Integrating GWAS and expression data for functional characterization of disease-associated SNPs: an application to follicular lymphoma

Abstract

Development of post-GWAS (genome-wide association study) methods are greatly needed for characterizing the function of trait-associated SNPs. Strategies integrating various biological data sets with GWAS results will provide insights into the mechanistic role of associated SNPs. Here, we present a method that integrates RNA sequencing (RNA-seq) and allele-specific expression data with GWAS data to further characterize SNPs associated with follicular lymphoma (FL). We investigated the influence on gene expression of three established FL-associated loci-rs10484561, rs2647012, and rs6457327-by measuring their correlation with human-leukocyte-antigen (HLA) expression levels obtained from publicly available RNA-seq expression data sets from lymphoblastoid cell lines. Our results suggest that SNPs linked to the protective variant rs2647012 exert their effect by a cis-regulatory mechanism involving modulation of HLA-DQB1 expression. In contrast, no effect on HLA expression was observed for the colocalized risk variant rs10484561. The application of integrative methods, such as those presented here, to other post-GWAS investigations will help identify causal disease variants and enhance our understanding of biological disease mechanisms.

Figure 1

ASE Test for Disease-Associated Variants ASE that is shared among multiple individuals can indicate the presence of an eQTL (i.e., individuals with ASE are heterozygous for the common causal regulatory variant), multiple rare regulatory variants (i.e., each individual has a private variant impacting expression), or epigenetic effects where one haplotype is silenced relative to the other. We have developed a method that assesses enrichment of ASE effects for individuals harboring both the risk and the protective alleles (i.e., individuals who are heterozygous for the GWAS variant) as compared to homozygous individuals. Here, the expectation is that functional differences will be more manifest for individuals who possess both the risk and protective alleles for genes involved in the etiology of the trait. This enrichment is represented in the figure in that more ASE events are present in individuals heterozygous for the GWAS variant; green ratios describe the relative transcript abundance. This test complements eQTL approaches in that it can add support to the presence of an eQTL, as well as indicate an enrichment of other potential causal effects (independent of frequency) (i.e., rare or private variants) underlying the difference in risk and protective haplotypes.

Figure 2

Genome-wide SNP-Probe Associations for rs4947344 in the GSE16921 Data Set SNP-probe association plot for rs4947344 and probes located across the genome. The strongest associations, represented as −log₁₀ of the Spearman’s observed p value, were observed for HLA class II genes located in cis with respect to rs4947344. A genome-wide association plot for all the rs2647012-linked variants is shown in Figure S3.