Skip to main content

Table 1 Alleles frequencies among FVG, 1000G and ExAC (Non Finnish European population) data of a selected list of SNPs reported as associated with specific drugs in the PharmGkB database

From: Pharmacogenetics driving personalized medicine: analysis of genetic polymorphisms related to breast cancer medications in Italian isolated populations

Snp id
(gene)
Drugs (reported as related by PharmGKB database) Alleles Af_FVG Af_1000G_EUR Af_ExAC_NFE Samples p value
vs EUR
p value
vs ExAC
rs3918290
(DPYD)
Capecitabine T/C 0.0006325 0.01 0.0058 1581 2.062E−05 2.20E−04
rs1136201
(ERBB2)
Trastuzumab G/A 0.1692 0.25 0.2396 1581 3.562E−05 2.37E−13
rs2369049
(TCL1A)
Exemestane G/A 0.1111 0.17 NA 1580 1.411E−04 NA
rs4244285
(CYP2C19)
Doxorubicin, cyclophosphamide, tamoxifen A/G 0.08485 0.15 0.1477 330 1.077E−03 7.27E−05
rs714368
(SLC22A16)
Doxorubicin, doxorubicinol C/T 0.2726 0.21 0.2218 1590 6.932E−03 1.73E−07
rs776746
(CYP3A5)
Tamoxifen T/C 0.08055 0.05 NA 1589 8.936E−03 NA
rs1801274
(FCGR2A)
Trastuzumab, doxorubicin, paclitaxel, cyclophosphamide G/A 0.4195 0.5 0.4942 1590 1.457E−02 9.20E−07
rs4880
(SOD2)
Cyclophosphamide G/A 0.5452 0.46 0.5162 1581 1.877E−02 7.81E−02
rs1801159
(DPYD)
Capecitabine C/T 0.217 0.17 0.1978 1581 2.155E−02 3.36E−02
rs2072671
(CDA)
Capecitabine C/A 0.397 0.33 0.3427 1587 2.326E−02 1.79E−05
rs2297595
(DPYD)
Fluorouracil, capecitabine C/T 0.09077 0.12 0.1027 1581 3.256E−02 5.40E−02
rs1048943
(CYP1A1)
Docetaxel, capecitabine C/T 0.06839 0.04 0.0332 1581 2.374E−02 5.66E−18
rs6214
(IGF1)
Tamoxifen T/C 0.3518 0.41 NA 1589 4.746E−02 NA
rs1695
(GSTP1)
Docetaxel, epirubicin, fluorouracil, doxorubicin, cyclophosphamide G/A 0.2761 0.32 0.3191 1590 8.264E−02 2.11E−04
rs12210538
(SLC22A16)
Doxorubicin, cyclophosphamide G/A 0.2125 0.25 0.2351 1581 8.411E−02 2.11E−02
rs9024
(CBR1, SETD4)
Doxorubicin, doxorubicinol A/G 0.1243 0.1 NA 1585 1.116E−01 NA
rs7349683
(EPHA5)
Paclitaxel T/C 0.4169 0.37 0.3588 1589 1.312E−01 8.26E−06
rs45589337
(DPYD)
Cyclophosphamide, fluorouracil, methotrexate C/T 0.004744 0.01 0.0155 1581 1.504E−01 2.90E−06
rs10509373
(C10orf11)
Tamoxifen C/T 0.469 0.42 NA 1258 1.544E−01 NA
rs1056836
(CYP1B1)
Docetaxel, paclitaxel, taxanes G/C 0.5728 0.63 0.5675 1580 1.551E−01 7.69E−01
rs723685
(SLC22A16)
Doxorubicin, cyclophosphamide G/A 0.1069 0.09 0.0886 1590 2.396E−01 1.28E−03
rs1143684
(NQO2)
Doxorubicin, cyclophosphamide T/C 0.7434 0.8 0.787 1588 2.401E−01 4.18E−02
rs9561778
(ABCC4)
Doxorubicin, cyclophosphamide, fluorouracil T/G 0.2085 0.18 NA 331 2.943E−01 NA
rs2032582
(ABCB1)
Anthracyclines and related substances, paclitaxel, doxorubicin, cyclophosphamide, taxanes C/A 0.6091 0.57 0.5523 1581 3.374E−01 9.99E−04
rs8133052
(CBR3)
Doxorubicin A/G 0.4817 0.45 0.5904 1587 3.647E−01 5.46E−09
rs2290272
(SLC28A1)
Capecitabine A/G 0.3569 0.38 0.3466 1590 4.403E−01 4.20E−01
rs1128503
(ABCB1)
Doxorubicin G/A 0.5317 0.57 0.5726 331 4.631E−01 2.78E−01
rs351855
(FGFR4)
Cyclophosphamide, fluorouracil, methotrexate A/G 0.309 0.29 0.3029 1581 4.805E−01 6.06E−01
rs7136446
(IGF1)
tamoxifen T/C 0.6372 0.61 NA 1589 5.265E−01 NA
rs1801133
(CLCN6,MTHFR)
Cyclophosphamide, fluorouracil A/G 0.3674 0.35 0.345 1584 5.661E−01 7.67E−02
rs1045642
(ABCB1)
Idarubicin, taxanes, cyclophosphamide, fluorouracil, epirubicin, anthracyclines and related substances, doxorubicin, paclitaxel, cytarabine, tamoxifen G/A 0.4894 0.47 0.4719 331 6.992E−01 6.17E−01
rs717620
(ABCC2)
Tamoxifen T/C 0.2009 0.21 0.1993 331 7.801E−01 9.71E−01
rs3740065
(ABCC2)
Tamoxifen G/A 0.1163 0.11 NA 331 8.022E−01 NA
rs1800566
(NQO1)
Fluorouracil, epirubicin doxorubicin, cyclophosphamide A/G 0.2044 0.2 0.188 1590 8.642E−01 6.10E−02
rs4646
(CYP19A1)
Letrozole C/A 0.7221 0.71 0.7481 331 8.697E−01 5.78E−01
rs9322336
(ESR1)
Exemestane T/C 0.7825 0.77 NA 331 8.729E−01 NA
rs8060157
(ZNF423)
Tamoxifen, raloxifene G/A 0.5548 0.56 NA 1258 9.202E−01 NA
rs1056892
(CBR3)
Doxorubicin A/G 0.3566 0.36 0.3481 1590 9.352E−01 5.05E−01
rs10509681
(CYP2C8)
Paclitaxel C/T 0.1086 0.11 0.1132 1589 9.719E−01 4.89E−01
rs20572
(CBR1, SETD4)
Doxorubicin, doxorubicinol T/C 0.0997 0.1 0.1144 331 1.00 3.18E−01
  1. Out of 41 variants selected for the analysis, thirteen of them (in italics) were found as significantly different in frequency in our sample as compared to the EUR cohort
  2. Snp id variant name, Gene target gene, Drugs medication reported to be correlated with a variant/gene in PharmGkB database (https://www.pharmgkb.org/), Alleles variant alleles (tested allele in italics), Af_FVG allele frequency of the FVG population, Af_1000G_EUR allele frequency of 1000G European population, Af_ExAC_NFE allele frequency in ExAC Non Finnish European populations, Samples sample number, p value vs EUR p value from Fisher test versus EUR population from 1000G (total sample size 379), p value vs ExAC p-value from Fisher test versus ExAC populations (total sample size 33,368)