SMuRF：一种用于鉴定体细胞点突变富集调控元件的新工具。
SMuRF: a novel tool to identify regulatory elements enriched for somatic point mutations.
机构信息
Princess Margaret Cancer Centre, The MaRS Center, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
出版信息
BMC Bioinformatics. 2018 Nov 26;19(1):454. doi: 10.1186/s12859-018-2501-y.
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 ).
背景
非编码顺式调控元件（CREs）中的单核苷酸变异（SNVs），包括体细胞点突变和单核苷酸多态性（SNPs），可以影响基因调控并导致疾病发生。已经开发了几种方法来识别高度突变的区域，但这些方法没有考虑到 CREs 的特定基因组背景和突变可能性。
结果
在这里，我们提出了 SMuRF（显著突变区域发现者），这是一种用户友好的命令行工具，用于从用户定义的基因组区间和 SNVs 中识别这些显著突变的区域。我们使用公开可用的数据集证明了这一点，其中 SMuRF 在肝癌中鉴定出 72 个显著突变的 CRE，包括已知突变的基因启动子以及以前未报道过的区域。
结论
SMuRF 是一种有用的工具，可以简单地识别显著突变的调控元件。它是开源的，并在 GitHub 上免费提供（https://github.com/LupienLab/SMURF）。
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