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

Tutkimustuotos: LehtiartikkeliArticleScientificvertaisarvioitu

102 Lataukset (Pure)

Abstrakti

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.

AlkuperäiskieliEnglanti
Sivut4112-4114
Sivumäärä3
JulkaisuBioinformatics (Oxford, England)
Vuosikerta34
Numero23
DOI - pysyväislinkit
TilaJulkaistu - 1 joulukuuta 2018
OKM-julkaisutyyppiA1 Julkaistu artikkeli, soviteltu

Sormenjälki Sukella tutkimusaiheisiin 'snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions'. Ne muodostavat yhdessä ainutlaatuisen sormenjäljen.

Siteeraa tätä