Defining Signatures of Arm-Wise Copy Number Change and Their Associated Drivers in Kidney Cancers.

ABSTRACT: Using pan-cancer data from The Cancer Genome Atlas (TCGA), we investigated how patterns in copy number alterations in cancer cells vary both by tissue type and as a function of genetic alteration. We find that patterns in both chromosomal ploidy and individual arm copy number are dependent on tumour type. We highlight for example, the significant losses in chromosome arm 3p and the gain of ploidy in 5q in kidney clear cell renal cell carcinoma tissue samples. We find that specific gene mutations are associated with genome-wide copy number changes. Using signatures derived from non-negative factorisation, we also find gene mutations that are associated with particular patterns of ploidy change. Finally, utilising a set of machine learning classifiers, we successfully predicted the presence

SUBMITTER: Benstead-Hume G 

PROVIDER: S-EPMC6887958 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature