SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT02428101

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

Relation of Genetic Polymorphism of ABCG2 Gene And Occurrence of Oxaliplatin - Induced Peripheral Neuropathy in Patients With Gastrointestinal Tract Cancer

This study will examine DNA from Gastrointestinal Tract of cancer patients treated with oxaliplatin to look for a variation (mutation) of the ABCG2 gene that may lead to drug-induced peripheral neuropathy in certain patients. The DNA will be extracted from patients' blood samples and are analyzed for the ABCG2 single nucleotide polymorphism (G34A - rs2231137 and A/A -rs3114018 genotypes) and correlated with peripheral neuropathy grades.

NCT02428101 Gastrointestinal Tract Cancer Peripheral Neuropathy
MeSH: Peripheral Nervous System Diseases Gastrointestinal Neoplasms
HPO: Abnormal peripheral nervous system morphology Malignant gastrointestinal tract tumors Neoplasm of the gastrointestinal tract Peripheral neuropathy Polyneuropathy

1 Interventions

Name: polymorphism analysis

Type: Genetic


Primary Outcomes

Description: Peripheral Neuropathy Toxicity will be assessed every cycle for six months using the National Cancer Institute Common Toxicity Criteria (NCI-CTCAE). Patients will be assigned to 4 groups according to the grades of neuropathy.

Measure: Correlation of single nucleotide polymorphisms of ABCG2 gene (G34A - rs2231137 and A/A -rs3114018 genotypes) with peripheral neuropathy grades, using the National Cancer Institute Common Toxicity Criteria (NCI-CTCAE)

Time: After 6 cycles of chemotherapy (each cycle is15 days), for six months

Time Perspective: Prospective

Cohort


There is one SNP

SNPs


1 G34A

The DNA will be extracted from patients' blood samples and are analyzed for the ABCG2 single nucleotide polymorphism (G34A - rs2231137 and A/A -rs3114018 genotypes) and correlated with peripheral neuropathy grades. --- G34A ---

Correlation of single nucleotide polymorphisms of ABCG2 gene (G34A - rs2231137 and A/A -rs3114018 genotypes) with peripheral neuropathy grades, using the National Cancer Institute Common Toxicity Criteria (NCI-CTCAE). --- G34A ---

- Neurologic disease or patients with disease impairing the neurologic function affecting Gastrointestinal Tract Cancer Peripheral Neuropathy Peripheral Nervous System Diseases Gastrointestinal Neoplasms Pharmacogenetic analysis/genotyping : Genotyping is conducted via High Resolution Melting (HRM) TECHNIQUE, To confirm the genotyping results, the Polymerase chain reaction (PCR) product of the samples will be examine via direct sequencing using 3500 Genetic analyzer from ThermoFisher (applied biosystem) at two ABCG2 loci using the following PCR primers: 1-ABCG2 G34A - rs2231137 Forward : 5'-TGC AAT CTC ATT TAT CTG GAC TA-'3 Reverse : 5'-AAT GCC TTC AGG TCA TTG GA-'3 -Annealing temp :57 -Product size : 163 2- ABCG2 A/A - rs3114018 Forward : 5'- TGATGTTCCTTCAGCCACTG-'3 Reverse : 5'-TTGTGGAAACCTCACAAAAGTG-'3 - Annealing temp : 59 - Product size : 124 --- G34A ---



