ERBB2 and breast cancer: When stratifying TransNEO and ARTemis + PBCP cohorts by the available BC subtypes, our cell-type-specific models retain good performance across subtypes (Supplementary Figure 3A–D), although the models for ER+,HER2− BC were more predictive than TNBC, possibly due to sample size limitations and the increased heterogeneity in TNBC.