Loss of genes in chromosome arms 5q and 16q in breast cancer.

Abstract

Losses of genetic material from chromosomes 5q and 16q commonly occur in sub-sets of breast cancer. Their significance from a pathophysiologic point of view is not well-defined. This study uses publicly available genomic data from extensive breast cancer datasets to define the landscape of losses in chromosomal arms 5q and 16q in the two sub-types of breast cancer they most commonly occur, basal-like and luminal A cancers, respectively. It is shown that dozens of genes from these chromosomal arms are putatively hemi-deleted in few samples each. No individual gene from either 5q or 16q shows an incidence of deep deletion above 10% in the cohorts with basal-like and luminal A cancers or in the whole cohorts. A few tumor suppressor genes are deleted in a small number of samples, less than 5% in each cohort. Losses of 5q or 16q confer no survival advantage in either the basal-like or the luminal A cohorts from TCGA that harbor them. Results suggest that there are no individual genes in chromosomes 5q and 16q whose loss can be implicated in a dominant pathophysiologic sequence of events in breast cancer or its sub-sets.