HPO Nodes


HPO:
Abnormal peripheral nervous system morphology
Genes 760
SLC25A46 TPM2 CDKN1A TPM3 CDKN1B MAG TACO1 HFE CDKN2B CDKN2C TREX1 ASXL1 AARS SCN11A ABCA1 ERCC1 SLC29A3 ERCC2 PNKP HINT1 AMER1 ERCC3 ERCC4 PDE4D ERCC5 ERCC6 HK1 CRLF1 RNF168 MANBA STUB1 HLA-B ACADS ACER3 PDGFRA PDSS1 SIGMAR1 PDHA1 HLA-DPA1 MAPT PYROXD1 HLA-DPB1 MARS PDK3 MAT1A AMACR CFL2 ACO2 SPEG SMC1A HLA-DRB1 MAX PDYN ACTA1 GDF6 GDAP1 ELOVL5 SCYL1 SLC5A7 PEX1 PEX6 PEX7 TCIRG1 PEX10 HMBS PEX12 PEX13 PEX14 CHAT RPS20 ANO5 AK9 EXT1 KLHL41 EXT2 EYA1 PLD3 MDH2 CHKB CHN1 COLQ TIMMDC1 TFG ADAR PLEKHG5 ATXN8 TTN LYST HNRNPA1 TTPA REEP2 TTR TRIP4 HNRNPA2B1 RTN2 KLRC4 ZNHIT3 CHRNA1 ARSI ADCY6 MEFV CHRNB1 NLRC4 RYR1 PGM3 CHRND TBC1D24 CHRNE SPG21 MEN1 SNAP29 MEOX1 MICU1 FAH ERCC8 TYROBP HOXB1 PNPT1 TUBB3 PHYH UBA1 AP1S1 SAMD9L FBN1 SERPINI1 NDRG1 SBF1 CLCN7 NALCN CLCNKB ATXN1 ATXN2 FKTN PIK3CA ATXN7 ATXN8OS FDX2 UBTF TPP1 CPT1C HPGD UCHL1 DSTYK ALG14 RAB3GAP2 SCN2A RNASEH2C SCN4A HACE1 AGXT SCN8A NPAP1 AHCY ATXN3 RETREG1 SNX10 SCN9A SCN10A PEX16 HRAS MLH1 GTF2H5 SCP2 FGF3 KMT2A CYP7B1 PLA2G6 CCR1 ALAD FGF14 ATXN10 ABCD1 MME FLRT1 CEP126 PWAR1 PLEC FH HSD17B4 TXN2 DNAJB2 GMPPB GMPPA DHTKD1 PLP1 NIPBL SLC30A10 MOCS1 MOCS2 HSPB1 SDHA SDHB SDHC VCP SDHD COL1A1 PMM2 WDR48 PMP2 MPL PMP22 COL3A1 HSPD1 COL4A1 POMT2 PMS1 VHL MPV17 MPZ FLI1 MRE11 FLII COL6A1 COL6A2 TRAPPC11 COL6A3 FLNC AMPD2 BIN1 PMS2 VRK1 FBLN5 PRRX1 FOXRED1 VPS37A COL12A1 MAGEL2 COL13A1 DEAF1 UBQLN2 MYOT FMR1 NDUFAF5 WAS COMP WIPF1 SLC25A4 PLEKHG4 CISD2 RNASEH2A DLL4 FKRP WFS1 LITAF SGCD SPTLC2 FOS FA2H KLHL40 RRM2B POLG FLVCR1 GNPTAB PEX3 COX6A1 CNTNAP1 NDUFAF3 BAG3 AGPAT2 SPTLC1 SLC19A2 ATL3 APC KLC2 ELP1 PHF6 COX15 TWNK OPA3 ALS2 XK SPG11 SAMHD1 XPA MSH2 CHD7 XPC POMT1 CPOX FXN XRCC1 PPARG XRCC4 APP SIX1 MORC2 IDUA FAS GDF3 TMEM127 GBA2 CRAT AR COA8 SHANK3 SLC2A1 PRX ALG2 YARS PEX26 CHMP2B PPOX FAN1 MTFMT JPH1 CRYAB UGT1A1 SPTBN4 TMEM106B HSD3B7 LIPT1 PPP2R2B RAB3GAP1 IFRD1 RAB18 IARS2 MLH3 NDUFAF4 RPIA