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This field, called pharmacogenomics, is a key area in the development of precision oncology. Deep learning (DL) methodology has emerged as a powerful technique to characterize and learn from rapidly accumulating pharmacogenomics data. We introduce the fundamentals and typical model architectures of DL. We review the use of DL in classification of cancers and cancer subtypes (diagnosis and treatment stratification of patients), prediction of drug response and drug synergy for individual tumors (treatment prioritization for a patient), drug repositioning and discovery and the study of mechanism\/mode of action of treatments. For each topic, we summarize current genomics and pharmacogenomics data resources such as pan-cancer genomics data for cancer cell lines (CCLs) and tumors, and systematic pharmacologic screens of CCLs. By revisiting the published literature, including our in-house analyses, we demonstrate the unprecedented capability of DL enabled by rapid accumulation of data resources to decipher complex drug response patterns, thus potentially improving cancer medicine. Overall, this review provides an in-depth summary of state-of-the-art DL methods and up-to-date pharmacogenomics resources and future opportunities and challenges to realize the goal of precision oncology.<\/jats:p>","DOI":"10.1093\/bib\/bbz144","type":"journal-article","created":{"date-parts":[[2019,10,24]],"date-time":"2019-10-24T19:10:41Z","timestamp":1571944241000},"page":"2066-2083","source":"Crossref","is-referenced-by-count":61,"title":["Deep learning of pharmacogenomics resources: moving towards precision oncology"],"prefix":"10.1093","volume":"21","author":[{"given":"Yu-Chiao","family":"Chiu","sequence":"first","affiliation":[{"name":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Hung-I Harry","family":"Chen","sequence":"additional","affiliation":[{"name":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"},{"name":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"}]},{"given":"Aparna","family":"Gorthi","sequence":"additional","affiliation":[{"name":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Milad","family":"Mostavi","sequence":"additional","affiliation":[{"name":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"},{"name":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"}]},{"given":"Siyuan","family":"Zheng","sequence":"additional","affiliation":[{"name":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"},{"name":"Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Yufei","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, the University of Texas at San Antonio, San Antonio, TX 78249, USA"},{"name":"Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA"}]},{"given":"Yidong","family":"Chen","sequence":"additional","affiliation":[{"name":"Greehey Children\u2019s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA"},{"name":"Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,12,8]]},"reference":[{"key":"2020120619235866600_ref1","doi-asserted-by":"crossref","first-page":"75","DOI":"10.3322\/caac.21329","article-title":"Translating cancer genomes and transcriptomes for precision oncology","volume":"66","author":"Roychowdhury","year":"2016","journal-title":"CA 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