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Homologous recombination (HR) DNA repair is of clinical relevance in breast cancer. Three DNA-based homologous recombination deficiency (HRD) scores (HRD-loss of heterozygosity score (LOH), HRD-telomeric allelic imbalance score (TAI), and HRD-large-scale state transition score (LST)) have been developed that are highly correlated with defects in  BRCA1/2 , and are associated with response to platinum therapy in triple negative breast and ovarian cancer. This study examines the frequency of  BRCA1/2  defects among different breast cancer subtypes, and the ability of the HRD scores to identify breast tumors with defects in the homologous recombination DNA repair pathway.    Methods  215 breast tumors representing all  ER/HER2  subtypes were obtained from commercial vendors. Next-generation sequencing based assays were used to generate genome wide SNP profiles,  BRCA1/2  mutation screening, and  BRCA1  promoter methylation data.    Results   BRCA1/2  deleterious mutations were observed in all breast cancer subtypes.  BRCA1  promoter methylation was observed almost exclusively in triple negative breast cancer.  BRCA1/2  deficient tumors were identified with  BRCA1 /2 mutations, or  BRCA1  promoter methylation, and loss of the second allele of the affected gene. All three HRD scores were highly associated with  BRCA1/2  deficiency (HRD-LOH:  P  = 1.3 × 10 -17 ; HRD-TAI:  P  = 1.5 × 10 -19 ; HRD-LST:  P  = 3.5 × 10 -18 ). A combined score (HRD-mean) was calculated using the arithmetic mean of the three scores. In multivariable analyses the HRD-mean score captured significant  BRCA1/2  deficiency information not captured by the three individual scores, or by clinical variables ( P  values for HRD-Mean adjusted for HRD-LOH:  P  = 1.4 × 10 -8 ; HRD-TAI:  P  = 2.9 × 10 -7 ; HRD-LST:  P  = 2.8 × 10 -8 ; clinical variables:  P  = 1.2 × 10 -16 ).    Conclusions  The HRD scores showed strong correlation with  BRCA1/2  deficiency regardless of breast cancer subtype. The frequency of elevated scores suggests that a significant proportion of all breast tumor subtypes may carry defects in the homologous recombination DNA repair pathway. The HRD scores can be combined to produce a more robust predictor of HRD. The combination of a robust score, and the FFPE compatible assay described in this study, may facilitate use of agents targeting homologous recombination DNA repair in the clinical setting.    Electronic supplementary material  The online version of this article (doi:10.1186/s13058-014-0475-x) contains supplementary material, which is available to authorized users.

Association of BRCA1/2defects with genomic scores predictive of DNA damage repair deficiency among breast cancer subtypes