PAPA: a flexible tool for identifying pleiotropic pathways using genome-wide association study summaries

Bioinformatics. 2016 Mar 15;32(6):946-8. doi: 10.1093/bioinformatics/btv668. Epub 2015 Nov 14.


: Pleiotropy is common in the genetic architectures of complex diseases. To the best of our knowledge, no analysis tool has been developed for identifying pleiotropic pathways using multiple genome-wide association study (GWAS) summaries by now. Here, we present PAPA, a flexible tool for pleiotropic pathway analysis utilizing GWAS summary results. The performance of PAPA was validated using publicly available GWAS summaries of body mass index and waist-hip ratio of the GIANT datasets. PAPA identified a set of pleiotropic pathways, which have been demonstrated to be involved in the development of obesity.

Availability and implementation: PAPA program, document and illustrative example are available at

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Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Genome-Wide Association Study*
  • Humans
  • Waist-Hip Ratio