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Table 2 Integrated analyses for drug response for either (A) Gemcitabine or (B) AraC

From: Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines

SNP Probe set GWAS
rslD Closest gene MAF Chr Position Region Probeset Gene symbol Chr R value (SNP vs IC50) P value (SNP vs IC50) R value (SNP vs Exp) P value (SNP vs Exp) R value (EXP vs IC50) P value (EXP vs IC50)
(A) Gemcitabine
rs316871 PLD5 0.097 1 240409507 Intron 225532_at CABLES1 18 -0.326 4.14E–05 -0.242 6.54E–05 0.347 3.12E–06
rs316823 PLD5 0.093 1 240422651 Intron 225532_at CABLES1 18 -0.288 2.88E–04 -0.257 2.05E–05 0.347 3.12E–06
rs402098 PLD5 0.093 1 240430321 Intron 225532_at CABLES1 18 -0.288 2.88E–04 -0.257 2.05E–05 0.347 3.12E–06
rs427498 PLD5 0.087 1 240424078 Intron 225532_at CABLES1 18 -0.280 4.43E–04 -0.256 2.28E–05 0.347 3.12E–06
rs316823 PLD5 0.093 1 240422651 Intron 225531_at CABLES1 18 -0.288 2.88E–04 -0.239 7.69E–05 0.321 1.72E–05
rs402098 PLD5 0.093 1 240430321 Intron 225531_at CABLES1 18 -0.288 2.88E–04 -0.239 7.69E–05 0.321 1.72E-05
rs4392391 C3orf23 0.419 3 44247970 Downstream 1555906_s_at C3orf23 3 -0.318 5.78E–05 -0.250 3.46E–05 0.263 4.86E–04
rs1565214 C3orf23 0.425 3 44309303 Upstream 1555906_s_at C3orf23 3 -0.308 1.35E–04 -0.251 4.09E–05 0.263 4.86E–04
rs9809107 C3orf23 0.419 3 44257938 Flanking_5UTR 1555906_s_at C3orf23 3 -0.301 1.46E–04 -0.242 5.97E–05 0.263 4.86E–04
rs967285 C3orf23 0.422 3 44250280 Downstream 1555906_s_at C3orf23 3 -0.301 1.48E–04 -0.247 4.36E–05 0.263 4.86E–04
rs9821268 C3orf23 0.413 3 44278128 Upstream 1555906_s_at C3orf23 3 -0.292 2.43E–04 -0.241 6.29E–05 0.263 4.86E–04
rs1565215 C3orf23 0.418 3 44309103 Upstream 1555906_s_at C3orf23 3 -0.291 2.64E–04 -0.246 4.62E–05 0.263 4.86E–04
rs10510741 C3orf23 0.445 3 44239198 Flanking_5UTR 1555906_s_at C3orf23 3 -0.283 3.68E–04 -0.275 4.71E–06 0.263 4.86E–04
rs9852733 C3orf23 0.451 3 44252343 Flanking_5UTR 1555906_s_at C3orf23 3 -0.279 4.59E–04 -0.268 8.53E–06 0.263 4.86E–04
rs6808448 C3orf23 0.451 3 44218611 Flanking_5UTR 1555906_s_at C3orf23 3 -0.273 6.19E–04 -0.273 5.38E–06 0.263 4.86E–04
rs9846155 C3orf23 0.456 3 44257844 Flanking_5UTR 1555906_s_at C3orf23 3 -0.272 6.33E–04 -0.262 1.38E–05 0.263 4.86E–04
rs9284879 C3orf23 0.433 3 44259588 Flanking_5UTR 1555906_s_at C3orf23 3 -0.264 9.43E–04 -0.253 2.65E–05 0.263 4.86E–04
rs12486452 C3orf23 0.433 3 44299569 Flanking_5UTR 1555906_s_at C3orf23 3 -0.264 9.43E–04 -0.241 6.45E–05 0.263 4.86E–04
rs12631341 C3orf23 0.433 3 44284272 Flanking_5UTR 1555906_s_at C3orf23 3 -0.264 9.43E–04 -0.241 6.45E–05 0.263 4.86E–04
