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Background  Women with breast cancer who have multiple affected relatives are more likely to have inherited genetic risk factors for the disease. All the currently known genetic risk factors for breast cancer account for less than half of the average familial risk. Furthermore, the genetic factor(s) underlying an increased cancer risk for many women from multiple-case families remain unknown. Rare genomic duplications and deletions, known as copy number variants (CNVs), cover more than 10% of a human genome, are often not assessed in studies of genetic predisposition, and could account for some of the so-called “missing heritability”.    Methods  We carried out a hypothesis-generating case-control study of breast cancer diagnosed before age 40 years (200 cases, 293 controls) using population-based cases from the Australian Breast Cancer Family Study. Genome-wide scanning for CNVs was performed using the Human610-Quad BeadChip and fine-mapping was conducted using PennCNV.    Results  We identified deletions overlapping two known cancer susceptibility genes, ( BRCA1  and  BLM) , and a duplication overlapping  SMARCB1 , associated with risk. The number of deletions across the genome was 1.5-fold higher for cases than controls ( P  = 10 -16 ), and 2-fold higher when only rare deletions overlapping genes (frequency <1%) were assessed ( P  = 5 × 10 -4 ). Association tests of CNVs, followed by experimental validation of CNV calls, found deletions overlapping the  OR4C11  and  OR4P4  genes were associated with breast cancer ( P  = 0.02 and  P  = 0.03, respectively).    Conclusion  These results suggest rare CNVs might have a role in breast cancer susceptibility, at least for disease at a young age.    Electronic supplementary material  The online version of this article (doi:10.1186/s13058-017-0825-6) contains supplementary material, which is available to authorized users.

Increased genomic burden of germline copy number variants is associated with early onset breast cancer: Australian breast cancer family registry