SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT01760148

Developed by Shray Alag, 2019.
SNP Clinical Trial Gene

Study of Parameters of Early Hepatitis C Virus Dynamics for Predicting the Outcome of Standard Interferon Therapy With Chinese Cohort (Second Phase)

The purpose of this study is to validate the first round HCV early dynamics discovery within a larger population.

NCT01760148 Hepatitis C, Chronic Liver Diseases Interferon Deficiency
MeSH: Hepatitis Hepatitis A Hepatitis C Liver Diseases Hepatitis C, Chronic
HPO: Abnormality of the liver Decreased liver function Elevated hepatic transaminase Hepatitis

1 Interventions

Name: interferon alpha 2b

Description: Interferon:dosage,5 million units/person;frequency,every other day (qod);duration,48 weeks;Subcutaneous injection. Ribavirin: dosage,15mg/kg/day;frequency,three times a day (t.i.d);duration,48 weeks;take orally.

Type: Drug

Interferon and ribavirin


Primary Outcomes

Description: Blood HCV RNA copies were assayed with Roche - COBAS® AmpliPrep/COBAS® TaqMan® HCV Test.

Measure: Absolute Blood HCV RNA Copies at designed time points

Time: 0hr,24hr,1wk,2wk,4wk,6wk,12wk,24wk,48wk,72wk

Secondary Outcomes

Description: IL28 gene polymorphism,rs8099917,rs12979860,etc

Measure: IL-28B polymorphism

Time: Baseline

Description: HCV NS5A is cloned into T vector and sequenced for evolutionary analysis.

Measure: HCV genotype

Time: Baseline

Description: ALT AST are assayed to detect the hepatic function.

Measure: Alanine Aminotransferase (ALT) and Aspartate transaminase (AST)

Time: Baseline,4wk,12wk,24wk,48wk

Description: Fibrosis is analyzed with Fibroscan.

Measure: Fibrosis stage

Time: Baseline,4wk,12wk,24wk,48wk

Description: The distribution and absolute count of the different types of blood cells are assayed.

Measure: Regular blood test

Time: Baseline,4wk,12wk,24wk,48wk

Description: Electrocardiography is taken to avoid severe side effects.

Measure: Electrocardiography

Time: Baseline,4wk,12wk,24wk,48wk

Description: Patients are asked whether they take alcohol or smoke cigarettes during the therapy period.

Measure: Alcohol ,smoking condition

Time: Baseline,4wk,12wk,24wk,48wk

Description: Patients will be asked about their drug usage history.

Measure: Drug abuse history

Time: Baseline

Time Perspective: Prospective

Cohort


There are 2 SNPs

SNPs


1 rs12979860

IL28 gene polymorphism,rs8099917,rs12979860,etc.


2 rs8099917

IL28 gene polymorphism,rs8099917,rs12979860,etc.



