Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes

Abstract

Genome-wide association studies of human gene expression promise to identify functional regulatory genetic variation that contributes to phenotypic diversity. However, it is unclear how useful this approach will be for the identification of disease-susceptibility variants. We generated gene expression profiles for 22 184 mRNA transcripts using RNA derived from peripheral blood CD4+ lymphocytes, and genome-wide genotype data for 516 512 autosomal markers in 200 subjects. We screened for cis-acting variants by testing variants mapping within 50 kb of expressed transcripts for association with transcript abundance using generalized linear models. Significant associations were identified for 1585 genes at a false discovery rate of 0.05 (corresponding to P-values ranging from 1 × 10(-91) to 7 × 10(-4)). Importantly, we identified evidence of regulatory variation for 119 previously mapped disease genes, including 24 examples where the variant with the strongest evidence of disease-association demonstrates strong association with specific transcript abundance. The prevalence of cis-acting variants among disease-associated genes was 63% higher than the genome-wide rate in our data set (P = 6.41 × 10(-6)), and although many of the implicated loci were associated with immune-related diseases (including asthma, connective tissue disorders and inflammatory bowel disease), associations with genes implicated in non-immune-related diseases including lipid profiles, anthropomorphic measurements, cancer and neurologic disease were also observed. Genetic variants that confer inter-individual differences in gene expression represent an important subset of variants that contribute to disease susceptibility. Population-based integrative genetic approaches can help identify such variation and enhance our understanding of the genetic basis of complex traits.

Figure 1.

(A) QQ plot of genome-wide screen for proximal eSNP in CD4+ lymphocytes. Dashed line denotes expected uniform (null) distribution. (B) Distribution of SNP-specific proportion of expression variation explained. Histogram includes 6706 SNPs with significant eQTL association findings.

Figure 2.

The proportion of expression–trait association results with population-based P-values <0.001 are plotted against distance from transcript boundaries for SNP within 1 Mb of transcript (6.86 million association tests). SNP distances were rounded up to the nearest kilobase, resulting in 2000 bins. A lowess curve with smoothing span of 0.1 is plotted in solid black. The line at 0.001 on the ordinate reflects the proportion of SNP that would be expected under the null hypothesis of no association. The red data points denote the 50 kb window considered for our primary association studies.

Figure 3.

Examples of disease-associated eQTL findings in peripheral blood CD4+ lymphocytes. For each of five panels (A–E), upper figure displays the –log₁₀P-values of population-based tests of association as a function of physical distance. Line colors correspond to results for individual genes (defined in legend), with relative position and strand orientation of genes depicted as arrows. Lower figure displays box plots of transcript intensity (log₂) as a function of disease-associated SNP genotype, the position of which is denoted by (*) in the upper figure. (A) Asthma, Crohn's and type I diabetes-associated ORMDL3/GSDML; (B) Crohn's disease/inflammatory bowel disease-associated IL23R; (C) lupus-associated BLK locus; (D) lipid-associated FADS1, FADS2, and FADS3; and (E) type I diabetes-associated SUOX.

Figure 3.

Examples of disease-associated eQTL findings in peripheral blood CD4+ lymphocytes. For each of five panels (A–E), upper figure displays the –log₁₀P-values of population-based tests of association as a function of physical distance. Line colors correspond to results for individual genes (defined in legend), with relative position and strand orientation of genes depicted as arrows. Lower figure displays box plots of transcript intensity (log₂) as a function of disease-associated SNP genotype, the position of which is denoted by (*) in the upper figure. (A) Asthma, Crohn's and type I diabetes-associated ORMDL3/GSDML; (B) Crohn's disease/inflammatory bowel disease-associated IL23R; (C) lupus-associated BLK locus; (D) lipid-associated FADS1, FADS2, and FADS3; and (E) type I diabetes-associated SUOX.

Figure 3.

Examples of disease-associated eQTL findings in peripheral blood CD4+ lymphocytes. For each of five panels (A–E), upper figure displays the –log₁₀P-values of population-based tests of association as a function of physical distance. Line colors correspond to results for individual genes (defined in legend), with relative position and strand orientation of genes depicted as arrows. Lower figure displays box plots of transcript intensity (log₂) as a function of disease-associated SNP genotype, the position of which is denoted by (*) in the upper figure. (A) Asthma, Crohn's and type I diabetes-associated ORMDL3/GSDML; (B) Crohn's disease/inflammatory bowel disease-associated IL23R; (C) lupus-associated BLK locus; (D) lipid-associated FADS1, FADS2, and FADS3; and (E) type I diabetes-associated SUOX.