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BMC Bioinformatics. 2018 Nov 26;19(1):454. doi: 10.1186/s12859-018-2501-y.

SMuRF: a novel tool to identify regulatory elements enriched for somatic point mutations.

Author information

1
Princess Margaret Cancer Centre, The MaRS Center, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada.
2
Princess Margaret Cancer Centre, The MaRS Center, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada. Mathieu.Lupien@uhnresearch.ca.
3
Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. Mathieu.Lupien@uhnresearch.ca.
4
Ontario Institute for Cancer Research, Toronto, ON, Canada. Mathieu.Lupien@uhnresearch.ca.

Abstract

BACKGROUND:

Single Nucleotide Variants (SNVs), including somatic point mutations and Single Nucleotide Polymorphisms (SNPs), in noncoding cis-regulatory elements (CREs) can affect gene regulation and lead to disease development. Several approaches have been developed to identify highly mutated regions, but these do not take into account the specific genomic context, and thus likelihood of mutation, of CREs.

RESULTS:

Here, we present SMuRF (Significantly Mutated Region Finder), a user-friendly command-line tool to identify these significantly mutated regions from user-defined genomic intervals and SNVs. We demonstrate this using publicly available datasets in which SMuRF identifies 72 significantly mutated CREs in liver cancer, including known mutated gene promoters as well as previously unreported regions.

CONCLUSIONS:

SMuRF is a helpful tool to allow the simple identification of significantly mutated regulatory elements. It is open-source and freely available on GitHub ( https://github.com/LupienLab/SMURF ).

KEYWORDS:

Cancer; Cis-regulatory elements; Enrichment; Mutations; Transcriptional regulation

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