SNPMiner Trials by Shray Alag


SNPMiner Trials: Clinical Trial Report


Report for Clinical Trial NCT03300414

Developed by Shray Alag, 2019.
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 Hepatitis A Carcinoma, Hepatocellular Hepatitis, Chronic Hepatitis B Liver Neoplasms Hepatitis B, Chronic
HPO: Chronic active hepatitis Chronic hepatitis 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:
Chronic active hepatitis
Genes 5
KRT8 ALMS1 C4B KRT18 AIRE
Chronic hepatitis
Genes 11
KRT8 ALMS1 RFXANK C4B KRT18 CIITA AIRE IL21R RFX5 RFXAP CD40LG
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
Hepatocellular carcinoma
Genes 54
PMS1 HFE KRAS MST1 FAH IL12A TGFBR2 MET IL12RB1 MSH6 RASGRP1 TCF4 BMPR1A SERPINA1 PMS2 MLH3 IGF2 IGF2R MMEL1 ATP7B SPIB PDGFRL PIK3CA GPR35 SLC25A13 JAG1 AHCY APC MLH1 TJP2 ABCB11 CASP8 HMBS POU2AF1 CASP10 PRKCD IRF5 RPS20 MSH2 SEMA4A CTNNB1 SPRTN UROD FAS FASLG EPCAM G6PC TNFSF15 SLC37A4 TNPO3 H19 TP53 AXIN1 FAN1
Neoplasm of the liver
Genes 94
BLK PMS1 CDKN1C CDKN2A HFE KRAS MST1 FAH IL12A TGFBR2 H19-ICR MET TMEM67 IL12RB1 MSH6 RASGRP1 TCF4 KLF11 HNF1A BMPR1A POU6F2 SERPINA1 PMS2 MLH3 NEUROD1 IGF2 IGF2R DIS3L2 RPGRIP1L MMEL1 ATP7B GPC3 BRCA1 CEL SPIB BRCA2 PDGFRL PIK3CA TRIM28 GPR35 INS INPP5E ABCC8 SLC25A13 JAG1 KCNJ11 SETBP1 AHCY GPC4 WT1 PDX1 APC MLH1 PRKAR1A TJP2 ABCB11 KCNQ1 CC2D2A CASP8 HMBS POU2AF1 CASP10 APPL1 PRKCD C11ORF95 IRF5 RPS20 RELA MSH2 GCK PAX4 REST SEMA4A CTNNB1 SPRTN UROD FAS HBB FASLG HNF4A TRIP13 KCNQ1OT1 EPCAM G6PC TNFSF15 SLC37A4 PALLD TNPO3 PALB2 H19 TP53 AXIN1 SMAD4 FAN1