Association of germline variants with somatic variants in breast tumors in a genome-wide study.

Background: In breast tumors, somatic mutation frequencies in and vary by tumor subtype and ancestry. HER2 positive and triple negative breast cancers (TNBC) have a higher frequency of somatic mutations than other subtypes. mutations are more frequently observed in hormone receptor positive tumors. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic or mutation status in breast tumors.

Methods: A genome-wide association study was conducted using breast cancer mutation status of and and functional mutation categories including gain of function (GOF) and loss of function mutations and activating/hotspot mutations. The discovery analysis consisted of 2850 European ancestry women from three datasets. Germline variants showing evidence of association with somatic mutations were selected for validation analyses based on predicted function, allele frequency, and proximity to known cancer genes or risk loci. Candidate variants were assessed for association with mutation status in a multi-ancestry validation study, a Malaysian study, and a study of African American/Black women with TNBC.

Results: The discovery Germline x Mutation (GxM) association study found five variants associated with one or more phenotypes with values <1×10, 33 variants associated with one or more phenotypes with values <1×10, and 44 variants associated with one or more phenotypes with values <1×10. In the multi-ancestry and Malaysian validation studies, germline locus variant, rs9383938, was associated with the presence of mutations overall ( values 6.8×10 and 9.8×10, respectively) and GOF mutations ( value 8.4×10). Multiple variants showed suggestive evidence of association with mutation status in the validation studies, but none were significant after correction for multiple comparisons.

Conclusions: We found evidence that germline variants were associated with and mutation status in breast cancers. Variants near the estrogen receptor alpha gene, were significantly associated with overall mutations and GOF mutations. Larger multi-ancestry studies are needed to confirm these findings and determine if these variants contribute to ancestry-specific differences in mutation frequency.