Concurrence Topology of Some Cancer Genomics Data

TL;DR

This paper applies concurrence topology, a topological data analysis method, to glioblastoma mutation data, revealing mutual exclusivity patterns and complex dependence structures among genes, with implications for understanding cancer genomics.

Contribution

It introduces the application of concurrence topology to cancer genomics data, uncovering higher-order dependence and mutual exclusivity among gene mutations.

Findings

Mutual exclusivity observed in dimension 1 analysis.

Triple mutation pattern involving PTEN, RB1, TP53 shows higher-order dependence.

Bootstrap analysis indicates such mutual exclusivity is common in the population.

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.