Fig. 4
From: Homologous recombination DNA repair defects in PALB2-associated breast cancers
Comparison of PALB2-associated breast cancers and non-BRCA1/2/PALB2-associated breast cancers. a, b Heatmap depicting the most recurrently mutated genes affecting 410 cancer genes identified in PALB2-associated breast cancers and non-BRCA1/2/PALB2-associated breast cancers from TCGA.19 Cases are shown in columns, genes in rows. Multi-Fisher’s exact test comparisons of mutational frequencies of the mutated genes were performed between a the 24 PALB2-associated breast cancers and the 683 ER+/HER2−, ER+/HER2+ and ER−/HER2− non-BRCA1/2/PALB2-associated breast cancers from TCGA, and b the 18 ER+/HER2− PALB2-associated breast cancers and the 441 ER+/HER2− non-BRCA1/2/PALB2-associated breast cancers from TCGA. P-value of each comparison is shown on the right side of the heatmap, with statistically significant P-values in bold. Indel, small insertion/deletion; SNV, single nucleotide variant. c Box and whisker plots showing the large-scale state transition (LST) scores of the PALB2-associated breast cancers with mono-allelic/bi-allelic PALB2 alterations, ER−/HER2− and ER+ non-BRCA1/2/PALB2-associated breast cancers, and ER−/HER2− and ER+/HER2− non-BRCA1/2/PALB2-associated breast cancers where LST scores could be inferred. The median value of LST scores, and the 75th and 25th percentiles are displayed at the top and bottom of the boxes, respectively. Each dot represents the LST score and/or mutational signature of a given case. Mutational signatures are color-coded according to the legend. *of the 601 ER−/HER2− and ER+ non-BRCA1/2/PALB2-associated breast cancers, the 34 cases lacking LST scores but displaying mutational signatures are not shown, three of these cases display signature 3. **of the 491 ER+/HER2− non-BRCA1/2/PALB2-associated breast cancers, the 29 cases lacking LST scores but displaying mutational signatures are not shown, three of these cases display signature 3. P-values of the comparisons of LST scores are shown using Fisher’s exact tests. N/A signatures not assessable, LST large-scale state transition
