Supplemental tableI. Design of primers used in genotyping of 19 candidate gene single nucleotide polymorphisms

Gene / SNP ID / PCR primer 1 / PCR Primer 2 / Extension Primer
ERCC1 / rs3212961 / ACGTTGGATGCTTGGAAGGGATTCAACAGC / ACGTTGGATGAGGTGGATGTGGTAAGCAGG / CATGGGCTGCTCCCTAGCCAGCCTCAC
ERCC1 / rs11615 / ACGTTGGATGTTGATGGCTTCTGCCCTTCG / ACGTTGGATGATAGTCGGGAATTACGTCGC / GGGTCCAAATTCCCAGGGCAC
ERCC2 / rs238415 / ACGTTGGATGTCGGCCTTGTGCTTCAATAG / ACGTTGGATGGCAAAGGTGTCTTAAGTAGG / GTTCAGTAGGACACAAAAGGCACCTG
ERCC2 / rs13181 / ACGTTGGATGCACCAGGAACCGTTTATGGC / ACGTTGGATGAGCAGCTAGAATCAGAGGAG / GAATCAGAGGAGACGCTG
ERCC2 / rs1052555 / ACGTTGGATGTCACAGATGCCAACCTCAAC / ACGTTGGATGTCTGCCGCAGGAAGTACTTG / CCCTGCCACCTGGACACCCTC
ERCC4 / rs1799802 / ACGTTGGATGAAAAGGAACTGGTCCTAGAA / ACGTTGGATGCTCTCCTTATTTTCTGCCTC / ATAATTCAGTCAGTGCCTCCCACTTTG
ERCC4 / rs1800067 / ACGTTGGATGCCGCTCCAAGAGTGATATAG / ACGTTGGATGGGTCAAGTACTGATTTGTGC / GATTTGTGCAAGTGATGACC
ERCC5 / rs4150388 / ACGTTGGATGATGATTCTGAGAGGCAGGTC / ACGTTGGATGGAGTCATCAAGCCTGAAAAG / CCCCAGGCTTTCAGATTCTAAAC
ERCC5 / rs17655 / ACGTTGGATGACCTGCCTCTCAGAATCATC / ACGTTGGATGTTCGCAGCTGTTCTCCTTTG / ATTAAAGATGAACTTTCAGCAT
ERCC5 / rs9514066 / ACGTTGGATGCAGTTTCTGTTGCCATGGAG / ACGTTGGATGTGTTATGCCTCTCTTCTGGG / CCTCTCTTCTGGGTTTTTC
ERCC5 / rs9514067 / ACGTTGGATGTAGAAGAGTCATCAAGCCTG / ACGTTGGATGATGATTCTGAGAGGCAGGTC / CCACAAATCCACCGCATGTATTCTTTC
XRCC1 / rs25487 / ACGTTGGATGAGGATAAGGAGCAGGGTTGG / ACGTTGGATGTAAGGAGTGGGTGCTGGACT / CCCCTCGGCGGCTGCCCTCCC
XRCC1 / rs25489 / ACGTTGGATGTTTGCCTGTCACTGCCCCCT / ACGTTGGATGTTTGTCTTCTCCAGTGCCAG / CCCTACAGTGCCAGCTCCAACTC
XRCC2 / rs3218536 / ACGTTGGATGTTCTTCTGATGAGCTCGAGG / ACGTTGGATGTCAGTGCTTAGAGAAGCTTG / GAGAGAAGCTTGTAAATGACTATC
XRCC4 / rs2891980 / ACGTTGGATGAGTCCTTGTGGAAGGTTTAG / ACGTTGGATGGAAACTTGGGTGTTCTTAATG / CCAATGAAATTATAGCCATTAGTTAC
XRCC4 / rs7734849 / ACGTTGGATGACTCTTTGAACAACGAAGTG / ACGTTGGATGACATACACAGATACACTGAC / TTAGATACACTGACACAGATC
XRCC4 / rs1056503 / ACGTTGGATGGCCTGATTCTTCACTACCTG / ACGTTGGATGCTGCTGTTTCTCAGAGTTTC / GAAGATGAGATGTGCTCCTTTTT
XRCC4 / rs963248 / ACGTTGGATGGTACTGCCTCAAACTTCTGG / ACGTTGGATGAAGCTGGGCATGATAGAGTG / GGGCGGTTTAGGTTGGAGGATC
XRCC5 / rs1051685 / ACGTTGGATGGCAAATGCTACTGCTTGCTC / ACGTTGGATGCTTAACCCTTTCCAGAGTCC / GGGGAATCCTCCAACAGCTGTCACA

*Abbreviations: SNP, single nucleotide polymorphism; PCR, polymerase chain reaction;ERCC, excision repair cross complenting gene; XRCC, X-ray repair cross complementing gene.

