Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

• DOI: 10.1371/journal.pgen.1000888
• Publication Date: 2010-04-01T19:21:31Z
• Authors: Dan L. Nicolae; Eric Gamazon; Wei Zhang; Shiwei Duan; M. Eileen Dolan; Nancy J. Cox
• Keywords: Genome-wide Association Study; International HapMap Project; Genetic Association; Minor allele frequency; SNP

Although genome-wide association studies (GWAS) of complex traits have yielded more reproducible associations than had been discovered using any other approach, the loci characterized to date do not account for much heritability such and, in general, led improved understanding biology underlying phenotypes. Using a web site we developed serve results expression quantitative trait locus (eQTL) lymphoblastoid cell lines from HapMap samples (http://www.scandb.org), show that single nucleotide polymorphisms (SNPs) associated with (from http://www.genome.gov/gwastudies/) are significantly likely be eQTLs minor-allele-frequency–matched SNPs chosen high-throughput GWAS platforms. These findings robust across range thresholds establishing (p-values 10−4–10−8), and broad spectrum human traits. Analyses data Wellcome Trust confirm annotating score reflecting strength evidence SNP is an eQTL can improve ability discover true clarify nature mechanism driving associations. Our showing trait-associated application this information enhance discovery phenotypes raise possibility utilize both increase explained by identifiable genetic factors gain better