NBDC Research ID: hum0075.v3
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
5. 329 patients with chronic HBV infection who were recruited at Chulalongkorn University in Bangkok, Thailand, and 318 healthy control individuals who were blood donors at the National Blood Center, The Thai Red Cross Society, in Bangkok, Thailand
| 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 |
| hum0075.v3.Thai-gwas.v1 | GWAS for 329 patients with chronic HBV infection and 318 healthy controls | Unrestricted-access | 2022/05/27 |
*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 |
| Participants/Materials |
329 patients with chronic HBV infection (ICD10: B169) [including liver cancer (ICD10: C220) patients] 318 healthy controls |
| 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 IMPUTE2 v2.3.2 software |
| Association Analysis (software) | PLINK v1.9 software |
| Filtering Methods |
pre-imputation QC: SNP call rate < 0.97, MAF P < 0.01, HWE P < 1 x10^-6 after imputation QC: SNPs with an info metric < 0.8 were excluded. |
| Marker Number (after QC) | 6,317,183 autosomal variants (GRCh37) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 600 MB (plink.assoc) |
| 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 | - |
| Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science Program for Basic and Clinical Research on Hepatitis, Japan Agency for Medical Research and Development (AMED) | Study for clinical sequening based on genome analysis of host and viral factors | JP20fk0210056 |
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 |
| 3 | Genome-wide association study for chronic hepatitis B infection in the Thai population | doi: 10.3389/fgene.2022.887121 | hum0075.v3.Thai-gwas.v1 |