Supplemental Table II. P-values of univariate analysis for imatinib treatment outcomes according to clinical variables

Referent parameter / Favorable parameter (n) / MCR / CCR / MMR / CMR / LOR / TF / OS
Age / >50 ( 85) / ≤50 (84) / 0.730 / 0450 / 0.430 / 0.450 / 0.567 / 0.753 / 0.617
sex / Male (96) / Female (73) / 0.345 / 0.830 / 0.301 / 0.466 / 0.099 / 0.312 / 0.269
Prior treatment / Presence (35) / Absence (134) / 0.080 / 0.380 / 0.310 / 0.275 / 0.648 / 0.628 / 0.782
Allo-HSCT / Done (7) / Not done (161) / 0.330 / 0.140 / 0.021 / 0.096 / 0.295 / 0.006 / 0.455
IM starting dose / ＞400mg (3) / ≤400 (165) / 0.642 / 0.222 / 0.816 / 0.674 / 0.192 / 0.881 / 0.682
Exposure days of IM / ≤1300adys(76) / ＞1300days (90) / 0.014 / 0.002 / 0.007 / 0.000 / 0.003 / 0.000 / 0.001
Add CG / Presence (23) / Absence (142) / 0.866 / 0.572 / 0.882 / 0.859 / 0.444 / 0.228 / 0.680
Sokal score / Low (48) / Intermediate/High (93) / 0.632 / 0.931 / 0.808 / 0.805 / 0.662 / 0.898 / 0.647

*Abbreviations: MCR, major cytogenetic response; CCR, complete cytogenetic response; MMR, major molecular response; CMR, complete molecular response LOR, loss of response;TF, treatment failure; OS, overall survival; Allo-HSCT,allogeneic hematopoietic stem cell transplantation; IM, imatinib; Add CG additional cytogenetic abnormality
Supplemental tableIII.P-values of univariate analysis for treatment outcomes according to the candidate genotypes in 169 chronic phase patients

Gene / SNP ID / Referent genotype (n) / Favorable genotype (n) / Call rate / MCR / CCR / MMR / CMR / LOR / TF / OS
ERCC1 / rs3212961 / AA/CC (80) / AC (78) / 94.1% / 0.136 / 0.389 / 0.382 / 0.950 / 0.992 / 0.550 / 0.218
ERCC1 / rs11615 / CC/CT (160) / TT (9) / 100% / 0.026 / 0.032 / 0.172 / 0.776 / 0.184 / 0.866 / 0.053
ERCC2 / rs238415 / CC/CG (126) / GG (41) / 98.8% / 0.152 / 0.211 / 0.061 / 0.182 / 0.237 / 0.151 / 0.345
ERCC2 / rs13181 / T(168) / 99.4% / - / - / - / - / - / -
ERCC2 / rs1052555 / TC (14) / CC (151) / 97.6% / 0.824 / 0.631 / 0.878 / 0.356 / 0.753 / 0.921 / 0.785
ERCC4 / rs1799802 / CC (169) / 100% / - / - / - / - / - / -
ERCC4 / rs1800067 / GG (168) / 99.4% / - / - / - / - / - / -
ERCC5 / rs4150388 / GG (168) / 99.4% / - / - / - / - / - / -
ERCC5 / rs17655 / GG (48) / CC/CG (69) / 69.2% / 0.128 / 0.026 / 0.070 / 0.211 / 0.312 / 0.074 / 0.296
ERCC5 / rs9514066 / CC (166) / 98.2% / - / - / - / - / - / -
ERCC5 / rs9514067 / CC (169) / 100% / - / - / - / - / - / -
XRCC1 / rs25487 / AA (7) / AG/GG (161) / 99.4% / 0.514 / 0.271 / 0.715 / 0.857 / 0.328 / 0.006 / 0.567
XRCC1 / rs25489 / AA (4) / AG/GG (164) / 99.4% / 0.475 / 0.952 / 0.869 / 0.752 / 0.026 / 0.488 / 0.541
XRCC2 / rs3218536 / GG (169) / 100% / - / - / - / - / - / -
XRCC4 / rs2891980 / TT/TC (72) / CC (93) / 97.6% / 0.569 / 0.847 / 0.769 / 0.338 / 0.326 / 0.338 / 0.898
XRCC4 / rs7734849 / AA/AT (146) / TT (9) / 91.7% / 0.939 / 0.806 / 0.152 / 0.163 / 0.334 / 0.327 / 0.477
XRCC4 / rs1056503 / GT/GG (159) / TT (9) / 99.4% / 0.890 / 0.801 / 0.144 / 0.169 / 0.317 / 0.303 / 0.443
XRCC4 / rs963248 / AG/GG (104) / AA (10) / 68.0% / 0.274 / 0.494 / 0.040 / 0.138 / 0.365 / 0.105 / 0.463
XRCC5 / rs1051685 / AG (17) / AA (150) / 99.4% / 0.172 / 0.407 / 0.940 / 0.631 / 0.611 / 0.746 / 0.481

*Abbreviations: SNP, single nucleotide polymorphism; ERCC, excision repair cross complementing gene; XRCC, X-ray repair cross complementing gene; MCR, major cytogenetic response; CCR, complete cytogenetic response; MMR, major molecular response; CMR, complete molecular response; LOR, loss of response; TF, treatment failure; TFS, transformation free survival; OS, overall survival

Supplemental table IV. Summary of internal validation using bootstrap survival analysis withERCC1 (rs11615) and ERCC5 (rs17655).