HPO Nodes


HPO:
Abnormality of the liver
Genes 848
MKKS TACO1 GLRX5 ABCA1 SLC29A3 BRIP1 LZTR1 ERCC4 ERCC6 ZMPSTE24 MAN2B1 ACADL ACADM ACADVL ACAT1 DNAJC19 MARS ACOX1 NCF1 TMEM216 ETFA ETFB ETFDH SCYL1 TCIRG1 DHDDS MCM4 IKZF1 RPS20 EWSR1 CD46 EXTL3 RRAS ACVRL1 RREB1 ADA ADAR F5 IL17F MECP2 IFT43 MEFV STN1 AXIN1 MEN1 FANCA FANCC FANCD2 FANCE ADK ARL6 FAH TTC8 MET FANCB FANCF FANCG SAA1 FBN1 FBP1 SFTPA2 CIITA SC5D COG6 ARHGAP31 FDX2 AGA AGL JAG1 RNASEH2C MIF FECH AHCY GPC4 WDR35 FGA MLH1 SCO1 CC2D2A ANTXR1 AKT2 NOP10 ALAS2 FGFR2 IFT80 MAD2L2 FH TRMT5 ALDOA DOCK6 ALDOB SLC30A10 SEC23B SDHA FOXF1 SDHB SDHC SDHD DUOXA2 MPI MPL MPV17 FLI1 COG2 KLF11 DCDC2 CLCA4 ANK1 OFD1 OSTM1 SLC25A4 RNASEH2A SFTPC CTC1 ACAD9 SGSH FOS PEX3 CEP290 AGPAT2 DOLK IYD LARS KCNAB2 BBIP1 APC AIRE XIAP SLC39A4 APOA1 NPC2 APOB MSH2 CHD7 FASTKD2 APOC2 TMEM107 APOE CCDC115 TARS2 FANCM SKI AP3B1 FAS NHP2 SKIV2L FASLG SLCO1B1 COA8 SLC2A1 CEP164 PEX26 COG8 RBCK1 SLC4A1 CASK FAN1 WDR19 SLC5A5 MST1 TRMU NBAS HSD3B7 LIPT1 MLH3 VIPAS39 NPHP3 TNFSF11 ARSA ARSB ATP6 GPIHBP1 UBE2T G6PC3 ARVCF KLF1 DYNC2LI1 TRIM32 ASAH1 SLC20A2 SLC25A1 RFXANK SLCO2A1 ASL CIDEC ND1 ND2 SLC22A5 ND3 ND4 ND5 ASS1 ND6 PTRH2 B9D1 ABCB11 DDRGK1 MPC1 TRNE C11ORF95 SMPD1 IFT122 FUCA1 TRNK TRNL1 ATM NGLY1 HAMP RERE TRNN TRNS1 OCLN TRNV TRNW STX11 PRDM16 BBS12 G6PC G6PD SLC37A4 PALLD TRIM37 SLX4 MMUT GAA H19 ALDH7A1 MVK INVS SON SOS1 SOS2 MYC GABRD TRAF3IP2 MYD88 SOX10 UBR1 ATP6V1B2 DNAJB11 INTU MYH9 ANKS6 GALE EOGT GALK1 ATP6AP1 ATP7A DIS3L2 ATP7B GALNS GALT SPIB ATRX SPINK1 AUH TNFSF12 RTEL1 C15ORF41 TMEM165 SPTA1 SDCCAG8 DZIP1L SPTB B2M NAGA NAGLU AKR1D1 CPLX1 GATA2 GATA6 FADD GBA BBS1 BBS2 GBE1 BBS4 SRP54 FGFRL1 UNC13D GCDH NCF2 NCF4 GCGR GCK TNFRSF11A PEX11B GNMT GDF2 ADA2 BCS1L BBS9 DPM1 DPM2 NAGS HESX1 NDUFS4 STAT1 NOD2 BLK BLVRA IFIH1 CDAN1 STK11 NEK1 BMPR1A STX1A NEU1 NEUROD1 GANAB PNPLA6 BPGM STXBP2 GPC3 BRCA1 GLB1 BRAF BRCA2 BTD ABCC8 SURF1 NFKB1 SUMF1 BTK NFKB2 VPS13A C1QBP C1S C4B BMPER GNAS SEMA4A COX4I2 