PIEZO2 POLR3B TNFSF11 IGF2 ARSA ARSB ATP6 SLC12A1 GNA14 DKK1 SLC12A3 COX1 COX2 COX3 CCT5 ARHGEF10 CYTB TRIM32 ASAH1 MTHFR SLC18A3 ASCL1 SLC25A1 SLCO2A1 FRG1 IGHMBP2 MTM1 TBK1 C12ORF65 ND1 ND2 ND3 ND4 ND4L ND5 ND6 MTTP MPLKIP PRKAR1A ZFHX2 KBTBD13 MTRR SIX5 MPC1 TRNE TRNF PRKCG SMN1 C11ORF95 ZFR NDUFAF6 CAVIN1 TRNH CTLA4 FUCA1 TRNK TRNL1 SELENOI NGLY1 SNAP25 FUS COASY ATP1A1 TRNQ TRNS1 TRNS2 C9ORF72 TDP1 RNASEH1 TRNV TRNW STX16 CTSD ABHD12 YME1L1 DNAJC3 SNRPN MUSK MEGF10 H19 PRNP RAI1 SOD1 MGME1 SEMA3E KIF1C PRPS1 MKRN3 ATP5F1E IL10 SNORD115-1 TET2 MYD88 SOX10 IL12A MYF6 IBA57 MYH7 CHCHD10 GALC NDUFS7 B4GALNT1 SETX PRTN3 ATP7A SPAST ATP7B PSAP DCAF8 PSEN1 SPG7 REEP1 ATRX KIF1A CHST14 ERAP1 MYO9A PET100 INS SEPTIN9 INPP5K MATR3 LRSAM1 B2M KIF1B APTX SPTBN2 IQSEC2 CYP27A1 GARS MAFA RNF113A INSR NAGA NAGLU HDAC8 BMS1 PTDSS1 DAB1 PDX1 IPW PWRN1 SPART GBE1 CDH23 NFASC PTPN22 GCDH DAXX GCGR SLC46A1 CCND1 GCH1 NDN GCK NDUFA2 TNFRSF11A NDUFA4 PLXND1 COL25A1 PEX11B GPR101 NEB NDUFA9 NDUFA10 ZC4H2 SUCLA2 WNK1 DCTN1 ADA2 NDUFB8 DDB2 GDNF RNF43 NDUFS1 NDUFS2 GFPT1 NDUFS3 BDNF SNORD116-1 NDUFV1 NAGS MFF NDUFS4 TTC19 STAT3 STAT4 NDUFS8 NDUFV2 TBC1D20 NOD2 SLC52A3 ELOVL4 JAK2 CBLIF IFIH1 TUBB6 NEFH FBXO38 GJA1 DES NEFL TTBK2 TIMM8A BMPR1A GJB1 CCM2 NEU1 KLHL9 KARS ADPRHL2 COCH DST NF1 PNPLA6 GLA DHH NDUFA12 BRAF NF2 KCNC3 ARL6IP1 SDHAF2 SACS FIG4 KCND3 WASHC5 GCLC FGD4 GLE1 SQSTM1 KCNJ1 SGPL1 ABCC8 SURF1 AP5Z1 DGUOK C19ORF12 KCNJ10 SUMF1 KCNJ11 MCM3AP MYPN AFG3L2 VAMP1 FAM126A VPS13A PEX19 MTMR2 NGF PEX2 SERPING1 MYMK PEX5 MFN2 RAB7A ALDH18A1 KCNQ2 KCNQ3 MAFB GNA11 C4A CACNA1G KIF5A NIPA1 GNAQ GNAS SEMA4A HERC2 SLC52A2 RMND1 NME1 DMPK PHOX2B CLP1 CPLANE1 DNA2 KIT KCNQ1OT1 DNASE1L3 HSPB8 DYNC1H1 IL23R NOTCH2 NOTCH3 CA2 DNM2 TBCE DNMT1 TBP RAD21 ADSSL1 RNASEH2B CACNA1A GPI KRAS DPAGT1 SLC12A6 SCO2 SH3TC2 DMXL2 SOST RAPSN TRIM2 HSPB3 AMN ATN1 SH2B3 GNE NDUFAF2 PRICKLE1 CALR BEAN1 TMPRSS6 NTRK1 MYO1H SMCHD1 DOK7 CAPN1 CAPN3 TPRKB ASCC1 DNAJB6 SLC19A3 