DOI: 10.1101/495903Dec 17, 2018Paper

Qtlizer: comprehensive QTL annotation of GWAS results

BioRxiv : the Preprint Server for Biology
Matthias MunzJeanette Erdmann

Abstract

Exploration of genetic variant-to-gene relationships by quantitative trait loci such as expression QTLs is a frequently used tool in genome-wide association studies. However, the wide range of public QTL databases and the lack of batch annotation features complicate a comprehensive annotation of GWAS results. In this work, we introduce the tool "Qtlizer" for annotating lists of variants in human with associated changes in gene expression and protein abundance using an integrated database of published QTLs. Features include incorporation of variants in linkage disequilibrium and reverse search by gene names. Analyzing the database for base pair distances between best significant eQTLs and their affected genes suggests that the commonly used cis-distance limit of 1,000,000 base pairs might be too restrictive, implicating a substantial amount of wrongly and yet undetected eQTLs. We also ranked genes with respect to the maximum number of datasets in which a most significant eQTL signal was consistent. For the top 100 genes we observed the strongest enrichment with housekeeping genes (P=2x10-6) and with the 10% highest expressed genes (P=0.005) after grouping eQTLs by r2>0.95, underlining the relevance of LD information in eQTL anal...Continue Reading

Related Concepts

Gene Expression
Genes
Quantitative Trait Loci
Gene Mutant
Active ingredient
REST gene
Genome-Wide Association Study
Gene Annotation

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