Additional file 2 of Multi-scale characterisation of homologous recombination deficiency in breast cancer

Additional file 2: Supplementary Data Table S1. Mutational signature phenotype clustering of the ICGC breast cancer cohort. Table S2. HRD classification and signature phenotype assignment of the TCGA-BRCA cohort. Table S3. ANOVA analysis of hypoxia levels as a function of ER, BRCA-defect, and HRD status in the TCGA-BRCA cohort. Table S4. The 228-gene HRD signature with centroid templates for each group developed using the TCGA-BRCA training cohort. Table S5. The reduced 26-gene HRD signature with importance values calculated using a graph attention network. Table S6. HRD scores and PRISM values of PARP inhibitor sensitivity for 26 breast cancer cell lines obtained from the Cancer Cell Line Encyclopaedia.