- 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]