rs7631790 C3orf23 0.433 3 44274209 Flanking_5UTR 1555906_s_at C3orf23 3 -0.264 9.43E–04 -0.241 6.45E–05 0.263 4.86E–04
rs4392391 C3orf23 0.419 3 44247970 Downstream 227978_s_at ZADH2 18 -0.318 5.78E–05 0.251 3.11E–05 -0.351 2.42E–06
rs1565214 C3orf23 0.425 3 44309303 Upstream 227978_s_at ZADH2 18 –0.308 1.35E–04 0.246 5.9E–05 -0.351 2.42E–06
rs9809107 C3orf23 0.419 3 44257938 Flanking_5UTR 227978_s_at ZADH2 18 -0.301 1.46E–04 0.273 5.72E–06 -0.351 2.42E–06
rs967285 C3orf23 0.422 3 44250280 Downstream 227978_s_at ZADH2 18 -0.301 1.48E–04 0.254 2.58E–05 -0.351 2.42E–06
rs9821268 C3orf23 0.413 3 44278128 Upstream 227978_s_at ZADH2 18 -0.292 2.43E–04 0.247 4.17E–05 -0.351 2.42E–06
rs1565215 C3orf23 0.418 3 44309103 Upstream 227978_s_at ZADH2 18 -0.291 2.64E–04 0.250 3.46E–05 -0.351 2.42E–06
rs4682949 C3orf23 0.398 3 44220159 Flanking_5UTR 227978_s_at ZADH2 18 -0.287 3.01E–04 0.247 4.14E–05 –0.351 2.42E–06
rs10510741 C3orf23 0.445 3 44239198 Flanking_5UTR 227978_s_at ZADH2 18 -0.283 3.68E–04 0.251 3.03E–05 –0.351 2.42E–06
rs9852733 C3orf23 0.451 3 44252343 Flanking_5UTR 227978_s_at ZADH2 18 –0.279 4.59E–04 0.239 7.38E–05 –0.351 2.42E–06
rs6808448 C3orf23 0.451 3 44218611 Flanking_5UTR 227978_s_at ZADH2 18 -0.273 6.19E–04 0.260 1.62E–05 -0.351 2.42E–06
rs9846155 C3orf23 0.456 3 44257844 Flanking_5UTR 227978_s_at ZADH2 18 -0.272 6.33E–04 0.260 1.58E–05 -0.351 2.42E–06
rs12486452 C3orf23 0.433 3 44299569 Flanking_5UTR 227978_s_at ZADH2 18 -0.264 9.43E–04 0.239 7.52E–05 -0.351 2.42E–06
rs12631341 C3orf23 0.433 3 44284272 Flanking_5UTR 227978_s_at ZADH2 18 -0.264 9.43E–04 0.239 7.52E–05 -0.351 2.42E–06
rs7631790 C3orf23 0.433 3 44274209 Flanking_5UTR 227978_s_at ZADH2 18 -0.264 9.43E–04 0.239 7.52E–05 -0.351 2.42E–06
rs12188464 PIK3RI 0.459 5 67999705 Flanking_5UTR 225935_at ––– 7 -0.309 9.69E–05 0.366 2.47E–06 -0.296 7.99E–05
rs13171512 PIK3RI 0.462 5 68000787 Flanking_5UTR 236170_x_at ––– 7 -0.313 7.86E–05 0.349 7.69E–06 -0.299 6.75E–05
rs13171512 PIK3RI 0.462 5 68000787 Flanking_5UTR 225935_at ––– 7 -0.313 7.86E–05 0.375 1.33E–06 -0.296 7.99E–05
rs7713001 PIK3RI 0.459 5 67999371 Flanking_5UTR 225935_at ––– 7 -0.309 9.69E–05 0.366 2.47E–06 -0.296 7.99E–05
rs12188464 PIK3RI 0459 5 67999705 Flanking_5UTR 201334_s_at ARHGEF12 11 -0.309 9.69E–05 0.380 9.03E–07 -0.339 5.35E–06
rs13171512 PIK3RI 0.462 5 68000787 Flanking_5UTR 201334_s_at ARHGEF12 11 -0.313 7.86E–05 0.372 1.59E–06 -0.339 5.35E–06
rs7713001 PIK3RI 0.459 5 67999371 Flanking_5UTR 201334_s_at ARHGEF12 11 -0.309 9.69E–05 0.380 9.03E–07 -0.339 5.35E–06
rs12188464 PIK3RI 0.459 5 67999705 Flanking_3UTR 238012_at DPP7 9 -0.309 9.69E–05 0.372 1.63E–06 -0.324 1.45E–05
