{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T19:23:55Z","timestamp":1774121035535,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,6,8]],"date-time":"2025-06-08T00:00:00Z","timestamp":1749340800000},"content-version":"vor","delay-in-days":38,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001102","name":"Cancer Council NSW","doi-asserted-by":"publisher","award":["RG20\u201312"],"award-info":[{"award-number":["RG20\u201312"]}],"id":[{"id":"10.13039\/501100001102","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Health and Medical Research Council Investigator","award":["1196405"],"award-info":[{"award-number":["1196405"]}]},{"name":"National Health and Medical Research Council Investigator","award":["5121190"],"award-info":[{"award-number":["5121190"]}]},{"name":"Tropical Australian Academic Health Centre Limited\u2014Research Seed","award":["SF000121"],"award-info":[{"award-number":["SF000121"]}]},{"DOI":"10.13039\/501100021954","name":"Tour De Cure","doi-asserted-by":"crossref","award":["RSP-379-FY2023"],"award-info":[{"award-number":["RSP-379-FY2023"]}],"id":[{"id":"10.13039\/501100021954","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The ability to identify patient-specific vulnerabilities to guide cancer treatments is a vital area of research. However, predictive bioinformatics tools are difficult to translate into clinical applications due to a lack of in vitro and in vivo validation. While the increasing number of personalised driver prioritisation algorithms (PDPAs) report powerful patient-specific information, the results do not easily translate into treatment strategies. Critical in addressing this gap is the ability to meaningfully benchmark and validate PDPA predictions. To address this, we developed Tumour-specific Algorithm for Ranking GEnetic Targets via Synthetic Lethality (TARGET-SL), which utilises PDPA predictions to produce a ranked list of predicted essential genes that can be validated in vitro and in vivo. This framework employs a novel strategy to benchmark PDPAs, by comparing predictions with ground truth gene essentiality data from large-scale CRISPR-knockout and drug sensitivity screens. Importantly TARGET-SL identifies vulnerabilities that are more exclusive to individual tumours than predictions based on canonical driver genes. We further find that TARGET-SL is better at identifying sample-specific vulnerabilities than other similar tools.<\/jats:p>","DOI":"10.1093\/bib\/bbaf255","type":"journal-article","created":{"date-parts":[[2025,6,8]],"date-time":"2025-06-08T02:54:37Z","timestamp":1749351277000},"source":"Crossref","is-referenced-by-count":3,"title":["TARGET-SL: precision essential gene prediction using driver prioritisation and synthetic lethality"],"prefix":"10.1093","volume":"26","author":[{"given":"Rhys","family":"Gillman","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences and Molecular and Cell Biology, College of Medicine and Dentistry, College of Science and Engineering, James Cook University , 1 James Cook Drive, Townsville, Queensland ,","place":["Australia"]},{"name":"Centre for Tropical Bioinformatics and Molecular Biology, James Cook University , 14-88 McGregor Road, Smithfield, QLD 4878 ,","place":["Australia"]}]},{"given":"Matt A","family":"Field","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences and Molecular and Cell Biology, College of Medicine and Dentistry, College of Science and Engineering, James Cook University , 1 James Cook Drive, Townsville, Queensland ,","place":["Australia"]},{"name":"Centre for Tropical Bioinformatics and Molecular Biology, James Cook University , 14-88 McGregor Road, Smithfield, QLD 4878 ,","place":["Australia"]},{"name":"Immunogenomics Lab, Garvan Institute of Medical Research , 384 Victoria St, Darlinghurst, NSW 2010 ,","place":["Australia"]},{"name":"Menzies School of Health Research, Charles Darwin University , Red 9, Casuarina campus, Univ Drive North, Casuarina, NT 0811 ,","place":["Australia"]}]},{"given":"Ulf","family":"Schmitz","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences and Molecular and Cell Biology, College of Medicine and Dentistry, College of Science and Engineering, James Cook University , 1 James Cook Drive, Townsville, Queensland ,","place":["Australia"]},{"name":"Centre for Tropical Bioinformatics and Molecular Biology, James Cook University , 14-88 McGregor Road, Smithfield, QLD 4878 ,","place":["Australia"]},{"name":"Faculty of Medicine & Health, The University of Sydney , Camperdown , Camperdown Campus, Parramatta Road, Sydney, NSW 2006,","place":["Australia"]}]},{"given":"Lionel","family":"Hebbard","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences and Molecular and Cell Biology, College of Medicine and Dentistry, College of Science and Engineering, James Cook University , 1 James Cook Drive, Townsville, Queensland ,","place":["Australia"]},{"name":"Centre for Tropical Bioinformatics and Molecular Biology, James Cook University , 14-88 McGregor Road, Smithfield, QLD 4878 ,","place":["Australia"]},{"name":"Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney , 176 Hawkesbury Rd, 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