Finding Mutated Subnetworks Associated with Survival in Cancer (1604.02467v2)

Abstract: Next-generation sequencing technologies allow the measurement of somatic mutations in a large number of patients from the same cancer type. One of the main goals in analyzing these mutations is the identification of mutations associated with clinical parameters, such as survival time. This goal is hindered by the genetic heterogeneity of mutations in cancer, due to the fact that genes and mutations act in the context of pathways. To identify mutations associated with survival time it is therefore crucial to study mutations in the context of interaction networks. In this work we study the problem of identifying subnetworks of a large gene-gene interaction network that have mutations associated with survival. We formally define the associated computational problem by using a score for subnetworks based on the test statistic of the log-rank test, a widely used statistical test for comparing the survival of two populations. We show that the computational problem is NP-hard and we propose a novel algorithm, called Network of Mutations Associated with Survival (NoMAS), to solve it. NoMAS is based on the color-coding technique, that has been previously used in other applications to find the highest scoring subnetwork with high probability when the subnetwork score is additive. In our case the score is not additive; nonetheless, we prove that under a reasonable model for mutations in cancer NoMAS does identify the optimal solution with high probability. We test NoMAS on simulated and cancer data, comparing it to approaches based on single gene tests and to various greedy approaches. We show that our method does indeed find the optimal solution and performs better than the other approaches. Moreover, on two cancer datasets our method identifies subnetworks with significant association to survival when none of the genes has significant association with survival when considered in isolation.