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Table 1 Significant SNPs (FDR q value < 0.005) associated with paclitaxel response along with statistical information

From: Bioinformatic analyses identifies novel protein-coding pharmacogenomic markers associated with paclitaxel sensitivity in NCI60 cancer cell lines

CHR Marker RS_ID Gene Name Gene Description A1 AF_R AF_S A2 UNADJ BONF FDR_BH CHISQ OR L95 U95
1p31.1 91699 rs371363 LPHN2 Latrophilin 2, G-protein coupled receptor A 0.5 0.0714 G 2.58E-06 0.2051 0.00477 22.11 13 3.741 45.17
2q14 1413956 rs1898705    A 0.571 0.0851 G 1.76E-06 0.1405 0.003902 22.84 14.33 3.975 51.69
2q14.3 1421343     C 0.438 0.0313 A 1.32E-07 0.01052 0.001169 27.84 24.11 5.296 109.8
2q31.2 1481588     T 0.25 0 C 1.02E-06 0.08144 0.003192 23.88 NA NA NA
2q33.1 1503580     A 0.5 0.0375 G 1.26E-06 0.1006 0.003354 23.48 25.67 4.721 139.5
2q35 1523870 rs6739040    A 0.286 0 G 1.39E-06 0.1104 0.003451 23.3 NA NA NA
2q36.3 1538316     T 0.375 0.0213 C 4.74E-07 0.03773 0.002331 25.37 27.6 4.902 155.4
3p24.3 1743877     C 0.286 0 A 2.32E-07 0.0185 0.001542 26.74 NA NA NA
3p14.2 1785132     G 0.333 0.0106 C 6.86E-07 0.05459 0.002481 24.66 46.5 4.628 467.2
3p12.3 1805457 rs1032966 ROBO1 roundabout, axon guidance receptor, homolog 1 (Drosophila) A 0.333 0.0111 G 1.20E-06 0.09528 0.003354 23.58 44.5 4.428 447.3
3q26.1 1876142 rs2404571    G 0.667 0.0854 A 2.81E-07 0.02238 0.001721 26.38 21.43 5.136 89.41
4p15.3 1929743 rs685064    C 0.313 0.0114 T 2.01E-06 0.1602 0.004162 22.58 39.55 4.224 370.3
5q23.2 2254477 rs959300    G 0.714 0.1111 A 9.98E-08 0.007946 0.001135 28.38 20 5.274 75.84
5q33.3 2292501 rs7715464 SGCD sarcoglycan, delta (35kDa dystrophin-associated glycoprotein) A 0.563 0.0851 G 1.04E-06 0.08298 0.003192 23.85 13.82 4.06 47.05
5q33.3 2294131     A 0.313 0.0102 G 5.15E-07 0.04098 0.002331 25.21 44.09 4.714 412.4
6p25.1 2325528 rs2073042    A 0.786 0.1622 G 1.12E-06 0.08914 0.003301 23.71 18.94 4.587 78.25
6p22.3 2343860     A 0.917 0.141 C 5.87E-09 0.000467 0.000156 33.88 67 7.85 571.8
6q14 2403189     A 0.333 0.0116 G 2.09E-06 0.1665 0.004162 22.51 42.5 4.227 427.3
6q22.1 2440993 rs594930    C 0.4 0.0217 T 1.38E-06 0.1098 0.003451 23.31 30 4.542 198.2
7q31.2 2626491 rs213988 CFTR Cystic fibrosis transmembrane conductance regulator G 0.438 0.0444 A 2.03E-06 0.1616 0.004162 22.57 16.72 4.093 68.31
8p12 2715222     G 0.25 0 A 1.72E-06 0.1373 0.003902 22.88 NA NA NA
8q11.22 2727769 rs2385525    C 0.429 0.0217 T 7.93E-08 0.006315 0.001052 28.82 33.75 5.829 195.4
8q11.22 2727770 rs2132528    G 0.5 0.0256 A 3.77E-08 0.003005 0.00063 30.26 38 6.591 219.1
8q11.22 2727954     T 0.583 0.0778 G 1.75E-06 0.1392 0.003902 22.85 16.6 4.165 66.17
8q11.22 2728154 rs318885 SNTG1 syntrophin, gamma 1 G 0.6 0.025 T 1.70E-09 0.000136 6.78E-05 36.29 58.5 8.841 387.1
