Table 1.

The “BRCAness” characteristics of breast tumors from TCGA database

The PAM50 status and TNBC status (absence of ER, PR and HER2) were taken from The Cancer Immunome Atlas (TCIA) https://tcia.at/home). The Lehmann subtyping was acquired from Lehmann at al [16].. P53 and PIK3CA mutation status were taken from cBioPortal (http://www.cbioportal.org)

Genomic instability measures represent median values calculated for each subtype using data on individual samples taken from iAtlas (https://www.cri-iatlas.org/about/). The values were considered positive for “BRCAness” (green cells) when they were equal or exceeded the threshold. The thresholds were as follows: 1). Frequencies of Basal type, P53 mutation, PIK3CA mutation and TNBC status expressed by BRCA1 germline mutation carriers 2). probability of pCR ≥30% and 3). The threshold for genomic instability measures represented the averaged value for all breast cancer types: 31.1 for SNV neoantigens, 1.54 for non-silent mutation rate, 234.3 for Number of segments, 0.59 for Fraction altered and 41.15 for HR recombination deficiency

*The pCR value given for BRCA2 germline mutation carriers applies to tumors expressing TNBC phenotype only [38] . The specific values for pCR vary depending on the type of therapy, but in most cases are higher for carriers of the germline mutations [39, 40]. pCR values for Lehmann subtypes were taken from Masuda at al. and Omarini at al. 2018 [28, 41]. pCR values for ER+ and HER2+ tumors were taken from I-SPY-2 TRIAL [42]