Additional file 2 of Genomic and transcriptomic analysis of breast cancer identifies novel signatures associated with response to neoadjuvant chemotherapy

Additional file 2: Table S1. The summary of clinical information and sequencing data of the NACBC sequencing set. Table S2. Characteristics of patients included in the NACBC sequencing and validation sets. Table S3. The relative weights of the COSMIC mutational signatures. Table S4. Changed somatic variants in CNR2, KIAA1549, or CCDC168 after NAC. Table S5. Differences in the expression levels of genes related to KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION, GOBP_POSITIVE_REGULATION_OF_GAMMA_DELTA_T_CELL_ACTIVATION, and HALLMARK_ANGIOGENESIS pathway between pre- and post-treatment. Table S6. Differences in the expression levels of genes related to HALLMARK_DNA_REPAIR pathway between the nonresponsive and responsive groups. Table S7. Significantly mutated genes in the pre-treatment tumors. Table S8. The frequency of non-synonymous SMG between the nonresponsive and responsive tumors.Table S9. Prediction of biological functional impact of somatic variants on protein functions. Table S10. Association of ADGRA2 or ADRB3 protein expression with clinicopathological parameters in the NACBC validation set.