The combination of next-generation sequencing technologies, subsequent analyses, validation of therapeutic targets, and testing of sensitivity for drugs in patient-derived xenografts (PDX) is a promising approach to aid treatment decisions in cancer patients. Presented in this protocol is proof-of-principal for this strategy, using ovarian tumors for genomic analyses and treatment testing as an example. The mate-pair next-generation sequencing (MPseq) protocol is used to identify chromosomal rearrangements, including gene fusions and copy number changes, in primary tumors. Further analysis is then performed to determine alterations that may be therapeutically targeted. Selected genomic alterations are validated with individualized primers for DNA chromosomal rearrangements in the tumor DNA (original and derived from PDX). The tumor is grown in immunocompromised mice until palpable, and treatments are administered with drugs that are selected based on genomic analyses. Results demonstrate a good correlation between the predicted and observed responses in the PDX model. This approach can be used to test the efficacy of combination treatments that include targeted drugs.