To confirm that our model predicts HRD based on the phenotypic differences between estrogen receptor-negative (ER −) and ER-positive (ER +) breast cancer samples, we calculated the receiving operating curve (ROC) and precision-recall curve (PRC) for the following subgroups: ER + /HER2 + , ER + /HER2 − , ER − /HER2 + , ER − /HER2 − achieving AUROCs of 0.66 ± 0.3, 0.8 ± 0.09, 0.72 ± 0.43, and 0.62 ± 0.11 (Additional File 5: Fig. 4A–H) indicating HRD could be predicted detached from morphological subtypes. Here, ERBB2 is linked to breast cancer.