NBDC Research ID: hum0014.v3

Click to Latest version.

 

SUMMARY

Aims: Identify disease-related genes in Japanese

Methods: Genomic DNA samples were genotyped by following methods: Human610-Quad BeadChip、HumanHap550v3 Genotyping BeadChip、OmniExpressExome BeadChip (Illumina), high-density oligonucleotide arrays (Perlegen Sciences), or Invader (Hologic Japan). Genome-Wide Association Studies (GWAS) for myocardial infarction (MI) and type II diabetes mellitus (T2DM) were performed using about 500K SNPs.

Participants/Materials: Participants for the Tailor-made Medical Treatment Program (BioBank Japan: BBJ)

URL: https://biobankjp.org/english/index.html

 

Data Set IDType of DataCriteriaRelease Date
hum0014.v1.freq.v1 GWAS for MI Open Access 2014/09/30
hum0014.v3.T2DM-1.v1 GWAS for T2DM [1] Open Access 2016/01/28
hum0014.v3.T2DM-2.v1 GWAS for T2DM [2] Open Access 2016/01/28

*Release Note

 

MOLECULAR DATA

hum0014.v1.freq.v1

Participants/Materials 1666 MI patients and 3198 controls
Targets genome wide SNVs
Target Loci for Capture Methods -
Platform Illumina [Human610-Quad BeadChip, HumanHap550v3 Genotyping BeadChip]
Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Illumina Human610-Quad Beadchip
Genotype Call Methods (software) GenCall software (GenomeStudio)
Filtering Methods Sample Call rate ≧ 0.98, SNP call rate ≧ 0.99, HWE P ≧ 1 x 10^-6
Marker Number (after QC) 455,781 SNPs (hg18/GRCh36)
NBDC Data Set ID

hum0014.v1.freq.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 71.3 MB (xlsx)
Comments (Policies) NBDC policy

 

hum0014.v3.T2DM-1.v1

Participants/Materials

T2DM: 9817 cases

6763 controls (healthy individuals and patients with Intracranial aneurysm, Esophageal cancer, Uterine cancer, Pulmonary emphysema, or Glaucoma [without T2DM])

Targets genome wide SNVs
Target Loci for Capture Methods -
Platform Illumina [OmniExpressExome Beadchip]
Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Illumina OmniExpressExome Beadchip kit
Genotype Call Methods (software) GenCall software (GenomeStudio)
Filtering Methods Sample Call rate < 0.98, SNP call rate < 0.99, MAF < 0.01 HWE P < 1 x 10^-6 in control
Marker Number (after QC) 552,915 SNPs (hg19)
NBDC Data Set ID

hum0014.v3.T2DM-1.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 84 MB (xlsx)
Comments (Policies) NBDC policy

 

hum0014.v3.T2DM-2.v1

Participants/Materials

T2DM: 5646 cases

19,420 controls (patients with Colorectal cancer, Breast cancer, Prostate cancer, Lung cancer, Gastric cancer,

Arteriosclerosis obliterans, Cardiac arrhythmias, Brain infarction, Myocardial infarction, Gallbladder cancer and Cholangiocarcinoma, Pancreatic cancer , Drug eruptions,

Rheumatoid arthritis, Amyotrophic lateral sclerosis, Liver cancer, Liver cirrhosis, Osteoporosis, or Uterine myoma [without T2DM])

Targets genome wide SNVs
Target Loci for Capture Methods -
Platform Illumina [Human610-Quad BeadChip]
Source gDNA extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Illumina Human610-Quad Beadchip kit
Genotype Call Methods (software) GenCall software (GenomeStudio)
Filtering Methods Sample Call rate < 0.98, SNP call rate < 0.99, MAF < 0.01 HWE P < 1 x 10^-6 in control
Marker Number (after QC) 479,088 SNPs (hg18)
NBDC Data Set ID

hum0014.v3.T2DM-2.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 72.6 MB (xlsx)
Comments (Policies) NBDC policy

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

 

DATA PROVIDER

Principal Investigator: Michiaki Kubo

Affiliation: RIKEN Center for Integrative Medical Sciences

Project / Group Name: Tailor-made Medical Treatment Program (Bio Bank Japan: BBJ)

URL: https://biobankjp.org/english/index.html

Funds / Grants (Research Project Number) :

NameTitleProject Number
Ministry of Education, Culture, Sports, Science and TechnologyJapan Taolor-made Medical Treatment Program (the 3rd phase) -

 

PUBLICATIONS

TitleDOIData Set ID
1 A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese. doi:10.1038/ejhg.2014.110 hum0014.v1.freq.v1
2 Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes doi: 10.1038/ncomms10531

hum0014.v3.T2DM-1.v1

hum0014.v3.T2DM-2.v1