NBDC Research ID: hum0074.v2

 

SUMMARY

Aims: Genome-wide association studies on Hepatitis C virus-related diseases and construction of genome database

Methods: SNP-based genome-wide association studies

Participants/Materials:

1. virologic response to PEG-INF/RBV treatment

   78 null virologic response (NVR)

   64 virologic response (VR)

   51 sustained virologic response (SVR)

2. decrease of PLT in response to PEG-IFN/RBV treatment

   107 HCV patients with decrease of PLT in response to PEG-IFN/RBV treatment

   196 HCV patients without decrease of PLT in response to PEG-IFN/RBV treatment

3. Hb reduction

   94 HCV patients with Hb reduction

   209 HCV patients without Hb reduction

4. hepatocellular carcinoma (HCC) development after eradication of HCV by IFN-based treatment

   123 patients who developed HCC at ≥1 year since the end of treatment

   333 patients who did not develop HCC at ≥5 years since the end of treatment

 

Data Set IDType of DataCriteriaRelease Date
hum0074.v1.vr.v1

GWAS for 78 NVR and 64 VR

GWAS for 78 NVR and 51 SVR

Un-restricted Access 2018/02/27
hum0074.v1.plt.v1 GWAS for 107 HCV patients with decrease of PLT in response to PEG-IFN/RBV treatment and 196 HCV patients without decrease of PLT in response to PEG-IFN/RBV treatment Un-restricted Access 2018/02/27
hum0074.v1.Hb.v1 GWAS for 94 HCV patients with Hb reduction and 209 HCV patients without Hb reduction Un-restricted Access 2018/02/27
hum0074.v2.hcc.v1

GWAS for HCC development after eradication of HCV by IFN-based treatment

123 patients who developed HCC

333 patients who did not develop HCC

Un-restricted Access 2018/09/25

*Release Note

*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more

 

MOLECULAR DATA

hum0074.v1.vr.v1

Participants/Materials

virologic response

   78 null virologic response

   64 virologic response

   51 sustained virologic response

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix Genome-Wide Human SNP Array 6.0
Library Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0
Genotype Call Methods (software) Birdseed version 3
Filtering Methods

Sample call rate < 0.95, SNP call rate < 0.95,

HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4

Marker Number (after QC)

NVR vs VR: 43 SNPs (hg18)

NVR vs SVR: 2 SNPs (hg18)

NBDC Data Set ID

hum0074.v1.vr.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 3 KB
Comments (Policies) NBDC policy

 

hum0074.v1.plt.v1

Participants/Materials

decrease of PLT in response to PEG-IFN/RBV treatment

   107 HCV patients with decrease of PLT

   196 HCV patients without decrease of PLT

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix Genome-Wide Human SNP Array 6.0
Library Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0
Genotype Call Methods (software) Birdseed version 3
Filtering Methods

Sample call rate < 0.95, SNP call rate < 0.95,

HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4

Marker Number (after QC) 66 SNPs (hg18)
NBDC Data Set ID

hum0074.v1.plt.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume

9 KB

Comments (Policies) NBDC policy

 

hum0074.v1.Hb.v1

Participants/Materials

Hb reduction

   94 HCV patients with Hb reduction

   209 HCV patients without Hb reduction

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix Genome-Wide Human SNP Array 6.0
Library Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0
Genotype Call Methods (software) Birdseed version 3
Filtering Methods

Sample call rate < 0.95, SNP call rate < 0.95,

HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4

Marker Number (after QC) 32 SNPs (hg18)
NBDC Data Set ID

hum0074.v1.Hb.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 5 KB
Comments (Policies) NBDC policy

 

hum0074.v2.hcc.v1

Participants/Materials

HCC development after eradication of HCV by IFN-based treatment (ICD10: C220)

   123 patients who developed HCC

   333 patients who did not develop HCC

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix Axiom Genome-Wide ASI 1 Array Plate, DigiTag2 Assay, TaqMan SNP Genotyping Assays
Library Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Affymetrix Axiom 2.0 Reagent Kit
Genotype Call Methods (software) Genotyping Console v4.1
Filtering Methods

Sample call rate < 0.95, SNP call rate < 0.95, MAF < 0.05,

HWE P < 0.001, Chi-square test (allelic model) P < 1 x 10^-4

Marker Number (after QC) 70 SNPs (hg18)
NBDC Data Set ID

hum0074.v2.hcc.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 22 KB (xslx)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Yasuhito Tanaka

Affiliation: Department of Virology, Graduate School of Medical Sciences, Nagoya City University

Project / Group Name: -

URL: https://nrd.nagoya-cu.ac.jp/profile/en.La-rbbQ.VwxrvKOhkZojag==.html

Funds / Grants (Research Project Number):

NameTitleProject Number
Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan Construction of hepatitis virus related database aiming at personalized medicine H19-kanen-013
Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan Database construction and therapeuitic applications including host genetic factors for hepatitis virus related diseases H22-kanen-005
Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan Genome-wide research on identification of host genetic factors to develop novel diagnostic and therapeutic methods for hepatitis. 15fk0210018h0003
Research Program on Hepatitis, Japan Agency for Medical Research and Development (AMED) Genome-wide research for identification of host factors associated with liver disease progression or improvement after hepatitis C virus eradication. 18fk0210001h0003

 

PUBLICATIONS

TitleDOIData Set ID
1 Genome-wide association of IL28B with response to pegylated interferon-α and ribavirin therapy for chronic hepatitis C doi: 10.1038/ng.449 hum0074.v1.vr.v1
2 Genome-wide association study identified ITPA/DDRGK1 variants reflecting thrombocytopenia in pegylated interferon and ribavirin therapy for chronic hepatitis C doi: 10.1093/hmg/ddr249

hum0074.v1.plt.v1

hum0074.v1.Hb.v1

3 Genome-wide Association Study Identifies TLL1 Variant Associated With Development of Hepatocellular Carcinoma After Eradication of Hepatitis C Virus Infection doi: 10.1053/j.gastro.2017.01.041 hum0074.v2.hcc.v1