Lookup NU author(s): Dr Ana Viñuela
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© 2017 Nature America, Inc.Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying causal variants remains difficult. Whole-genome sequencing (WGS) can help by providing complete knowledge of all genetic variants, but it is financially prohibitive for well-powered GWAS studies. We performed mapping of expression quantitative trait loci (eQTLs) with WGS and RNA-seq, and found that lead eQTL variants called with WGS were more likely to be causal. Through simulations, we derived properties of causal variants and used them to develop a method for identifying likely causal SNPs. We estimated that 25-70% of causal variants were located in open-chromatin regions, depending on the tissue and experiment. Finally, we identified a set of high-confidence causal variants and showed that these were more enriched in GWAS associations than other eQTLs. Of those, we found 65 associations with GWAS traits and provide examples in which genes implicated by expression are functionally validated as being relevant for complex traits.
Author(s): Brown AA, Vinuela A, Delaneau O, Spector TD, Small KS, Dermitzakis ET
Publication type: Article
Publication status: Published
Journal: Nature Genetics
Print publication date: 01/12/2017
Online publication date: 23/10/2017
Acceptance date: 27/09/2017
ISSN (print): 1061-4036
ISSN (electronic): 1546-1718
Publisher: Nature Publishing Group
PubMed id: 29058714
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