Parameter / Gene / SNP ID / Bootstrap p-value (95% C.I.)
MCR / ERCC1 / rs11615 / 0.020 (0.000, 0.822)
ERCC5 / rs17655 / 0.162 (0.008, 0.9316)
CCR / ERCC1 / rs11615 / 0.030(0.000, 0.812)
ERCC5 / rs17655 / 0.040 (0.000, 0.662)
MMR / ERCC1 / rs11615 / 0.001 (0.000, 0.241)
ERCC5 / rs17655 / 0.096 (0.001, 0.896)
CMR / ERCC1 / rs11615 / 0.548 (0.004,0.997)
ERCC5 / rs17655 / 0.200 (0.002,0.939)
LOR / ERCC1 / rs11615 / 0.998 (0.998,0.999)
ERCC5 / rs17655 / 0.296 (0.007,0.973)
TF / ERCC1 / rs11615 / 0.997 (0.997,0.998)
ERCC5 / rs17655 / 0.062(0.000,0.858)
OS / ERCC1 / rs11615 / 0.999 (0.998, 0.999)
ERCC5 / rs17655 / 0.32 (0.014, 0.996)

*Abbreviations: MCR, major cytogenetic response; CCR, complete cytogenetic response; MMR, major molecular response; CMR, complete molecular response; LOR, loss of response; TF, treatment failure; OS, overall survival; ERCC, excision repair cross complementing gene; XRCC, X-ray repair cross complementing gene; SNP, single nucleotide polymorphisms; CI, confidence interval

Supplemental table V. Results of multivariate analysis for treatment outcomes with clinical variable and significant genotypes

P-value
HR[95%C.I.] / MCR / CCR / MMR / CMR / LOR / TF / OS
ERCC1
(rs11615) / 0.002
5.14[1.83-14.43] / 0.012
3.47[1.31-9.17] / 0.001
5.71[2.13-15.30] / 0.277
2.25 [0.52-9.75] / 0.989
0[-] / 0.979
0[-] / 0.994
0[-]
ERCC5
(rs17655) / 0.699
1.10 [0.68-1.78] / 0.263
1.35[0.80-2.28] / 0.246
1.41[0.79-2.54] / 0.582
1.20[0.63-2.26] / 0.227
0.40[0.09-1.78] / 0.352
0.67[0.29-1.55] / 0.803
0.80[0.14-4.72]
XRCC1
(rs25489) / 0.222
0.52 [0.18-1.49] / 0.478
0.65[0.20-2.15] / 0.468
0.64[0.19-2.14] / 0.907
0.92[0.21-4.04] / 0.193
0.33[0.06-1.76] / 0.835
0.86[0.20-3.70] / 0.992
1.6E6[0.00-]
Allo HSCT
(done vs not done) / 0.789
0.82 [0.19-3.49] / 0.343
0.38[0.05-2.83] / 0.395
0.42[0.06-3.13] / 0.595
0.57[0.07-4.53] / 0.993
0[-] / 0.051
3.51[0.99-12.40] / 0.93
0.89[0.07-11.3]
Exposure days of IM
(≤1300 vs >1300 days) / 0.006
2.18 [1.25-3.80] / 0.015
1.99[1.15-3.47] / 0.243
1.43[0.79-2.60] / 0.026
2.48[1.11-5.53] / 0.062
0.21[0.04-1.08] / 0.000
0.11[0.04-0.31] / 0.004
0.04[0.00-0.35]
Add CG abnormality (presence vs absence) / 0.465
0.32 [0.33-1.68] / 0.175
0.53[0.21-1.33] / 0.287
0.57[0.20-1.61] / 0.882
0.92[0.31-2.77] / 0.113
4.56[0.70-29.81] / 0.012
3.46[1.31-9.10] / 0.954
0.11[0.11-8.48]
Sokal score
(low /Int. high) / 0.576
1.15 [0.70-1.89] / 0.786
1.07[0.64-1.80] / 0.987
1.01[0.58-1.75] / 0.936
0.98[0.53-1.80] / 0.570
0.65[0.14-2.93] / 0.428
0.72[0.31-1.64] / 0.843
0.84[0.14-4.9]

*Abbreviations: HR, hazard ratio; C.I., confidence interval; add GC abnormality, additional cytogenetic abnormality; Int, intermediate; ERCC, excision repair cross complementing gene; XRCC, X-ray repair cross complementing gene; MCR, major cytogenetic response; CCR, complete cytogenetic response; MMR, major molecular response; CMR, complete molecular response; LOR, loss of response; TF, treatment failure; OS, overall survival

Supplemental figure I.Linkage disequilibrium plot of SNPs evaluated in the present study