SNPMiner Trials by Shray Alag


SNPMiner SNPMiner Trials (Home Page)


Report for Clinical Trial NCT03300414

Developed by Shray Alag, 2020.
SNP Clinical Trial Gene

Biologic Basis of Liver Cancer From Chronic Hepatitis B

The focus of the study is to identify viral factors and host immune responses that differentiate HBV-related HCC patients from HBV patients who have not progressed to HCC. To that end, the investigators will compare gene expression levels between HCC patients and non-HCC patients categorized into high and low risk profiles. The investigators will perform ANOVA to compare three groups (HCC, high risk, low risk). Multiple comparison corrections will be performed using Benjamini and Hochberg False Discovery Rate (FDR) with a 90% confidence that the discovery lists will contain no more than 5% false positives (FDR<0.05) (PMID: 12584122, 11682119). A p-value <0.05 is considered statistically significant using this multiple comparison correction approach. Post-hoc Student-Newman-Keuls or Tukey tests will be used following ANOVA for comparisons of HCC patients with high risk and low risk. If data are not normally distributed when log-transformed, then Kruskall-Wallis tests will be used. ANCOVA will be used to adjust for the effects of covariates, such as age, gender, and HBV genotype (B or C). Further, the investigators often use an additional 2-fold change criterion for significance because the investigators consider a fold change of this magnitude to be biologically significant. Hierarchical clustering analyses and principal component analyses will be used to visualize how well the genes separate the groups, or to discover new subgroups. For the analysis of SNVs, the exact binomial test will be performed and p-values will be adjusted by the Benjamini-Hochberg correction.

NCT03300414 Hepatocellular Carcinoma Hepatitis B, Chronic
MeSH: Hepatitis A Hepatitis B Hepatitis B, Chronic Carcinoma, Hepatocellular Liver Neoplasms Hepatitis
HPO: Hepatitis Hepatocellular carcinoma Neoplasm of the liver

1 Interventions

Name: One time blood draw

Description: Same as part 1

Type: Other

Collection of blood specimen


Primary Outcomes

Description: In order to meet this aim, blood samples will be obtained from 10 consented subjects. The DNA extracted from these samples will be used as part of an ongoing study comparing viral sequences and gene expression profiles across Asian ethnic groups, we will analyze the same data comparing individuals with high and low HCC risk factors (i.e. the presence and absence of cirrhosis, high HBV viral load, men who have sex with men).

Measure: Associate viral sequences and host gene expression signatures with established HCC risk factors in Asian Americans.

Time: 1 year

Time Perspective: Prospective

Cohort


There is one SNP

SNPs


1 G1764A

Carcinogenesis 2008) Viral mutants including the A1762T/G1764A basal core promoter mutations and Pre-S region deletions are also associated with poor HCC outcomes and may be the result of selection by host immune responses and activation of endogenous cytidine deaminase by pro-inflammatory cytokines (e.g. --- G1764A ---



HPO Nodes


HPO:
Hepatitis
Genes 90
CD247 CTNNB1 ATP7B CASP10 PIEZO1 GUSB BLNK SHPK CYP7A1 IL17RA IGF2R CASP8 SH2D1A SLC25A15 BTK BTK C4B CD79B VPS33B XIAP SERPINA1 PIK3R1 GLIS3 POU2AF1 CIITA FOXP3 TPP2 RFX5 CIITA RASGRP1 RFXANK SLC25A15 AXIN1 TCF4 CD3D TP53 IL12A PRKCD CD40LG BTK IGHM IL17RC ALMS1 TRAF3IP2 KRT8 FAS LRRC8A FAS IL17F XIAP SPIB C1S RFX5 RFXAP MST1 TTC7A COG8 SKIV2L VIPAS39 IGLL1 PDGFRL TNFSF15 HSD3B7 CD3E AMACR ATP7B FASLG RFXANK IL12RB1 TCF3 CD79A KRT18 IRF5 MET PIK3CA MMEL1 ITCH TBX19 IL21R AIRE RFXAP TTC7A CLEC7A GPR35 ATP7A CYP7B1 STAT1 PGM1 APC TNPO3
Hepatocellular carcinoma
Genes 65
AHCY CTNNB1 CASP10 IGF2R JAG1 CASP8 HFE BMP2 HFE MLH1 PMS2 POU2AF1 HMBS FAH MSH6 SLC25A13 RASGRP1 EPCAM UROD AXIN1 TCF4 TP53 IL12A PRKCD SLC37A4 TGFBR2 SEMA4A JAK2 FAN1 FAS BMPR1A FAS KRAS FAH SPIB MSH2 HMBS MST1 MLH3 G6PC SPRTN SLC37A4 PIK3CA PDGFRL SERPINA1 TNFSF15 ATP7B IGF2 ABCB11 FASLG IL12RB1 SLC25A13 IRF5 RPS20 MET PIK3CA MMEL1 HFE H19 PMS1 F5 GPR35 APC TJP2 TNPO3
Neoplasm of the liver
Genes 132
TTC37 REST GPC3 TMEM67 AHCY HNF1A TRIP13 IGF2R HFE MLH1 PMS2 APC INS ABCC8 PALLD POU2AF1 BRCA2 HMBS HBB STAT6 MSH6 APC SLC25A13 RASGRP1 UROD INPP5E TP53 PRKCD KRAS SLC37A4 FAN1 SETBP1 NEUROD1 SKIV2L RPGRIP1L FAS KRAS WT1 MSH2 HMBS G6PC SPRTN PAX4 PIK3CA RELA SERPINA1 PDX1 TNFSF15 ATP7B ABCB11 RPS20 BRCA1 HFE H19 PRKAR1A TRIM28 KLF11 APC F5 GPR35 MLH1 APC BLK WT1 CTNNB1 CASP10 H19-ICR CEL GPC4 TRIM28 JAG1 HNF1A CASP8 HFE BMP2 BRCA2 MSH6 POU6F2 KCNQ1OT1 H19 NAB2 GCK KCNQ1 SMPD1 HNF4A FAH EPCAM AXIN1 TCF4 MSH2 APC KCNJ11 IL12A TGFBR2 SEMA4A JAK2 DIS3L2 FAS APPL1 APC BMPR1A TP53 FAH CDKN1C SPIB SMAD4 PHKG2 HBB C11ORF95 MST1 MLH3 GPC3 PALB2 IGF2 SLC37A4 PHKA2 PDGFRL SETBP1 IGF2 FASLG IL12RB1 SLC25A13 IRF5 MET PIK3CA MMEL1 H19 PMS1 CDKN2A CC2D2A TJP2 TNPO3