Table 2. Summary of available samples in this study.

Summary	Total	Good	Poor	Control
Phase I
Samples with mutations discovered by exome sequencing	108	45	26	36
Patients with paired exome sequencing	49	21	11	17
Patients with exome sequencing from either sample	59	24	15	20
Patients with exome sequencing in baseline	52	22	12	18
Patients with exome sequencing in surgery	56	23	14	19
Phase I and II
Samples with targeted sequencing	163	64	59	40
Patients with targeted sequencing from either sample	86	33	33	20
Patients with paired targeted sequencing	77	31	26	20
Patients with targeted sequencing in baseline	84	32	32	20
Patients with targeted sequencing in surgery	79	32	27	20

Analyses on the mutational load and the mutational clusters were performed on phase I samples with exome sequencing available. Analyses based on 77 breast cancer-related genes were performed on the combined set of phase I and II samples. As indicated in the text, some analyses were performed on patients with paired baseline and surgery samples only.