NBDC Research ID: hum0075.v2
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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
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0075.v1.gwas.v1 | GWAS for 181 HBV carriers and 184 controls | Unrestricted-access | 2017/09/25 |
| hum0075.v1.virus.v1 | GWAS for 181 HBV carriers and 185 spontaneously HBV-resolved individuals | Unrestricted-access | 2017/09/25 |
| hum0075.v1.clear.v1 | GWAS for 185 spontaneously HBV-resolved individuals and 184 controls | Unrestricted-access | 2017/09/25 |
| hum0075.v2.hcc.v1 | GWAS for 473 HBV-positive HCC patients and 516 HBV carriers | Unrestricted-access | 2019/02/19 |
*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
| 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 Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 14 KB (csv) |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 12 KB (csv) |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 12 KB (csv) |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID |
(Click the Dataset ID to download the 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 |
