PT  - JOURNAL ARTICLE
AU  - Tingting Jiang
AU  - Uri Shaham
AU  - Fabio Parisi
AU  - Ruth Halaban
AU  - Anton Safonov
AU  - Harriet Kluger
AU  - Sherman Weissman
AU  - Joseph Chang
AU  - Yuval Kluger
TI  - Methods for detecting co-mutated pathways in cancer samples to inform treatment selection
AID  - 10.1101/082552
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 082552
4099  - http://biorxiv.org/content/early/2016/10/22/082552.short
4100  - http://biorxiv.org/content/early/2016/10/22/082552.full
AB  - Tumor genomes evolve through a selection of mutations. These mutations may complement each other to promote tumorigenesis. To better understand the functional interactions of different processes in cancer, we studied mutation data of a set of tumors and identified significantly co-mutated pathways. Fisher’s exact test is a standard approach that can be used to assess the significance of the joint dysregulation of pathways pairs across a patient population. We developed a robust test to identify co-occurrence using DNA mutations, which overcomes deficiencies of the Fisher’s exact test by taking into account the large variability in overall mutation load and sequencing depth. Applying our method to a study of six common cancer types, we identify enrichment of co-mutated signal transduction pathways such as IP3 synthesis and PI3K and pairs of co-mutated pathways involving other processes such as immunity and development. We observed enrichment of clonal co-mutation of the proteasome and apoptosis pathways in colorectal cancer, which suggests potential mechanisms for immune evasion.