Table 1.

DNA repair pathways and 123 genes employed in this study for overall survival (OS) prediction.

DNA Repair Pathway	Genes
Direct reversal repair (DRR)	ALKBH2, ALKBH3, MGMT
Base excision repair (BER)	APEX1, APEX2, APTX, FEN1, LIG1, LIG3, MBD4, MPG, MUTYH, NEIL1, NEIL2, NEIL3, NTHL1, OGG1, PARP1, PARP2, PCNA, PNKP, POLB, POLD1, POLE, POLL, WRN, SMUG1, TDG, UNG, XRCC1
Non-homologous end-joining (NHEJ)	DCLRE1C, XRCC6, XRCC5, LIG4, NHEJ1, POLM, PRKDC, XRCC4
Mismatch repair (MMR)	EXO1, MLH1, MLH3, MSH2, MSH3, MSH6, PMS1, PMS2
Translesion synthesis (TLS)	POLH, POLI, POLK, POLN, POLQ, REV1, REV3L
DNA damage signaling (DDS)	ATM, ATR, ATRIP, BLM, BRCA1, CCNH, CDK7, CDKN1A, CHEK1, CHEK2, COPS5, DCLRE1A, DCLRE1B, FANCA, FANCC, GPS1, HUS1, MDC1, MNAT1, MRE11A, NBN, RAD1, RAD17, RAD18, RAD23A, RAD50, RAD9A, RFC1, RFC2, RFC3, RFC4, RFC5, TOPBP1, TP53
Homologous recombination repair (HRR)	BRCA2, FAAP24, EME1, EME2, FANCB, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, MSH4, MSH5, MUS81, RAD51, RAD52
Nucleotide excision repair (NER)	ERCC8, ERCC6, CUL4A, DDB1, DDB2, ERCC1, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MMS19, RAD23B, RPA1, XPA, ERCC3, XPC, ERCC2, ERCC4, ERCC5