KCNQ1OT1 TALDO1 MYRF AP3D1 GNS ABCG5 ABCG8 NOTCH1 TBX1 ALG1 NOTCH2 CA2 GP1BB NPC1 GPD1 NPHP1 GPI IFT27 TCF4 HNF1A HNF1B TCF3 SLC25A20 RPGRIP1L SLC11A2 NRAS CALR GPR35 TMPRSS6 HGSNAT BAZ1B CASP8 CASP10 CASR IL17RC ADAMTS13 LMNB2 SPECC1L CAV1 BBS5 SLC7A7 TERC TERT TF CBS TFAM CLDN1 POLR3A KRIT1 TFR2 TG TGFB1 MMAA HAVCR2 TBX19 TGFBR2 B9D2 MSH6 GTF2I THRA THRB CD19 MS4A1 DCLRE1C CD27 CD28 GUSB GYPC BTNL2 SCARB2 GYS2 GUCY2D CD40LG TNFRSF13C LRRC8A TNFRSF13B CD70 PLPBP CD79A CD79B CD81 PARN HADHA MRPL3 PAX4 HADHB HADH TNFRSF1A TNFRSF1B SEC63 HBA1 HBA2 POLG2 SLC25A19 KAT6B HBB PC MMAB HBG1 PCCA HBG2 PCCB TNPO3 PCK1 PCK2 TP53 CEP19 COX14 XPR1 PIGM TPI1 CDKN1A HEXB PCSK1 CDKN1B CFH CDKN1C CDKN2A HFE TPO CDKN2B TPP2 CDKN2C H19-ICR TMEM67 USP18 TREX1 POU6F2 HK1 CEL TRHR HLA-B PDGFB PDGFRA MICOS13 PDGFRL PDGFRB VPS45 AMACR CTSC HLA-DRB1 SLC26A4 CFTR PEPD BLNK CTRC PEX1 CLEC7A PEX6 DNAJC21 DPM3 PEX10 HMBS PEX12 PEX13 PEX14 TSC1 TSC2 HMGCL TSHB ATP8B1 TSHR HMGCS2 HMOX1 PFKM HNF4A TRIP13 LYST HNRNPA1 HNRNPA2B1 NLRC4 PGM1 TUFM HIRA RNU4ATAC ABCB4 PHKA2 ERCC8 PHKB PHKG2 LONP1 SERPINA1 AP1S1 ICOS PIGA CLCN7 HOXD13 HPD PIK3CA PIK3R1 HPGD SHPK UCP2 RECQL4 UFD1 A2ML1 PKD1 SNX10 PKD2 PEX16 PKLR PKHD1 TJP2 CYP7B1 ALG8 PLAGL1 IL17RA UQCRC2 ABCC2 PLG UROD UROS HSD17B4 PLIN1 ALG6 EIF2AK3 COG4 VCP PMM2 HJV PMS1 VHL TRAPPC11 PMS2 KIF23 COMT CLIP2 DLL4 WHCR NSD2 NELFA INPP5E IARS POLD1 RRM2B POLG GNPTAB LZTFL1 COX6B1 WT1 POMC COX8A COX10 POU1F1 DUOX2 POU2AF1 COX15 CP TWNK CPA1 XK RFX6 SAMHD1 CPOX PPARG XRCC2 CPT1A XRCC4 IDS CPT2 GTF2IRD1 IDUA NSMCE2 CFI CR2 CTSA SP110 SLC40A1 ZAP70 ALG2 UGT1A1 IFNGR1 IGF2 IGF2R MMEL1 SEC24C LACC1 PRF1 NEK8 IGHM TTC37 IL21R SETBP1 IQCB1 RBPJ LPIN2 PRKAR1A NKX2-5 SLC13A5 APPL1 PRKCD CTBP1 CAVIN1 CTLA4 PRKCSH IGLL1 CTNS CTNNB1 GFM1 IL1RN IL2RA CTSK IL2RG IL6 NEUROG3 ADAMTSL2 IL7R PROP1 ATPAF2 CYBA CYBB CYC1 COX20 TET2 LDLRAP1 IL12A IL12RB1 PRSS1 PRSS2 IFT140 NDUFS7 PSAP TRAF3IP1 EARS2 CYP7A1 PET100 INS IFT172 CYP19A1 PIEZO1 INPPL1 CYBC1 