{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T23:20:20Z","timestamp":1774308020484,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T00:00:00Z","timestamp":1719532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["U54 CA274502"],"award-info":[{"award-number":["U54 CA274502"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","award":["P41 GM103504"],"award-info":[{"award-number":["P41 GM103504"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Predicting cancer drug response requires a comprehensive assessment of many mutations present across a tumor genome. While current drug response models generally use a binary mutated\/unmutated indicator for each gene, not all mutations in a gene are equivalent.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we construct and evaluate a series of predictive models based on leading methods for quantitative mutation scoring. Such methods include VEST4 and CADD, which score the impact of a mutation on gene function, and CHASMplus, which scores the likelihood a mutation drives cancer. The resulting predictive models capture cellular responses to dabrafenib, which targets BRAF-V600 mutations, whereas models based on binary mutation status do not. Performance improvements generalize to other drugs, extending genetic indications for PIK3CA, ERBB2, EGFR, PARP1, and ABL1 inhibitors. Introducing quantitative mutation features in drug response models increases performance and mechanistic understanding.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code and example datasets are available at https:\/\/github.com\/pgwall\/qms.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae209","type":"journal-article","created":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T09:25:33Z","timestamp":1719566733000},"page":"i160-i168","source":"Crossref","is-referenced-by-count":5,"title":["Representing mutations for predicting cancer drug response"],"prefix":"10.1093","volume":"40","author":[{"given":"Patrick","family":"Wall","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of California San Diego , La Jolla, CA 92093, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California San Diego , La Jolla, CA 92093, United States"},{"name":"Department of Medicine, University of California San Diego , La Jolla, CA 92093, United States"},{"name":"Department of Computer Science and Engineering, University of California San Diego , La Jolla, CA 92093, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,6,28]]},"reference":[{"key":"2024071814122889800_btae209-B1","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1056\/NEJMoa1813904","article-title":"Alpelisib for PIK3CA-Mutated, hormone receptor\u2013positive advanced breast cancer","volume":"380","author":"Andr\u00e9","year":"2019","journal-title":"N Engl J 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