Concurrence Topology of Some Cancer Genomics Data

Abstract

The topological data analysis method "concurrence topology" is applied to mutation frequencies in 69 genes in glioblastoma data. In dimension 1 some apparent "mutual exclusivity" is found. By simulation of data having approximately the same second order dependence structure as that found in the data, it appears that one triple of mutations, PTEN, RB1, TP53, exhibits mutual exclusivity that depends on special features of the third order dependence and may reflect global dependence among a larger group of genes. A bootstrap analysis suggests that this form of mutual exclusivity is not uncommon in the population from which the data were drawn.