LAMA2 LAMB2 CRPPA DNM1L GJC2 CASR SALL4 GRN RELA SYT2 AIP CAV1 RET REV3L PRRT2 RFC1 CUBN GRM1 TYMP ECHS1 CHAMP1 SELENON TBL1XR1 ATP13A2 TFAP2A ANKH OPA1 MSTO1 NARS2 EDN3 DARS2 NLRP3 EDNRB ATL1 GSN SIL1 POLR3A KRIT1 MKRN3-AS1 RNF170 TGFB1 NDUFA13 TGFBR2 LIFR TGFBR3 KY TARDBP LMOD3 MSH6 ANGPTL6 LRPPRC GTF2E2 LDB3 VPS13D AAAS OTX2 ERLIN2 THPO LMNA LMNB1 MTMR14 SMC3 EGR2 INF2 MYH14 SETD5 ATAD3A PABPN1 AIFM1 IL12A-AS1 CD28 TK2 DDHD1 BTNL2 SLC25A15 SBF2 SAR1B TLR4 CTDP1 MED25 TREM2 CD59 LRP4 LRP5 GAN SPRED1 TRPV4 CYP2U1 UBAC2 ZFYVE26 GNB4 BSCL2 HADHA LTBP3 HADHB HADH HARS OSMR SLC39A14 TNFRSF1A TNFRSF1B POLG2 SLC25A19 HBB PDCD10 ENG EPCAM CLCF1 AGRN TNXB SLC33A1 PIK3R5 TOP3A COQ7 TP53 LARGE1 TPI1
Malignant gastrointestinal tract tumors
Genes 32
APC MLH1 MST1 FLCN TGFBR2 STK11 MSH6 TCF4 AKT1 BMPR1A PMS2 MSH2 FGFR3 MLH3 GREM1 CTNNB1 DLC1 NRAS DCC EPCAM PIK3CA GPR35 POLD1 EP300 NTHL1 POLE MUTYH AXIN2 SMAD4 SRC BUB1B WRN
Neoplasm of the gastrointestinal tract
Genes 211
CDKN1A CDKN1B CDKN1C CDKN2A HFE CDKN2B CDKN2C CDKN2D IL12A H19-ICR TMEM67 IL12RB1 TREX1 ERBB2 POU6F2 BRIP1 DIS3L2 ATP7B PSAP WWOX CEL SPIB ACD ATRX PDGFRA PDGFRL TNFSF12 INS SRC MC1R PDX1 BARD1 HMBS IRF1 NBN IRF5 RPS19 DAXX RPS20 GCK KEAP1 ACVRL1 DCC PTCH1 PTEN MDM2 GDF2 HNF4A TRIP13 GDNF RNF43 TERF2IP STAT1 AXIN1 AXIN2 BAP1 MEN1 BLK BLM FAH MET STK11 PTPN3 BMPR1A SERPINA1 NEUROD1 DLC1 ICOS GPC3 MGMT BRCA1 BRCA2 PIK3CA ABCC8 JAG1 NFKB1 KCNJ11 NFKB2 BUB1 BUB1B MITF AHCY GPC4 MLH1 CTHRC1 TJP2 KCNQ1 CC2D2A COL14A1 AKT1 BCL10 DLEC1 FGFR3 FGFR2 GNAS SEMA4A UROD FH KIT KCNQ1OT1 TNFSF15 SEC23B SDHA SDHB SDHC SDHD RAD21 FOXE1 RAD51 RAD51C PMS1 RAD51D KRAS MRE11 TCF4 KLF11 HNF1A SEMA3C PMS2 RPGRIP1L NRAS COMP RHBDF2 KLF6 NRTN DOCK8 GPR35 INPP5E POLD1 NTHL1 POLE POT1 SH3KBP1 WRN ASCC1 WT1 APC CASP8 POU2AF1 CASP10 RELA MSH2 MSH3 MINPP1 REST RET ECE1 FAS FASLG CR2 AAGAB TERT DICER1 PALB2 EDN3 EDNRB FAN1 RAD50 MSR1 MST1 TGFBR2 MSH6 RASGRP1 SEMA3D KLLN MLH3 PIEZO2 IGF2 ARSA IGF2R MMEL1 LMNA RNF6 CD19 MS4A1 TRIM28 SLC25A13 SETBP1 CHEK2 PTCH2 TNFRSF13C PRKAR1A ABCB11 TNFRSF13B FLCN APPL1 PRKCD C11ORF95 CD81 HABP2 PAX4 GREM1 CTNNB1 SPRTN BUB3 HBB SUFU CEP57 ENG CDH1 EPCAM G6PC SLC37A4 PALLD TNPO3 EP300 MUTYH H19 TP53 SMAD4 CDK4
