{"id":96,"date":"2023-04-17T07:20:40","date_gmt":"2023-04-17T07:20:40","guid":{"rendered":"https:\/\/kurir-health.com\/?p=96"},"modified":"2023-05-25T11:47:01","modified_gmt":"2023-05-25T11:47:01","slug":"software-developed-by-townsend-lab-analyzes-somatic-driver-variants-introducing-cancereffectsizer","status":"publish","type":"post","link":"https:\/\/kurir-health.com\/?p=96","title":{"rendered":"Software Developed by Townsend Lab Analyzes Somatic Driver Variants: Introducing &#8216;cancereffectsizeR&#8217;"},"content":{"rendered":"\n<p>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.<\/p>\n\n\n\n<p>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.&nbsp;This unique algorithm organizes somatic variant data to facilitate mutational signature analyses and calculate site-specific mutation rates.&nbsp;The software is also capable of testing customizable epistatic and stage-specific models of selection.<\/p>\n\n\n\n<p>The tool, which is available in an easy-to use package, tutorial and publication, will allow for widespread quantification of mutations&#8217; 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.<\/p>\n\n\n\n<p>Researchers said that their cancer effect metric was a better predictor than standard tools of oncogenic pathogenicity.<\/p>\n\n\n\n<p>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.&nbsp;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.<\/p>\n\n\n\n<p>The details of the new technology have been published in&nbsp;<em>Cancer Research<\/em>, on 5 December.&nbsp;The paper&#8217;s lead author is Jeffrey Mandell, Ph.D. student at Yale in the Computational Biology and Bioinformatics Program.&nbsp;Townsend, who is also the co-leader for Yale&#8217;s Genomics, Genetics, &amp; Epigenetics Program, is the corresponding writer.&nbsp;Vincent Cannataro, a professor in the Department of Biology at Emmanuel College, is a coauthor.<\/p>\n\n\n\n<p>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 &#8211; a crucial component of cancer causation, that has so far eluded analysis.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"768\" height=\"403\" src=\"https:\/\/kurir-health.com\/wp-content\/uploads\/2023\/05\/image-22.png\" alt=\"\" class=\"wp-image-158\" srcset=\"https:\/\/kurir-health.com\/wp-content\/uploads\/2023\/05\/image-22.png 768w, https:\/\/kurir-health.com\/wp-content\/uploads\/2023\/05\/image-22-300x157.png 300w\" sizes=\"auto, (max-width: 768px) 100vw, 768px\" \/><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>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 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":158,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5],"tags":[],"class_list":["post-96","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-medical-devices"],"_links":{"self":[{"href":"https:\/\/kurir-health.com\/index.php?rest_route=\/wp\/v2\/posts\/96","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/kurir-health.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/kurir-health.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/kurir-health.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/kurir-health.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=96"}],"version-history":[{"count":2,"href":"https:\/\/kurir-health.com\/index.php?rest_route=\/wp\/v2\/posts\/96\/revisions"}],"predecessor-version":[{"id":276,"href":"https:\/\/kurir-health.com\/index.php?rest_route=\/wp\/v2\/posts\/96\/revisions\/276"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/kurir-health.com\/index.php?rest_route=\/wp\/v2\/media\/158"}],"wp:attachment":[{"href":"https:\/\/kurir-health.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=96"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/kurir-health.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=96"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/kurir-health.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=96"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}