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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
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Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000660

Type of data
Imputation data and index data for 180,882 patients from BBJ 1st cohort
Access criteria
Controlled-access (Type I)
Total data volume
11.1 TB
File formats
  • VCF
  • TBI
Research
hum0311
Date published
2022-08-12
Date modified
2022-08-12
DDBJ Search
JGAD000660 (opens in a new tab)
JGA Study
JGAS000541 (opens in a new tab)

Analysis method

Genotyping by array

Materials and participants
180,882 patients from BBJ 1st cohort
ICD10: A15-A16, B16-B17.0, B18.0-B18.1, B17.1, B18.2, C15, C16, C18, C22, C23-C24, C25, C33-C34, C50, C53, C54, C56, C61, C81, D25, E05, E10, E78.0-E78.5, G12, G40-G41, H25-H26, H40-H42, I20, I21-I22, I44-I49, I50, I60, I69.0, I63, I69.3, I70, J30, J41-J44, J45-J46, J80-J84, K05, K74.3-K74.6, L00-L99, L20, M05-M06, M80-M82, N04, N20-N23, N80, R00-R9
  • Health status
    Affected
  • Subject count
    180,882 (Individual)
  • Population
    East Asian
Sample description
DNAs extracted from peripheral blood cells or saliva
  • Tissue
    Peripheral blood, Saliva
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
HumanExome BeadChip Kit
HumanOmniExpress BeadChip Kit
HumanOmniExpressExome BeadChip Kit
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Reference genome
GRCh38
QC and filtering
Before imputation, we excluded SNPs using the following criteria:

Heterozygosity count for each chip < 5
P-value for Hardy-Weinberg equilibrium (HWE) for each chip < 1.0 x 10^-6
*- Genotype concordance rate with whole-genome sequencing (WGS) for 939 samples < 99.5% and its non-reference discordance rate >= 0.5%
Lower call rate SNPs if the position was the same when merging datasets
Call rate < 99%*
P-values for chrX SNPs were calculated by using female samples

We also excluded samples using the following criteria:

Call Rate < 98%
Samples whose inferred sex was not matched with the clinical information
Lower call rate samples for duplicated or monozygotic twin in the dataset
Outliers from East Asian clusters from principal component analysis with 1KGp3v5 samples.
Imputation
Eagle software (v2.4.1) without a reference panel
Minimac4 software (v1.0.2)
Analysis method
GenomeStudio Software
Variant count
Autosomes: 515,587 SNVs
X chromosome: 11,140 SNVs
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)