Germline copy number variants are not associated with globally acquired copy number changes in familial breast tumours

A characteristic of sporadic and familial breast tumours is genomic instability, resulting from either inherited mutations in genes that control genome integrity or mutations that are acquired in somatic cells during development. It is well established that abnormal chromosome number and structural changes to chromosomes play an important role in the cause and progression of breast cancer. Familial BRCA1 breast tumours are characterised by basal-like phenotype and high-histological grade which are typically associated with increased genomic instability. Consistent with previous studies, the genomes with the greatest number of base pairs covered by copy number change were typically found in basal-like and/or high-histological grade breast tumours within our cohort. Moreover, we show that luminal A tumours that are high grade had significantly less copy number variant (CNV) coverage than the more clinically aggressive high-grade luminal B tumours, suggesting that chromosomal instability rather than cellular differentiation contributes to the aggressive nature of luminal B tumours. It has previously been proposed that germline CNVs may contribute to somatically acquired chromosome changes in the tumour, but this is the first study to address this idea in breast cancer. By comparing germline CNVs and tumour-specific CNVs in matched breast tumour and normal tissue using data from the Illumina Human CNV370 duo beadarray, we provide evidence that germline CNVs do not tend to act as a foundation on which larger chromosome copy number aberrations develop in tumour cells. Further studies are required with increased sequence resolution that will detect smaller CNVs and define CNV breakpoints to comprehensively assess the relationship between inherited genomic variation and genome evolution in breast cancer.