rs13171512 PIK3RI 0.462 5 68000787 Flanking_3UTR 238012_at DPP7 9 -0.313 7.86E–05 0.378 1.08E–06 -0.324 1.45E–05
rs7713001 PIK3RI 0.459 5 67999371 Flanking_3UTR 238012_at DPP7 9 -0.309 9.69E–05 0.372 1.63E–06 -0.324 1.45E–05
rs12188464 PIK3RI 0.459 5 67999705 Flanking_3UTR 225086_at FAM98B 15 -0.309 9.69E–05 0.345 9.5E–06 -0.352 2.18E–06
rs13171512 PIK3RI 0.462 5 68000787 Flanking_3UTR 225086_at FAM98B 15 -0.313 7.86E–05 0.354 5.38E–06 -0.352 2.18E–06
rs3135351 HLA–DRA 0.137 6 32500923 Flanking_5UTR 1566082_at ––– 10 0.265 9.48E–04 0.277 4.24E–06 0.320 1.88E–05
rs2472476 NIPSNAP3B 0.389 9 106571777 Intron 200988_s_at PSME3 17 0.338 1.92E–05 -0.239 7.6E–05 -0.350 .60E–06
rs2928445 IPMK 0.267 10 58816782 Flanking_3UTR 227482_at ADCK1 14 -0.331 2.76E–05 0.247 4.09E–05 -0.293 9.45E–05
rs12244977 IPMK 0.195 10 58762688 Flanking_3UTR 1569396_at RAB40C 16 -0.308 1.03E–04 -0.243 5.72E–05 0.303 5.47E–05
rs12256364 IPMK 0.195 10 58765694 Flanking_3UTR 1569396_at RAB40C 16 -0.308 1.03E–04 -0.243 5.72E–05 0.303 5.47E–05
rs2928445 IPMK 0.267 10 58816782 Flanking_3UTR 226987_at RBM15B 3 -0.331 2.76E–05 0.263 1.2E–05 -0.354 1.90E–06
rs4774760 PIGB 0.416 15 53376504 upstreaintronm 224856_at FKBP5 6 0.326 3.63E–05 -0.241 6.7E–05 -0.411 2.15E–08
rs7174876 PIGB 0.416 15 53406853 Upstream 224856_at FKBP5 6 0.284 4.06E–04 -0.237 9.71E–05 -0.411 2.15E–08
rs2290344 PIGB 0.253 15 53407088 Coding 224856_at FKBP5 6 0.339 1.75E–05 -0.266 9.87E–06 -0.393 9.66E–08
rs4774760 PIGB 0.416 15 53376504 Upstream 204560_at FKBP5 6 0.326 3.63E–05 -0.282 2.7E–06 -0.393 9.66E–08
rs12050587 PIGB 0.45 15 53414820 Intron 224856_at FKBP5 6 0.305 1.23E–04 -0.256 2.27E–05 -0.393 9.66E–08
rs28668016 PIGB 0.365 15 53398725 5UTR 204560_at FKBP5 6 0.304 1.31E–04 -0.261 1.49E–05 -0.393 9.66E–08
rs11636687 PIGB 0.421 15 53392444 Flanking_5UTR 224856_at FKBP5 6 0.302 1.53E–04 -0.252 3.34E–05 -0.393 9.66E–08
rs2414409 PIGB 0.448 15 53419009 Intron 204560_at FKBP5 6 0.299 1.62E–04 -0.264 1.17E–05 -0.393 9.66E–08
rs7183960 PIGB 0.451 15 53409987 Intron 224856_at FKBP5 6 0.292 2.37E–04 -0.262 1.37E–05 -0.393 9.66E–08
rs7174876 PIGB 0.423 15 53406853 Intron 204560_at FKBP5 6 0.284 4.06E–04 -0.274 6.06E–06 -0.393 9.66E–08
rs2290344 PIGB 0.253 15 53407088 Coding 224856_at PIGB 15 0.339 1.75E–05 -0.301 4.81E–07 -0.294 8.98E–05
rs4774760 PIGB 0.416 15 53376504 Upstream 242760_x_at PIGB 15 0.326 3.63E–05 -0.240 6.85E–05 -0.294 8.98E–05
rs8024695 PIGB 0.285 15 53426597 Intron 242760_x_at PIGB 15 0.321 5.00E–05 -0.282 2.56E–06 -0.294 8.98E–05
rs28668016 PIGB 0.365 15 53398725 5UTR 242760_x_at PIGB 15 0.304 1.31E–04 -0.274 5.28E–06 -0.294 8.98E–05