Peripheral neuropathy
Genes 553
SLC25A46 MAG TACO1 HFE TREX1 AARS SCN11A ABCA1 ERCC1 ERCC2 PNKP HINT1 ERCC3 ERCC4 PDE4D ERCC5 ERCC6 HK1 RNF168 MANBA STUB1 HLA-B ACER3 PDSS1 SIGMAR1 PDHA1 HLA-DPA1 MAPT HLA-DPB1 MARS PDK3 AMACR ACO2 SMC1A HLA-DRB1 PDYN GDAP1 ELOVL5 SCYL1 SLC5A7 PEX1 PEX6 PEX7 PEX10 HMBS PEX12 CHAT RPS20 PLD3 TIMMDC1 TFG ADAR PLEKHG5 ATXN8 LYST HNRNPA1 TTPA REEP2 TTR TRIP4 HNRNPA2B1 RTN2 KLRC4 ARSI MEFV NLRC4 RYR1 PGM3 TBC1D24 SPG21 MEN1 SNAP29 MICU1 FAH ERCC8 TUBB3 PHYH AP1S1 SAMD9L FBN1 SERPINI1 NDRG1 SBF1 CLCNKB ATXN1 ATXN2 PIK3CA ATXN7 ATXN8OS FDX2 TPP1 CPT1C HPGD UCHL1 DSTYK RAB3GAP2 SCN2A RNASEH2C SCN4A AGXT SCN8A NPAP1 AHCY ATXN3 RETREG1 SCN9A SCN10A MLH1 GTF2H5 SCP2 KMT2A CYP7B1 CCR1 ALAD FGF14 ABCD1 MME FLRT1 PWAR1 HSD17B4 TXN2 DNAJB2 GMPPA DHTKD1 PLP1 NIPBL SLC30A10 HSPB1 SDHA VCP COL1A1 PMM2 WDR48 MPL PMP22 HSPD1 PMS1 VHL MPV17 MPZ FLI1 MRE11 FLII TRAPPC11 AMPD2 BIN1 PMS2 FBLN5 FOXRED1 VPS37A MAGEL2 COL13A1 DEAF1 MYOT FMR1 NDUFAF5 WAS COMP WIPF1 SLC25A4 PLEKHG4 CISD2 RNASEH2A WFS1 LITAF SPTLC2 FOS FA2H RRM2B POLG FLVCR1 GNPTAB COX6A1 NDUFAF3 BAG3 AGPAT2 SPTLC1 SLC19A2 ATL3 KLC2 ELP1 PHF6 COX15 TWNK OPA3 ALS2 XK SPG11 SAMHD1 XPA MSH2 XPC CPOX FXN XRCC1 PPARG XRCC4 APP MORC2 IDUA FAS GBA2 CRAT AR COA8 SHANK3 SLC2A1 PRX YARS PPOX FAN1 MTFMT JPH1 SPTBN4 HSD3B7 LIPT1 PPP2R2B RAB3GAP1 IFRD1 RAB18 IARS2 MLH3 RPIA PIEZO2 POLR3B IGF2 ARSA ARSB ATP6 SLC12A1 GNA14 DKK1 SLC12A3 COX1 COX2 COX3 CCT5 CYTB MTHFR SLC18A3 SLC25A1 SLCO2A1 IGHMBP2 C12ORF65 ND1 ND2 ND3 ND4 ND4L ND5 ND6 MPLKIP PRKAR1A ZFHX2 MPC1 TRNE TRNF PRKCG C11ORF95 ZFR NDUFAF6 CAVIN1 TRNH CTLA4 FUCA1 TRNK TRNL1 SELENOI NGLY1 SNAP25 FUS COASY ATP1A1 TRNQ TRNS1 TRNS2 TDP1 RNASEH1 TRNV TRNW STX16 CTSD ABHD12 DNAJC3 SNRPN