NBDC Research ID: hum0075.v2

 

SUMMARY

Aims: Search for susceptibility genes to hepatitis virus B (HBV)-related diseases

Methods: SNP-based genome-wide association study (GWAS)

Participants/Materials:

1. 181 HBV carriers and 184 controls

2. 181 HBV carriers and 185 spontaneously HBV-resolved individuals

3. 185 spontaneously HBV-resolved individuals and 184 controls

4. 473 HBV-positive hepatocellular carcinoma (HCC) patients and 516 HBV carriers including chronic hepatitis and asymptomatic carriers

 

Data Set IDType of DataCriteriaRelease Date
hum0075.v1.gwas.v1 GWAS for 181 HBV carriers and 184 controls Un-restricted Access 2017/09/25
hum0075.v1.virus.v1 GWAS for 181 HBV carriers and 185 spontaneously HBV-resolved individuals Un-restricted Access 2017/09/25
hum0075.v1.clear.v1 GWAS for 185 spontaneously HBV-resolved individuals and 184 controls Un-restricted Access 2017/09/25
hum0075.v2.hcc.v1 GWAS for 473 HBV-positive HCC patients and 516 HBV carriers Un-restricted Access 2019/02/19

*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

hum0075.v1.gwas.v1

Participants/Materials 181 HBV carriers and 184 controls
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) Genotyping Console v4.1 software (Birdseed v1)
Filtering Methods

Sample call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001

Chi-square test P < 1.0x10^-4

Marker Number (after QC) 104 autosomal SNPs (ref: Build 36.3)
NBDC Data Set ID

hum0075.v1.gwas.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 14 KB (csv)
Comments (Policies) NBDC policy

 

hum0075.v1.virus.v1

Participants/Materials 181 HBV carriers and 185 spontaneously HBV-resolved individuals
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) Genotyping Console v4.1 software (Birdseed v1)
Filtering Methods

Sample call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001

Chi-square test P < 1.0x10^-4

Marker Number (after QC) 88 autosomal SNPs (ref: Build 36.3)
NBDC Data Set ID

hum0075.v1.virus.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 12 KB (csv)
Comments (Policies) NBDC policy

 

hum0075.v1.clear.v1

Participants/Materials 185 spontaneously HBV-resolved individuals and 184 controls
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) Genotyping Console v4.1 software (Birdseed v1)
Filtering Methods

Sample call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001

Chi-square test P < 1.0x10^-4

Marker Number (after QC) 90 autosomal SNPs (ref: Build 36.3)
NBDC Data Set ID

hum0075.v1.clear.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 12 KB (csv)
Comments (Policies) NBDC policy

 

hum0075.v2.hcc.v1

Participants/Materials

473 HBV-positive HCC patients (ICD10: B181)

516 HBV carriers including chronic hepatitis and asymptomatic carriers

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix Axiom Genome-Wide ASI 1 Array
Library Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Axiom 2.0 Reagent Kit
Genotype Call Methods (software) Genotyping Console v4.2.0.26 software
Filtering Methods

Sample call rate < 0.97, SNP call rate < 0.95, MAF P < 0.03, HWE P < 0.001

Chi-square test P < 0.05

Marker Number (after QC) 24,123 autosomal SNPs
NBDC Data Set ID

hum0075.v2.hcc.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 5.8 MB (xls)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Masashi Mizokami

Affiliation: Department of Liver Diseases, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine

Project / Group Name: Genome Medical Science Project

Funds / Grants (Research Project Number):

NameTitleProject Number
Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan Database construction and therapeutic applications including host genetic factors related with viral hepatitis H22-kanen-005
Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan Development of diagnostics and treatment for hepatitis B related diseases based on genome-wide genetic analysis H23-kanen-005
Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan Identification of genes associated with hepatitis B virus-related diseases by genome-wide analyses H26-kanen-004
Grant-in-aid from the Ministry of Health, Labour, and Welfare of Japan Identification of HLA allelss and immume-related genes associated with chronic hepatitis B and viral clearance H25-kanen-012
KAKENHI Grant-in-Aid for Young Scientists (B) Identification of host genetic factors related with chronic hepatitis B 25870178
Miyakawa Memorial Research Foundation Identification of host genetic factors related with chronic hepatitis B and HBV-related cancer -

 

PUBLICATIONS

TitleDOIData Set ID
1 Genome-Wide Association Study Confirming Association of HLA-DP with Protection against Chronic Hepatitis B and Viral Clearance in Japanese and Korean doi: 10.1371/journal.pone.0039175

hum0075.v1.gwas.v1

hum0075.v1.virus.v1

hum0075.v1.clear.v1

2 Genome-wide association study identified new susceptible genetic variants in HLA class I region for hepatitis B virus-related hepatocellular carcinoma doi: 10.1038/s41598-018-26217-7 hum0075.v2.hcc.v1