Variant Set Enrichment: an R package to identify disease-associated functional genomic regions

Musaddeque Ahmed; Richard C Sallari; Haiyang Guo; Jason H Moore; Housheng Hansen He; Mathieu Lupien

doi:10.1186/s13040-017-0129-5

Variant Set Enrichment: an R package to identify disease-associated functional genomic regions

BioData Min. 2017 Feb 22:10:9. doi: 10.1186/s13040-017-0129-5. eCollection 2017.

Authors

Musaddeque Ahmed^{1

2}, Richard C Sallari³, Haiyang Guo^{1

2}, Jason H Moore⁴, Housheng Hansen He^{1

2}, Mathieu Lupien^{1

5}

Affiliations

¹ Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada.
² Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.
³ Massachusetts Institute of Technology (MIT), Cambridge, MA USA.
⁴ Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
⁵ Ontario Institute for Cancer Research, Toronto, ON Canada.

Abstract

Background: Genetic predispositions to diseases populate the noncoding regions of the human genome. Delineating their functional basis can inform on the mechanisms contributing to disease development. However, this remains a challenge due to the poor characterization of the noncoding genome. Here, we propose an R package that can pinpoint which genomic features are etiologically important based on the genetic predispositions.

Results: Variant Set Enrichment (VSE) is an R package to calculate the enrichment of a set of disease-associated variants across functionally annotated genomic regions, consequently highlighting the mechanisms important in the etiology of the disease studied.

Conclusions: VSE is implemented as an R package and can easily be implemented in any system with R.

Keywords: AVS; Disease; Enrichment; GWAS; Noncoding region; Regulatory region.

Abstract

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