Iterative sure independent ranking and screening for drug response prediction

BACKGROUND: Prediction of drug response based on multi-omics data is a crucial task in the research of personalized cancer therapy. RESULTS: We proposed an iterative sure independent ranking and screening (ISIRS) scheme to select drug response-associated features and applied it to the Cancer Cell Line Encyclopedia (CCLE) dataset. For each drug in CCLE, we incorporated multi-omics data including copy number alterations, mutation and gene expression and selected up to 50 features using ISIRS. Then a linear regression model based on the selected features was exploited to predict the drug response. Cross validation test shows that our prediction accuracies are higher than existing methods for most drugs. CONCLUSIONS: Our study indicates that the features selected by the marginal utility measure, which measures the conditional probability of drug responses given the feature, are helpful for drug response prediction.