Fixed Effects Meta-analyses for Previously Unreported Association Signals Forest plots for fixed effects meta-analyses of beta-coefficients associated with LDL-C.

Figure 3

Haploview Plots of SNPs Showing Significant Associations with LDL-C before and after Variable Selection in Whitehall II Haploview plots for LDL-C-associated SNPs significant by univariate analysis (at p < 10⁻⁵) and those retained after variable selection (red boxes). Bar charts show the −log₁₀ p value for each SNP from the univariate analysis, with those in red corresponding to the values for SNPs retained after variable selection. For LDL-C and the chr 19 APOE cluster, orange boxes designate SNPs that were not retained after inclusion in the model of the APOE E2, E3, E4 variants that had been previously genotyped in WH-II.

Figure 4

Haploview Plots of SNPs Showing Significant Associations with HDL-C before and after Variable Selection in Whitehall II Haploview plots for HDL-C-associated SNPs significant by univariate analysis (at p < 10⁻⁵) and those retained after variable selection (red boxes). Bar charts show the −log₁₀ p value for each SNP from the univariate analysis, with those in red corresponding to the values for SNPs retained after variable selection.

Figure 5

Haploview Plots of SNPs Showing Significant Associations with Triglycerides before and after Variable Selection in Whitehall II Haploview plots for triglyceride-associated the SNPs significant by univariate analysis (at p < 10⁻⁵) and those retained after variable selection (red boxes). Bar charts show the −log₁₀ p value for each SNP from the univariate analysis, with those in red corresponding to the values for SNPs retained after variable selection.

Figure 6

Heat Plot of the Associations of the 195 Significant SNPs across All the Lipid and Lipoprotein Variables Analyzed

Figure 7

Pie Charts Showing the Contribution of SNPs to the Genetic Variance of Lipid, Lipoprotein, and Apolipoprotein Traits Contribution of SNPs retained after variable selection to the genetic variance of the (A) LDL-C and ApoB, (B) HDL-C and ApoAI, and (C) triglycerides. Inset in each figure is shown as a proportion of the total variance of the trait compared to the variance of the trait explained by age and gender.

Figure 8

Frequency Distribution of the Gene Count Scores for LDL-C and Triglycerides Frequency distribution of the gene count score for (A) LDL-C and (B) TG with the fitted line representing the effect of gene score on trait level, with increasing score. Below each gene score histogram is a plot of the odds ratio for being in either the top or bottom 10% of the trait distribution at different cut points of the respective gene score below. The medians (interquartile ranges) of the gene counts were 27 (25–30) for LDL-C and 13 (11–14) for TG.