Genomic Signature of Homologous Recombination Deficiency in Breast and Ovarian Cancers

Homologous recombination deficiency, mainly resulted from BRCA1 or BRCA2 inactivation (so called BRCAness), is found in breast and ovarian cancers. Detection of actual inactivation of BRCA1/2 in a tumor is important for patients’ treatment and follow-up as it may help predicting response to DNA damaging agents and give indication Homologous recombination deficiency, mainly resulted from BRCA1 or BRCA2 inactivation (so called BRCAness), is found in breast and ovarian cancers. Detection of actual inactivation of BRCA1/2 in a tumor is important for pat for genetic testing. This protocol describes how to detect impairment of homologous recombination based on the tumor genomic profile measured by SNP-array. The proposed signature of BRCAness is related to the number of large-scale chromosomal breaks in a tumor genome calculated after filtering and smoothing small-scale alterations. The procedure strongly relies on good quality SNP-arrays preprocessed to absolute copy number and allelic content (allele-specific copy number) profiles. This genomic signature of homologous recombination deficiency was shown to be highly reliable in predicting BRCA1/2 inactivation in triple-negative breast carcinoma (97% accuracy; for more details, see Popova et al., 2012) and predictive of survival in ovarian carcinoma (unpublished data). Authors are grateful to Dominique Stoppa-Lyonnet, Anne Vincent-Salomon, Thierry Dubois, and Xavier Sastre-Garau for their contributions. (Patent was deposited: Reference number EP12305648.3, June 7, 2012)