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

 

Data Set IDType of DataCriteriaRelease 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
JGAS00000000120 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
JGAS00000000120 Genotypes for genome wide SNPs using the Affymetrix Axiom Genome-Wide ASI 1 Array Controlled Access (Type I) 2017/10/03

*Release Note

* Data users need to apply the Form 2 (Application Form 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/JGAS00000000120

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 Data set ID JGAD00000000130
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 Data Set ID

hum0082.v1.AFFY6.0.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume

Stats: 69 MB (csv)

Genotype data: about 30 GB (CEL, CHP)

Comments (Policies) NBDC policy

 

hum0082.v1.Axiom.v1/JGAS00000000120

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 Data set ID JGAD00000000131
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 Data Set ID

hum0082.v1.Axiom.v1

(Click the Data Set ID to download the file)

Dictionary 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):

NameTitleProject 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

TitleDOIData Set ID
1 A polymorphism in CCR1/CCR3 is associated with narcolepsy doi: 10.1016/j.bbi.2015.05.003

hum0082.v1.AFFY6.0.v1

JGAD00000000130

2 Genome-wide association study of HLA-DQB1*06:02 negative essential hypersomnia doi: 10.7717/peerj.66

hum0082.v1.AFFY6.0.v1

JGAD00000000130

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

JGAD00000000131

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

JGAD00000000131

 

USERS (Controlled Access Data)

PIAffiliationData in Use (Data Set ID)Period of Data Use
- - - -