H19 RAI1 KIF1C PRPS1 MKRN3 ATP5F1E IL10 SNORD115-1 TET2 MYD88 SOX10 IL12A MYF6 IBA57 CHCHD10 GALC NDUFS7 B4GALNT1 SETX PRTN3 ATP7A SPAST ATP7B PSAP DCAF8 SPG7 REEP1 KIF1A CHST14 ERAP1 MYO9A PET100 INS SEPTIN9 INPP5K MATR3 LRSAM1 B2M KIF1B APTX SPTBN2 IQSEC2 CYP27A1 GARS RNF113A INSR NAGA NAGLU HDAC8 DAB1 PDX1 IPW PWRN1 SPART GBE1 PTPN22 SLC46A1 CCND1 GCH1 NDN GCK NDUFA2 NDUFA4 PEX11B GPR101 NDUFA9 NDUFA10 SUCLA2 WNK1 ADA2 NDUFB8 DDB2 NDUFS1 NDUFS2 NDUFS3 SNORD116-1 NDUFV1 NAGS MFF NDUFS4 STAT3 STAT4 NDUFS8 NDUFV2 TBC1D20 SLC52A3 ELOVL4 JAK2 CBLIF IFIH1 NEFH NEFL TTBK2 TIMM8A BMPR1A GJB1 KLHL9 KARS DST PNPLA6 GLA DHH NDUFA12 BRAF NF2 KCNC3 ARL6IP1 SACS FIG4 KCND3 WASHC5 GCLC FGD4 GLE1 KCNJ1 SGPL1 ABCC8 SURF1 AP5Z1 DGUOK C19ORF12 KCNJ10 KCNJ11 MCM3AP AFG3L2 VAMP1 FAM126A VPS13A MTMR2 NGF SERPING1 PEX5 MFN2 RAB7A ALDH18A1 KCNQ2 KCNQ3 GNA11 C4A CACNA1G KIF5A NIPA1 GNAS SEMA4A HERC2 SLC52A2 RMND1 CLP1 KCNQ1OT1 DNASE1L3 HSPB8 DYNC1H1 IL23R NOTCH2 NOTCH3 CA2 DNM2 TBCE DNMT1 TBP RAD21 RNASEH2B CACNA1A GPI KRAS SLC12A6 SCO2 SH3TC2 DMXL2 TRIM2 HSPB3 AMN ATN1 SH2B3 NDUFAF2 PRICKLE1 CALR BEAN1 TMPRSS6 NTRK1 CAPN1 ASCC1 SLC19A3 LAMA2 DNM1L GJC2 CASR RELA SYT2 AIP CAV1 PRRT2 RFC1 CUBN GRM1 TYMP ECHS1 CHAMP1 ATP13A2 OPA1 MSTO1 DARS2 NLRP3 EDNRB ATL1 GSN SIL1 POLR3A MKRN3-AS1 RNF170 TGFB1 NDUFA13 TGFBR2 LIFR MSH6 GTF2E2 LDB3 VPS13D AAAS ERLIN2 THPO LMNA MTMR14 SMC3 EGR2 INF2 MYH14 SETD5 ATAD3A AIFM1 IL12A-AS1 CD28 TK2 DDHD1 BTNL2 SLC25A15 SBF2 SAR1B TLR4 CTDP1 MED25 CD59 GAN TRPV4 CYP2U1 UBAC2 ZFYVE26 GNB4 BSCL2 HADHA HADHB HADH HARS TNFRSF1A TNFRSF1B POLG2 SLC25A19 HBB EPCAM CLCF1 AGRN TNXB SLC33A1 PIK3R5 TOP3A COQ7 TP53 TPI1
Polyneuropathy
Genes 52
SLC12A6 MYD88 ERCC8 SH3TC2 DMXL2 LDB3 RPIA SETX ERCC6 MYOT ATP7B ATP6 PSAP DHH COX3 ARL6IP1 CYTB GCLC AIFM1 PDK3 SEPTIN9 DGUOK PDYN C12ORF65 ND1 ND2 ND4 ND4L ND5 FAM126A ND6 CD59 PEX12 CYP7B1 ALAD FUCA1 ABCD1 NGLY1 PEX11B GRM1 SLC25A19 ABHD12 TTR PIK3R5 NAGS COQ7 EDNRB GSN TBC1D24 PMM2 SNAP29 PRPS1