snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions

A1 Journal article (refereed)


Internal Authors/Editors


Publication Details

List of Authors: Nousiainen K, Kanduri K, Ricano-Ponce I, Wijmenga C, Lahesmaa R, Kumar V, Lahdesmaki H
Publisher: OXFORD UNIV PRESS
Publication year: 2018
Journal: Bioinformatics
Journal acronym: BIOINFORMATICS
Volume number: 34
Start page: 4112
End page: 4114
Number of pages: 3
ISSN: 1367-4803


Abstract

Motivation: Co-localization of trait associated SNPs for specific transcription-factor binding sites or regulatory regions in the genome can yield profound insight into underlying causal mechanisms. Analysis is complicated because the truly causal SNPs are generally unknown and can be either SNPs reported in GWAS studies or other proxy SNPs in their linkage disequilibrium. Hence, a comprehensive pipeline for SNP co-localization analysis that utilizes all relevant information about both the genotyped SNPs and their proxies is needed.Results: We developed an R package snpEnrichR for SNP co-localization analysis. The software integrates different tools for random SNP generation and genome co-localization analysis to automatize and help users to create custom SNP co-localization analysis. We show via an example that including proxy SNPs in SNP co-localization analysis enhances the sensitivity of co-localization detection.

Last updated on 2019-15-10 at 03:12

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