MRPL44 CYP27A1 KIAA0586 VPS33A INSR PSMB4 TMEM199 PSMB8 PSMB9 PDX1 CD55 SLCO1B3 IRF5 DAXX NHLRC2 MCCC1 PTEN NPHP4 RNF43 PLEKHM1 DDOST ITK MKS1 HELLPAR FBXL4 FAM111B JAK2 JAK3 PTPN3 TRMT10C PTPN11 CEP120 PTPRC ALMS1 MOGS CLPB VPS33B TINF2 PAX8 CCDC47 KCNH1 DGUOK DHCR7 DHFR KCNJ11 TMEM70 PEX19 ABCD3 PEX2 PEX5 MFN2 KCNN4 DKC1 KCNQ1 DLD PYGL ATP11C RBM8A DMD RFT1 RMND1 TMEM231 DMPK CARS2 HYMAI KIT TNFSF15 DNASE1L3 RAB27A NR1H4 JAM3 PCSK9 FERMT3 FOXP3 RAD51 RAD51C RNASEH2B KRAS DPAGT1 RAF1 RAG1 RPGRIP1 RAG2 KRT6A KRT6B EFL1 KRT8 PNPLA2 B3GLCT ITCH KRT16 SRD5A3 LHX4 KRT17 RHBDF2 RASA2 WDR34 KRT18 USB1 GNE LYRM4 DYNC2H1 COG7 PIGS GLIS3 AGGF1 FARSB WDR60 MRPS16 FANCL RELA LHX3 LBR REST LCAT RFC2 WRAP53 TYMP BOLA3 RFX5 RFXAP LDLR JMJD1C WDPCP PALB2 LETM1 RHAG NLRP3 TSFM RFWD3 YARS2 BBS10 CEP55 ESCO2 RIT1 TTC7A SLC17A5 LHX1 RMRP MRPS7 RASGRP1 MLXIPL LIG4 LRPPRC LIMK1 LIPA LIPE ABHD5 IL36RN NDUFAF1 LMNA TRIM28 BBS7 SBDS FANCI IER3IP1 SLC25A13 ALG9 SLC25A15 SAR1B CEP83 TTC21B STEAP3 LRP5 BSCL2 ELN LTBP3 C8ORF37 DCTN4 TANGO2 SPRTN SH2D1A LYZ ENG EPCAM CSPP1 TBL2 CD96 EPB41 EPB42 SMAD4 TCTN2 ALG13
Decreased liver function
Genes 188
NPC1 CYC1 NHLRC1 TACO1 COX20 MPV17 RNU12 UBR1 IL12A TMEM67 USP18 IL12RB1 CACNA1S COG2 SCO2 TCF4 SLC25A20 EPM2A RPGRIP1L ATP7B GALT SPIB ATRX HLA-B OSTM1 USB1 MICOS13 RTEL1 CTC1 GPR35 COG7 MARS PET100 INPP5E IFT172 IARS ACAD9 AMACR FOS HLA-DRB1 POLG PEX3 NDUFAF3 AGPAT2 COX6B1 TMEM199 AKR1D1 LARS SCYL1 FADD GBA PEX1 PEX6 COX8A COX10 FARSB GBE1 PEX10 PORCN PEX12 PEX13 POU2AF1 XIAP PEX14 PTPN22 IRF5 DAXX IKZF1 FASTKD2 CAV1 CCDC115 PPARG ACVRL1 CPT1A PEX11B WRAP53 SLC7A7 CPT2 GDF2 COQ2 NHP2 LARS2 TERC SP110 TERT BCS1L F5 NDUFB8 TFAM COA8 NDUFS2 CEP164 DDOST F13A1 MEFV NDUFS4 F13B RYR1 PEX26 STT3B ADK BLVRA JAK2 MST1 TRMU FAH MRPS7 NBAS HSD3B7 LIPT1 OTC SERPINA1 TRMT10C LIPA GANAB MMEL1 ATP6 ALMS1 MOGS TINF2 SC5D CCDC47 SURF1 TTC37 DGUOK BTNL2 ALG9 JAG1 SLC25A15 MTM1 IL21R ND1 ND2 ND3 ND4 FECH ND5 ND6 VPS13A PEX19 PEX16 ABCD3 PEX2 SCO1 TJP2 PEX5 DKC1 CC2D2A DLD CYP7B1 ALG8 PARN NOP10 CAVIN1 BSCL2 IFT122 HADHA TRNK TRNL1 HADHB HADH UQCRC2 TRNN RMND1 TRNS1 FH OCLN TRNT TRNV TRNW SH2D1A ALDOB GFM1 ENG TALDO1 ALG6 EIF2AK3 SLC30A10 TNFSF15 TNPO3 COG4 PCK1 PCK2 NR1H4 ALG1 SMAD4 COX14 MPI
