PGA: post-GWAS analysis for disease gene identification

Abstract Summary Although the genome-wide association study (GWAS) is a powerful method to identify disease-associated variants, it does not directly address the biological mechanisms underlying such genetic association signals. Here, we present PGA, a Perl- and Java-based program for post-GWAS anal...

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Bibliographic Details
Published in:Bioinformatics 2018-05, Vol.34 (10), p.1786-1788
Main Authors: Lin, Jhih-Rong, Jaroslawicz, Daniel, Cai, Ying, Zhang, Quanwei, Wang, Zhen, Zhang, Zhengdong D
Format: Article
Language:English
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Summary:Abstract Summary Although the genome-wide association study (GWAS) is a powerful method to identify disease-associated variants, it does not directly address the biological mechanisms underlying such genetic association signals. Here, we present PGA, a Perl- and Java-based program for post-GWAS analysis that predicts likely disease genes given a list of GWAS-reported variants. Designed with a command line interface, PGA incorporates genomic and eQTL data in identifying disease gene candidates and uses gene network and ontology data to score them based upon the strength of their relationship to the disease in question. Availability and implementation http://zdzlab.einstein.yu.edu/1/pga.html Supplementary information Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btx845