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Table 5 The top seven SNPs in PIGB that were associated with gemcitabine cytotoxicity and its expression in LCLs by integrated analysis

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

SNP Gene SNP vs. IC50 SNP vs. Expression Expression vs. IC50
 rsID Chr Position Region MAF  Probeset Gene symbol  Chr R value  P value  R value  P value  R value  P value
rs2290344 15 53407088 Coding 0.253 205452_at PIGB 15 0.339 1.75E-05 −0.340 1.06E-08 −0.212 5.31E-03
rs2290344 15 53407088 Coding 0.253 242760_x_at PIGB 15 0.339 1.75E-05 −0.301 4.81E-07 −0.294 8.98E-05
rs4774760 15 53376504 5′-upstream 0.416 205452_at PIGB 15 0.326 3.63E-05 −0.283 2.48E-06 −0.212 5.31E-03
rs4774760 15 53376504 5′-upstream 0.416 242760_x_at PIGB 15 0.326 3.63E-05 −0.240 6.85E-05 −0.294 8.98E-05
rs8024695 15 53426597 Intron 0.285 205452_at PIGB 15 0.321 5.00E-05 −0.326 4.60E-08 −0.212 5.31E-03
rs8024695 15 53426597 Intron 0.285 242760_x_at PIGB 15 0.321 5.00E-05 −0.282 2.56E-06 −0.294 8.98E-05
rs12050587 15 53414820 Intron 0.450 205452_at PIGB 15 0.305 1.23E-04 −0.246 4.54E-05 −0.212 5.31E-03
rs28668016 15 53398725 5′-UTR 0.365 205452_at PIGB 15 0.304 1.31E-04 −0.346 5.97E-09 −0.212 5.31E-03
rs28668016 15 53398725 5′-UTR 0.365 242760_x_at PIGB 15 0.304 1.31E-04 −0.274 5.28E-06 −0.294 8.98E-05
rs11636687 15 53392444 5′-upstream 0.421 205452_at PIGB 15 0.302 1.53E-04 −0.287 2.22E-06 −0.212 5.31E-03
rs7174876 15 53406853 Intron 0.423 205452_at PIGB 15 0.284 4.06E-04 −0.261 1.64E-05 −0.212 5.31E-03
  1. R values represent correlation coefficients for associations. We performed integrated analysis among the SNPs and mRNA expression of the PIGB gene as well as gemcitabine cytotoxicity. The only cis- associated SNPs with PIGB gene expression were listed.