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

Kari Nousiainen, Kartiek Kanduri, Isis Ricaño-Ponce, Cisca Wijmenga, Riitta Lahesmaa, Vinod Kumar, Harri Lähdesmäki

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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. Availability and implementation: The software is available at https://github.com/kartiek/snpEnrichR.

Original languageEnglish
Pages (from-to)4112-4114
Number of pages3
JournalBioinformatics (Oxford, England)
Volume34
Issue number23
DOIs
Publication statusPublished - 1 Dec 2018
MoE publication typeA1 Journal article-refereed

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