NBDC Research ID: hum0136.v3
SUMMARY
Aims: To identify host genetic factors associated with response to a HB vaccination
Methods: Genome-wide association study
Participants/Materials: 1,193 Japanese individuals vaccinated with a HB vaccine (Bimmugen) and 555 Japanese individuals vaccinated with a HB vaccine (Heptavax)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0136.v1.gwas.v1 | GWAS for 1,193 Japanese individuals vaccinated with a HB vaccine (Bimmugen) | Unrestricted-access | 2018/05/22 |
| hum0136.v2.hep-gwas.v1 | GWAS for 555 Japanese individuals vaccinated with a HB vaccine (Heptavax) | Unrestricted-access | 2021/03/05 |
| JGAS000341 | Genotypes for 1,193 Japanese individuals vaccinated with a HB vaccine (Bimmugen) | Controlled-access (Type I) | 2021/10/01 |
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*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
hum0136.v1.gwas.v1 / JGAS000341
| Participants/Materials |
1,193 Japanese individuals vaccinated with a HB vaccine (Bimmugen) - Low responders (n=107, HBsAb ≤ 10mIU/mL) - Intermediate responders (n=351, 10mIU/mL < HBsAb ≤ 100mIU/mL) - High responders (n=735, HBsAb >100mIU/mL) 864 Japanese individuals under the age of 30 years vaccinated with a HB vaccine (Bimmugen) - Low responders (n=56, HBsAb ≤ 10mIU/mL) - Intermediate responders (n=226, 10mIU/mL < HBsAb ≤ 100mIU/mL) - High responders (n=582, HBsAb >100mIU/mL) |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Axiom Genome-Wide ASI 1 Array] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix AXIOM 2.0 Reagent Kit |
| Genotype Call Methods (software) | GenCall software (Genotyping Console ver. 4.2.0.26) |
| Filtering Methods |
overall call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001, MAF < 0.05, Regression P < 0.05 |
| Marker Number (after QC) |
I. Regression analysis for low (0), intermediate (1), and high (2) responders (covariates: age nad gender): 22,044 SNPs (hg19) [Figure 2] II. Regression analysis for low (0), intermediate (1), and high (2) responders under the age of 30 years (covariates: age nad gender): 21,580 SNPs (hg19) [Supplementary Figure 4] III. Regression analysis for low (0) and high (1) responders (covariates: age nad gender): 23,765 SNPs (hg19) [Supplementary Figure 4] |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000452 |
| Total Data Volume |
hum0136.v1.gwas.v1: 7.3 MB JGAD000452: 34.4 GB（CEL） |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
555 Japanese individuals vaccinated with a HB vaccine (Heptavax) - Low responders (n=66, HBsAb ≤ 10mIU/mL) - Intermediate responders (n=184, 10mIU/mL < HBsAb ≤ 100mIU/mL) - High responders (n=305, HBsAb >100mIU/mL) |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Axiom Genome-Wide ASI 1 Array] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix AXIOM 2.0 Reagent Kit |
| Genotype Call Methods (software) | GenCall software (Genotyping Console ver. 4.2.0.26) |
| Filtering Methods |
overall call rate < 0.95, SNP call rate < 0.95, HWE P < 0.001, MAF < 0.05, Regression P < 0.05 |
| Marker Number (after QC) |
I. GWAS for low responders (n=66) and responders (n=489) with Heptavax (after imputation): 279,671 SNPs (hg19) [Figure 1a] II. GWAS for low responders (n=66) and high responders (n=305) with Heptavax (after imputation): 292,028 SNPs (hg19) [Figure 1b] III. GWAS for low responders (n=66) and responders (n=489) with Heptavax (before imputation): 22,770 SNPs (hg19) [Supplementary Figure 1a] IV. GWAS for low responders (n=66) and high responders (n=305) with Heptavax (before imputation): 23,717 SNPs (hg19) [Supplementary Figure 1b] V. GWAS for low responders (n=66 + 107) and responders (n=489 + 1086) with Heptavax and Bimmugen (after imputation): 310,312 SNPs (hg19) [Supplementary Figure 2a] VI. GWAS for low responders (n=66 + 107) and high responders (n=305 + 735) with Heptavax and Bimmugen (after imputation): 317,176 SNPs (hg19) [Supplementary Figure 2b] VII. GWAS for low responders with Heptavax (n=66) and low responders with Bimmugen (n=107) (after imputation): 285,687 SNPs (hg19) [Supplementary Figure 3a] VIII. GWAS for intermediate responders with Heptavax (n=184) and intermediate responders with Bimmugen (n=351) (after imputation): 312,192 SNPs (hg19) [Supplementary Figure 3b] IX. GWAS for high responders with Heptavax (n=305) and high responders with Bimmugen (n=735) (after imputation): 321,074 SNPs (hg19) [Supplementary Figure 3c] |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 500 MB |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masashi Mizokami
Affiliation: Natinal Center for Global Health and Medicine
Project / Group Name: Genome Medical Science Project
URL: http://www.ncgmkohnodai.go.jp/genome/english/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science Program for an Integrated Database of Clinical and Genomic Information | Construction of integrated clinical genome database regarding hepatitis B related diseases | JP16kk0205007 |
| Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science Program for Basic and Clinical Research on Hepatitis | Identification of genes associated with hepatitis B virus-related diseases by genome-wide analyses | JP16fk021010 |
| Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science Program on the Innovative Development and the Application of New Drugs for Hepatitis B | Elucidation of the pathogenesis for HBV clearance, chronic hepatitis B infection, and hepatocellular carcinoma | JP17fk0310115 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Comprehensive understanding for the relationship between HLA class II genes and chronic hepatitis B infection | 16K09387 |
| Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science Program for Basic and Clinical Research on Hepatitis | Study for clinical sequening based on genome analysis of host and viral factors | JP20fk0210056 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Key HLA‐DRB1‐DQB1 haplotypes and role of the BTNL2 gene for response to a hepatitis B vaccine | doi: 10.1002/hep.29876 | hum0136.v1.gwas.v1 |
| 2 | Importance of HBsAg recognition by HLA molecules as revealed by responsiveness to different hepatitis B vaccines | doi: 10.1038/s41598-021-82986-8 | hum0136.v2.hep-gwas.v1 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Taku Miyagawa | Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science | Japan | Search for genes involved in the pathogenesis of sleep disorders presenting with hypersomnia (various hypersomnias, circadian rhythm sleep disorders, sleep apnea syndrome, sleep-related movement disorders, sleep paralysis, etc.) and study of their functions and autoantigen-specific responses of peripheral blood lymphocytes | JGAD000452 | 2023/07/20-2027/03/31 |
