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 IDType of DataCriteriaRelease 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

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

*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

hum0136.v1.gwas.v1

(Click the Dataset ID to download the file)

Dictionary 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

 

hum0136.v2.hep-gwas.v1

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

hum0136.v2.hep-gwas.v1

(Click the Dataset ID to download the file)

Dictionary 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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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