8q24.21 2806750 rs2568409    G 0.643 0.0455 T 4.79E-10 3.81E-05 3.81E-05 38.76 37.8 8.573 166.7
9p23 2835786     G 0.25 0 A 6.07E-07 0.04836 0.002418 24.89 NA NA NA
9p23 2836025 rs7470838 PTPRD protein tyrosine phosphatase, receptor type, D T 0.857 0.2245 C 1.47E-06 0.1168 0.003538 23.19 20.73 4.311 99.66
9p23 2836880     T 0.714 0.1413 C 1.26E-06 0.1005 0.003354 23.48 15.19 4.143 55.72
9p22.2 2845463     G 0.25 0 A 7.88E-07 0.06275 0.002728 24.39 NA NA NA
9p21.2 2856599 rs2060439    G 0.25 0 A 6.07E-07 0.04836 0.002418 24.89 NA NA NA
9q21.33 2897567     G 0.6 0.0488 A 1.24E-07 0.009894 0.001169 27.95 29.25 5.814 147.2
11q14.1 494182 rs7927911    A 0.429 0.0256 C 8.37E-07 0.06661 0.002775 24.27 28.5 4.912 165.4
12q21 629187     G 0.25 0 A 3.61E-07 0.02874 0.002053 25.89 NA NA NA
13q13.3 709113 rs7335400    A 0.563 0.0714 C 1.58E-07 0.01257 0.001251 27.49 16.71 4.781 58.43
13q21.33 748668     G 0.857 0.1628 A 3.96E-08 0.003151 0.00063 30.17 30.86 6.213 153.2
13q32.1 779846 rs727299 DCT dopachrome tautomerase T 0.313 0.01 C 3.92E-07 0.03122 0.002081 25.73 45 4.812 420.8
16p13.3 997458 rs714181 BTBD12 BTB (POZ) domain containing 12 A 0.313 0.0104 G 6.76E-07 0.05379 0.002481 24.68 43.18 4.616 404
16p13.12 1011445 rs251919    C 0.438 0.0385 T 2.41E-06 0.1918 0.004566 22.24 19.44 4.257 88.81
16q23.3 1071765     G 0.571 0.0745 C 5.27E-07 0.04196 0.002331 25.16 16.57 4.476 61.35
18p11.22 1162169 rs3975417    T 0.333 0.0116 C 2.09E-06 0.1665 0.004162 22.51 42.5 4.227 427.3
19q13.12 1266548 rs958305 ZNF607 zinc finger protein 607 C 0.5 0.061 T 2.18E-06 0.1738 0.004239 22.43 15.4 4.058 58.44
21q21.3 1647581 rs457531 GRIK1 glutamate receptor, ionotropic, kainate 1 T 0.5 0.0349 C 1.73E-07 0.01377 0.001251 27.31 27.67 5.504 139.1
  1. Significant SNPs were traced back to their genes using dbSNP Build 131 in order to identify which protein-coding genes they belonged to. (CHR = Chromosome loci, Marker = SNP ID number on Affymetrix 125 k SNP Array, RS_ID = SNP rs number, Gene Name = Notation for gene as found on Human Genome Organization Gene Nomenclature Committee website, A1 = Associated SNP allele, A2 = Alternate variant allele, AF_R = Frequency of associated allele in resistant cell lines, AF_S = frequency of associated allele in sensitive cell lines, UNADJ = unadjusted p value, BONF = Bonferroni correction value, FDR_BH = FDR correction value, CHISQ = Chi-Squared Value, OR = Odds Ratio, L95 = Lower Bound of 95% confidence interval for odds ratio, U95 = Upper Bound of 95% confidence interval for odds ratio). Statistics with NA written indicate that the statistic could not be calculated. This GWAS was performed using only 58 of the 62 cell lines which had drug response data available since the remaining 4 cell lines lacked available genotype data.
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BMC Medical Genomics

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