NBDC Research ID: hum0082.v2
SUMMARY
Aims : Genome-wide SNP genotyping for healthy Japanese
Methods : (1) Genotyping for about 900,000 SNPs by using of Affymetrix Human SNP Array 6.0
(2) Genotyping for about 600,000 SNPs by using of Affymetrix Axiom ASI 1 Array
Materials : 419 healthy Japanese
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0082.v1.AFFY6.0.v1 | Genotype count for genome wide SNPs on the Affymetrix Genome-Wide Human SNP Array 6.0 | Unrestricted-access | 2017/09/26 |
| JGAS000120 | Genotypes for genome wide SNPs on the Affymetrix Genome-Wide Human SNP Array 6.0 | Controlled-access (Type I) | 2017/10/03 |
| hum0082.v1.Axiom.v1 | Genotype count for genome wide SNPs on the Affymetrix Axiom Genome-Wide ASI 1 Array | Unrestricted-access | 2017/09/26 |
| JGAS000120 | Genotypes for genome wide SNPs using the Affymetrix Axiom Genome-Wide ASI 1 Array | Controlled-access (Type I) | 2017/10/03 |
*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
hum0082.v1.AFFY6.0.v1/JGAS000120
| Materials | 418 healthy Japanese |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Genome-Wide Human SNP Array 6.0] |
| 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 (softwares) | Birdseed version 2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000130 |
| Filtering Methods | overall call rate < 0.97, SNP call rate < 0.95, HWE P < 0.001, MAF < 0.01 |
| Marker Numbers (after QC) | 647,318 SNPs (hg19) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume |
Stats: 69 MB (csv) Genotype data: about 30 GB (CEL, CHP) |
| Comments (Policies) | NBDC policy |
hum0082.v1.Axiom.v1/JGAS000120
| Materials | 419 healthy Japanese |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Axiom Genome-Wide ASI 1 Array] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix AXIOM 2.0 Reagent Kit |
| Genotype Call Methods (softwares) | Genotyping Console v4.1 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000131 |
| Filtering Methods | overall call rate < 0.97, SNP call rate < 0.95, HWE P < 0.001, MAF < 0.01 |
| Marker Numbers (after QC) | 490,744 SNPs (hg19) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume |
Stats: 41 MB (csv) Genotype data: about 30 GB (CEL, CHP) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Katsushi Tokunaga
Affiliation: The University of Tokyo, Graduate School of Medicine
URL: http://www.humgenet.m.u-tokyo.ac.jp/index.en.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| JSPS KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Genome Sciences | 221S0002 |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | HLA and diseases | 22133008 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | A polymorphism in CCR1/CCR3 is associated with narcolepsy | doi: 10.1016/j.bbi.2015.05.003 |
hum0082.v1.AFFY6.0.v1 JGAD000130 |
| 2 | Genome-wide association study of HLA-DQB1*06:02 negative essential hypersomnia | doi: 10.7717/peerj.66 |
hum0082.v1.AFFY6.0.v1 JGAD000130 |
| 3 | Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population | doi: 10.1016/j.ajhg.2012.08.010 |
hum0082.v1.Axiom.v1 JGAD000131 |
| 4 | IKZF1, a new susceptibility gene for cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis with severe mucosal involvement | doi: 10.1016/j.jaci.2014.12.1916 |
hum0082.v1.Axiom.v1 JGAD000131 |
USERS (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 | JGAD000131 | 2023/07/20-2027/03/31 |
