In order to build the predictive model, we utilized publicly available datasets27 of clinicopathological and WXS data from neoadjuvant treated HER2+ breast cancer for training (TransNEO cohort; 57 HER2+ pre-treatment tumour biopsies) (Supplementary Table 9) and independent test set (ARTemis/PBCP cohort; 18 HER2+ pre-treatment tumour biopsies; Supplementary Table 10). Here, ERBB2 is linked to breast cancer.