(B) AraC
rs10495285 KIAA0133 (URB2) 0.171 1 227871618 Downstream 219526_at C14orf169 14 0.393 4.13E–07 -0.240 6.97E–05 -0.318 1.86E–05
rs9861198 Probable leucyl–tRNA synthetase 0.086 3 45310394 Upstream 235936_at LOC254559 15 0.308 9.07E–05 0.274 5.12E–06 0.294 8.27E–05
rs9816196 U3 small nucleolar RNA 0.055 3 45321382 Upstream 235936_at LOC254559 15 0.315 6.70E–05 0.242 7.05E–05 0.294 8.27E–05
rs6441911 RIS1 0.055 3 45322523 Flanking_5UTR 235936_at LOC254559 15 0.315 6.20E–05 0.250 3.26E–05 0.294 8.27E–05
rs9878275 Probable leucyl–tRNA synthetase 0.055 3 45331043 Upstream 235936_at LOC254559 15 0.311 8.31E–05 0.249 3.79E–05 0.294 8.27E–05
rs9846284 U3 small nucleolar RNA 0.055 3 45331970 Upstream 235936_at LOC254559 15 0.315 6.20E–05 0.250 3.37E–05 0.294 8.27E–05
rs9850725 LARS2 0.055 3 45332431 Flanking_5UTR 235936_at LOC254559 15 0.315 6.20E–05 0.250 3.26E–05 0.294 8.27E–05
rs9861198 Probable leucyl–tRNA synthetase 0.086 3 45310394 Upstream 206603_at SLC2A4 17 0.308 9.07E–05 0.239 7.63E–05 0.345 3.18E–06
rs9816196 U3 small nucleolar RNA 0.055 3 45321382 Upstream 206603_at SLC2A4 17 0.315 6.70E–05 0.294 1.21E–06 0.345 3.18E–06
rs6441911 RIS1 0.055 3 45322523 Flanking_5UTR 206603_at SLC2A4 17 0.315 6.20E–05 0.301 4.80E–07 0.345 3.18E–06
rs9878275 Probable leucyl–tRNA synthetase 0.055 3 45331043 Upstream 206603_at SLC2A4 17 0.311 8.31E–05 0.300 5.67E–07 0.345 3.18E–06
rs9846284 U3 small nucleolar RNA 0.055 3 45331970 Upstream 206603_at SLC2A4 17 0.315 6.20E–05 0.301 5.03E–07 0.345 3.18E–06
rs9850725 LARS2 0.055 3 45332431 Flanking_5UTR 206603_at SLC2A4 17 0.315 6.20E–05 0.301 4.80E–07 0.345 3.18E–06
rs9816196 U3 small nucleolar RNA 0.055 3 45321382 Upstream 1553755_at NXNL1 19 0.315 6.70E–05 0.237 9.98E–05 0.312 2.82E–05
rs6441911 RIS1 0.055 3 45322523 Flanking_5UTR 1553755_at NXNL1 19 0.315 6.20E–05 0.245 4.73E–05 0.312 2.82E–05
rs9878275 Probable leucyl–tRNA synthetase 0.055 3 45331043 Upstream 1553755_at NXNL1 19 0.311 8.31E–05 0.244 5.26E–05 0.312 2.82E–05
rs9846284 U3 small nucleolar RNA 0.055 3 45331970 Upstream 1553755_at NXNL1 19 0.315 6.20E–05 0.245 4.88E–05 0.312 2.82E–05
rs9850725 LARS2 0.055 3 45332431 Flanking_5UTR 1553755_at NXNL1 19 0.315 6.20E–05 0.245 4.73E–05 0.312 2.82E–05
rs17564430 IGSF4 (CADM1) 0.155 11 114548784 Flanking_3UTR 206571_s_at MAP4K4 2 -0.337 1.74E–05 0.237 8.48E–05 -0.322 1.51E–05
rs11215406 IGSF4 (CADM1) 0.138 11 Intron114570292 Intron 206571_s_at MAP4K4 2 -0.335 1.92E–05 0.248 3.93E–05 -0.322 1.51E–05
rs11215406 IGSF4 (CADM1) 0.138 11 114570292 Intron 204201_s_at PTPN13 4 -0.335 1.92E–05 0.243 5.49E–05 -0.301 5.30E–05
