Fig. 3

Landscape of somatic single nucleotide variants in 70 patients with HER2-positive breast cancer, stratified by early response assessed using MRI after two cycles of neoadjuvant treatment. DNA sequencing was conducted using a custom-designed gene panel encompassing 769 frequently mutated genes in solid tumours. Gene mutations were analysed in relation to early response, which was assessed by MRI after the first two cycles of TCbH treatment according to the Response Evaluation Criteria in Solid Tumours (RECIST) version 1.1. Patients with a partial response (n = 37) were defined as those showing at least a 30% reduction in the sum of the longest diameters of all target lesions from baseline; patients not meeting this criterion were classified as having stable disease (n = 33). The types of gene mutations identified in each patient are annotated, with the mutation rate for each type presented on the left. Additionally, the status of pathological markers, including estrogen receptor (ER), progesterone receptor (PR), and HER2, as determined by immunohistochemistry (IHC), as well as menopause status and pyrotinib treatment, are also shown