Table 1 Step I: SNPs with P<0.05 in univariate analysis of PFS, OS and grades 3–4 toxicity

PFS

ATM rs1801516 (Asp1853Asn) Ataxia telangiectasia mutated gene

Regulator of tumour suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9 and DNA repair protein NBS1.

ERCC5 rs1047768 (T335C, His46His)

Involved in excision repair of UV-induced DNA damage.

XPG, excision repair cross-complementing (5) gene

GADD45A rs532446 (T3812C) Growth arrest and DNA-damage-inducible gene, α

The protein product of this gene responds to environmental stresses by mediating activation of the p38/JNK pathway through MTK1/MEKK4 kinase.

RAD51 rs1801320 (G287C, Arg 96Pro)

Involved in the homologous recombination and repair of DNA.

RecA homologue gene

ATM rs609429 (IVS48+238 C>G) Ataxia telangiectasia mutated gene

Regulator of tumour suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, and DNA repair protein NBS1.

OGG1 rs1052133 (Ser 326Cys) 8-Oxoguanine DNA glycosylase gene

Excision of 8-oxoguanine, a mutagenic base by-product that occurs as a result of exposure to reactive oxygen.

BRCA2 rs15869 (105 bp 3′of STP A>C) Breast cancer 2, early onset gene

Involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair.

OS

LIG4 rs1805388 (−176 C>T, Thr 9Ile) DNA ligase IV gene

DNA ligase that joins single-strand breaks through non-homologous end joining. This protein forms a complex with the X-ray repair cross-complementing protein 4 (XRCC4).

BARD1 rs2070093 (His 506His)

Forms a complex with BRCA1 that may be an essential aspect of tumour suppression by BRCA1.

BRCA1-associated RING domain 1 gene

OGG1 rs1052133 (Ser 326Cys) 8-Oxoguanine DNA glycosylase gene

Excision of 8-oxoguanine, a mutagenic base by-product that occurs as a result of exposure to reactive oxygen.

GADD45A rs532446 (T3812C) Growth arrest and DNA-damage-inducible gene, α

The protein product of this gene responds to environmental stresses by mediating activation of the p38/JNK pathway through MTK1/MEKK4 kinase.

ATM rs609429 (IVS48+238 C>G) Ataxia telangiectasia mutated gene

Regulator of tumour suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, and DNA repair protein NBS1.

LIG4 rs1805389 (−194 C>T) DNA ligase IV gene

DNA ligase that joins single-strand breaks through non-homologous end joining. This protein forms a complex with the X-ray repair cross-complementing protein 4 (XRCC4).

MUTYH rs3219489 (Gln 324His) MUT Y homologue

Encodes a DNA glycosylase involved in oxidative DNA damage repair; excises adenine bases that are inappropriately paired with, eg 8-oxo-7,8-dihydroguanine (major oxidative DNA damage).

XRCC1 rs25487 (G1301A, Arg 399Gln) X-ray repair complementing defective repair (1)

Involved in the efficient repair of DNA single-strand breaks formed by exposure to ionizing radiation and alkylating agents.

Toxicity

ERCC2 rs238406 (C499A, Arg156Arg) XPD (excision repair cross-complementing rodent repair deficiency, complementation group 2)

The protein encoded by this gene is involved in transcription-coupled nucleotide excision repair of damaged DNA, and is an integral member of the basal transcription factor BTF2/TFIIH complex.

MGMT rs1803965 (C171T, Leu 53Leu)

DNA repair gene regulated by p53, confers resistance to alkylating agents

O-6-methylguanine-DNA methyltransferase

MGMT rs12917 (C262T, Leu 84Phe)

DNA repair gene regulated by p53, confers resistance to alkylating agents

O-6-methylguanine-DNA methyltransferase

LIG1 rs3730849 (IVS2+12 C>T) DNA ligase I

LIG1 encodes DNA ligase I, with functions in DNA replication and the base excision repair process. Mutations in LIG1 that lead to DNA ligase I deficiency result in immunodeficiency and increased sensitivity to DNA-damaging agents.