NCI has used a panel of 60 diverse human cancer cell lines to screen >100K chemical compounds for anticancer activity. We identify common chemosensitivity biomarkers by developing a novel statistical pharmacogenomic approach “Co-eXpression ExtrapolatioN” (COXEN), which can effectively identify concordant genomic chemosensitivity biomarkers between two independent expression profiling data sets, extrapolating the genomic expression patterns of NCI-60 biomarkers with those of clinical tumors. Applying COXEN, we predicted anticancer drug activities on completely independent bladder cancer, which is not included in the NCI-60 panel, and on breast cancer patients treated with commonly used chemotherapeutics with >80% accuracy. We also used COXEN for in silico screening of 45,545 compounds and identify a novel agent with superior growth inhibition activity against human bladder cancer.