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. © 2013 The American Society of Human Genetics.
CITATION STYLE
Conde, L., Bracci, P. M., Richardson, R., Montgomery, S. B., & Skibola, C. F. (2013). Integrating GWAS and expression data for functional characterization of disease-associated SNPs: An application to follicular lymphoma. American Journal of Human Genetics, 92(1), 126–130. https://doi.org/10.1016/j.ajhg.2012.11.009
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