Elevated hepatic transaminase
Genes 203
CYC1 CFH CDKN2A HFE TMEM67 USP18 TREX1 GLRX5 MYH9 ERCC4 ATP6AP1 ATP7B ACADM ATRX HLA-B MICOS13 TNFSF12 DNAJC19 MARS IFT172 AMACR TMEM165 ACOX1 MRPL44 KIAA0586 PSMB4 TMEM199 AKR1D1 PSMB8 PSMB9 DNAJC21 DPM3 SRP54 PEX13 DHDDS DAXX IKZF1 HMGCL CD46 ATP8B1 GNMT GDF2 HNF4A ADAR ADA2 BCS1L F5 DPM1 DPM2 DDOST PGM1 HELLPAR FBXL4 ABCB4 ADK JAK2 IFIH1 FAH PHKA2 PHKG2 SERPINA1 TRMT10C FBP1 ICOS BRCA1 ALMS1 BRCA2 CLPB VPS33B SC5D COG6 AGL DGUOK JAG1 NFKB1 NFKB2 RNASEH2C VPS13A AHCY PEX19 PEX16 ABCD3 WDR35 C1QBP CC2D2A DLD CYP7B1 PYGL ALAS2 UQCRC2 GNAS DMD HSD17B4 ALDOB ALG6 EIF2AK3 SLC30A10 COG4 NR1H4 SDHD PMM2 FOXP3 HJV GPD1 RNASEH2B KRAS DPAGT1 MPV17 TRAPPC11 COG2 TCF4 HNF1A HNF1B PNPLA2 DCDC2 SLC25A20 KIF23 RPGRIP1L SRD5A3 OFD1 SLC25A4 GNE RNASEH2A GPR35 COG7 INPP5E IARS ACAD9 POLD1 FOS RRM2B POLG AGPAT2 DOLK LARS FARSB TWNK MRPS16 SAMHD1 CAV1 LBR CCDC115 PPARG CPT1A SLC7A7 CPT2 NSMCE2 TYMP CFI CR2 SP110 CBS TFAM PALB2 COG8 RBCK1 YARS2 TFR2 FAN1 MST1 LHX1 TRMU NBAS HSD3B7 LIPT1 VIPAS39 ABHD5 CD19 MS4A1 SBDS ASL IER3IP1 SLC25A13 SLC25A15 GYS2 SAR1B SLC22A5 TNFRSF13C TNFRSF13B STEAP3 PRKCD CD81 CAVIN1 BSCL2 HADHA MRPL3 ATM HADHB NGLY1 HAMP HADH C8ORF37 TANGO2 OCLN POLG2 HBB CSPP1 G6PC SLC37A4 PALLD TP53 MVK SMAD4
Hepatitis
Genes 74
TTC7A MST1 TRAF3IP2 TPP2 TBX19 IL12A MET IL12RB1 RASGRP1 TCF4 HSD3B7 KRT8 SERPINA1 TCF3 VIPAS39 ATP7A IGF2R MMEL1 ATP7B ALMS1 SPIB KRT18 VPS33B CIITA PDGFRL PIK3CA GPR35 CYP7A1 GUSB PIK3R1 AMACR RFXANK SHPK IGHM PIEZO1 SLC25A15 BTK IL21R CD40LG BLNK GLIS3 APC CLEC7A AIRE LRRC8A CASP8 POU2AF1 XIAP CASP10 C1S CYP7B1 PRKCD CD79A CD79B IRF5 C4B IL17RC IL17RA IGLL1 CTNNB1 FAS SKIV2L FASLG SH2D1A RFX5 IL17F RFXAP TNFSF15 TNPO3 PGM1 STAT1 TP53 AXIN1 FOXP3