title: pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels.
abstract: We recently described a methodology that reliably predicted chemotherapeutic response in multiple independent clinical trials. The method worked by building statistical models from gene expression and drug sensitivity data in a very large panel of cancer cell lines, then applying these models to gene expression data from primary tumor biopsies. Here, to facilitate the development and adoption of this methodology we have created an R package called pRRophetic. This also extends the previously described pipeline, allowing prediction of clinical drug response for many cancer drugs in a user-friendly R environment. We have developed several other important use cases; as an example, we have shown that prediction of bortezomib sensitivity in multiple myeloma may be improved by training models on a large set of neoplastic hematological cell lines. We have also shown that the package facilitates model development and prediction using several different classes of data.
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Paul
authors.initials: P
authors.lastname: Geeleher
authors.affiliation: Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Nancy
authors.initials: N
authors.lastname: Cox
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: R Stephanie
authors.initials: RS
authors.lastname: Huang
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology / Q000627:therapeutic use; D019295:Computational Biology / Q000379:methods*; D066264:Datasets as Topic; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009369:Neoplasms / Q000188:drug therapy / Q000235:genetics; D010597:Pharmacogenetics / Q000379:methods*; D016896:Treatment Outcome; D064878:Web Browser
chemical_list: D000970:Antineoplastic Agents