rs17564430 IGSF4 (CADM1) 0.155 11 114548784 Flanking_3UTR 204880_at MGMT 10 -0.337 1.74E–05 -0.236 9.07E–05 0.332 7.44E–06
rs17564430 IGSF4 (CADM1) 0.155 11 114548784 Flanking_3UTR 1556095_at UNC13C 15 -0.337 1.74E–05 0.256 2.21E–05 -0.354 1.60E–06
rs17564430 IGSF4 (CADM1) 0.155 11 114548784 Flanking_3UTR 1556096_s_at UNC13C 15 -0.337 1.74E–05 0.240 7.07E–05 -0.337 5.47E–06
rs17564430 IGSF4 (CADM1) 0.155 11 114548784 Flanking_3UTR 1569969_a_at UNC13C 15 -0.337 1.74E–05 0.257 1.93E–05 -0.332 7.56E–06
rs11215406 IGSF4 (CADM1) 0.138 11 114570292 Intron 1556095_at UNC13C 15 -0.335 1.92E–05 0.276 4.27E–06 -0.354 1.60E–06
rs11215406 IGSF4 (CADM1) 0.138 11 114570292 Intron 1556096_s_at UNC13C 15 -0.335 1.92E–05 0.255 2.29E–05 -0.337 5.47E–06
rs11215406 IGSF4 (CADM1) 0.138 11 114570292 Intron 1569969_a_at UNC13C 15 -0.335 1.92E–05 0.270 7.08E–06 -0.332 7.56E–06
rs11215416 IGSF4 (CADM1) 0.147 11 114582537 Intron 1556095_at UNC13C 15 -0.346 9.57E–06 0.260 1.59E–05 -0.354 1.60E–06
rs11215416 IGSF4 (CADM1) 0.147 11 114582537 Intron 1556096_s_at UNC13C 15 -0.346 9.57E–06 0.242 6.21E–05 -0.337 5.47E–06
rs11215416 IGSF4 (CADM1) 0.147 11 114582537 Intron 1569969_a_at UNC13C 15 -0.346 9.57E–06 0.258 1.84E–05 -0.332 7.56E–06
rs2008801 IGSF4 (CADM1) 0.126 11 114513385 Flanking_3UTR 225532_at CABLES1 18 -0.317 5.42E–05 -0.254 2.54E–05 0.271 2.92E–04
rs2507905 IGSF4 (CADM1) 0.126 11 114513815 Downstream 225532_at CABLES1 18 -0.317 5.42E–05 -0.254 2.54E–05 0.271 2.92E–04
rs7122402 IGSF4 (CADM1) 0.126 11 114521517 Downstream 225532_at CABLES1 18 -0.317 5.42E–05 -0.261 1.43E–05 0.271 2.92E–04
rs4938179 IGSF4 (CADM1) 0.132 11 114538635 Downstream 225532_at CABLES1 18 -0.289 2.56E–04 -0.247 4.34E–05 0.271 2.92E–04
rs17564430 IGSF4 (CADM1) 0.155 11 114548784 Flanking_3UTR 225532_at CABLES1 18 -0.337 1.74E–05 -0.242 6.19E–05 0.271 2.92E–04
  1. “Integrated analyses” with the top expression probe sets that were associated with SNPs within loci with gemcitabine IC50 (SNP vs. Expression P value <10–4, and Expression vs. IC50 P value < 10–4), except for C3orf23 (SNP vs. Expression P value < 10–4, and Expression vs. IC50 P value ≈ 10–4). Eighteen unique probe sets, representing 12 annotated genes that were associated with 66 SNPs within 7 loci and were significantly correlated with gemcitabine IC50 values are listed. (B) “Integrated analyses” for AraC. Eleven unique probe sets, representing 6 annotated genes that were associated with 15 SNPs within 3 loci and were significantly correlated with AraC IC50 values are listed. R values represent correlation coefficients for each association.