Fig. 2. Association of DEPTH scores with genomic instability.

a The positive correlations between tumor mutation burden (TMB) and DEPTH scores in pan-cancer and in 11 individual cancer types. Spearman’s correlation test, false discovery rate (FDR), and correlation coefficient (ρ) are shown. The FDR was estimated by the Benjamini and Hochberg method⁶⁶ to adjust for p-values in multiple tests. TMB, the total somatic mutation count in the tumor. b TP53-mutated tumors display significantly higher DEPTH scores than TP53-wildtype tumors in pan-cancer and in multiple individual cancer types (FDR < 0.05). c MSI-high (MSI-H) tumors have significantly higher DEPTH scores than MSI-low (MSI-L)/microsatellite stability (MSS) tumors in COAD, STAD, and ESCA (p ≤ 0.05). MSI, microsatellite instability. d The positive associations between the expression of DNA mismatch repair proteins (PCNA, MSH6, and MSH2) and DEPTH scores within multiple individual cancer types (two-sided Student’s t test, FDR < 0.05). e The four DNA damage response-associated pathways more highly enriched in high-DEPTH-score than in low-DEPTH-score tumors within multiple individual cancer types identified by GSEA³⁴ (FDR < 0.05). high-DEPTH-score, DEPTH scores in the upper third. low-DEPTH-score, DEPTH scores in the bottom third. They also apply to the following figures. f Comparison of DEPTH scores between the pathway-gene-mutated and pathway-gene-wildtype groups for nine DDR pathways. DDR, DNA damage repair. BER, base excision repair. MMR, mismatch repair; BER, base excision repair. NER, nucleotide excision repair. FA, Fanconi Anemia. HDR, homology-dependent recombination. NHEJ, non-homologous DNA end joining. DR, direct damage reversal/repair. TLS, translesion DNA synthesis. g The positive correlation between DEPTH scores and HRD scores in pan-cancer and in 11 individual cancer types. HRD, homologous recombination deficiency. *FDR < 0.05, **FDR < 0.01, ***FDR < 0.001, NS: not significant. It also applies to the following figures.