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

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

Musaddeque Ahmed  1   2 , Richard C Sallari  3 , Haiyang Guo  1   2 , Jason H Moore  4 , Housheng Hansen He  1   2 , Mathieu Lupien  1   5
Affiliations

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

Musaddeque Ahmed et al. BioData Min. .

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.

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Figures

Fig. 1
Fig. 1
Enrichment of Breast, Prostate, Lung and Colorectal cancer AVS across different genomic maps in cancer-type specific cells. The box and whisker plots show the enrichment score distribution of match null set. The bar inside the box corresponds to the median enrichment score of the null set. The significantly enriched genome regions (Bonferroni corrected P-value < 0.01) are marked in red. The histone modifications are profiled in MCF7, LNCaP, A549 and HCT-116/Caco-2 for breast, prostate, lung and colorectal cancer, respectively
See this image and copyright information in PMC

References

    1. Cowper-Sal·lari R, et al. Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat Genet. 2012;44:1191–1198. doi: 10.1038/ng.2416. - DOI - PMC - PubMed
    1. Maurano MT, et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012;337:1190–1195. doi: 10.1126/science.1222794. - DOI - PMC - PubMed
    1. Schaub MA, et al. Linking disease associations with regulatory information in the human genome. Genome Res. 2012;22:1748–1759. doi: 10.1101/gr.136127.111. - DOI - PMC - PubMed
    1. Hindorff LA, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009;106:9362–9367. doi: 10.1073/pnas.0903103106. - DOI - PMC - PubMed
    1. Welter D, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014;42:D1001–D1006. doi: 10.1093/nar/gkt1229. - DOI - PMC - PubMed

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