Software Developed by Townsend Lab Analyzes Somatic Driver Variants: Introducing ‘cancereffectsizeR’

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The Townsend Lab has developed a new open-source program called cancereffectsizeR that greatly enhances the ability of clinical analysts and data scientists to pinpoint specific mutations in genetic code that cause cancer.

The software, created in the R platform (which is widely available), calculates the effect size of single-nucleotide variations in cancer. It also quantifies the impact on cancer cell proliferation and survival in humans. This unique algorithm organizes somatic variant data to facilitate mutational signature analyses and calculate site-specific mutation rates. The software is also capable of testing customizable epistatic and stage-specific models of selection.

The tool, which is available in an easy-to use package, tutorial and publication, will allow for widespread quantification of mutations’ contribution to somatic evolution. This quantification has appeared in many publications by our lab, but has never been widely made accessible with a simple-to-use software, tutorial and publication.

Researchers said that their cancer effect metric was a better predictor than standard tools of oncogenic pathogenicity.

Researchers write that they validated the usefulness of cancer effect in a pancancer data set by showing that somatic variations classified as likely pathogenic and pathogenic in ClinVar have significantly higher effects than other variants. In fact, a multiple logit regression shows that cancer effect is a better predictor than variant prevalence and functional impact scores like SIFT or PolyPhen-2.

The details of the new technology have been published in Cancer Research, on 5 December. The paper’s lead author is Jeffrey Mandell, Ph.D. student at Yale in the Computational Biology and Bioinformatics Program. Townsend, who is also the co-leader for Yale’s Genomics, Genetics, & Epigenetics Program, is the corresponding writer. Vincent Cannataro, a professor in the Department of Biology at Emmanuel College, is a coauthor.

The Townsend Lab has recently been awarded a $250,000 Grant from the JMR Barker Foundation. This grant will allow the team to expand its software analysis to include mutations which eliminate, duplicate or multifurcate genes in the genome – a crucial component of cancer causation, that has so far eluded analysis.

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