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We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

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

JGAD000893

Type of data
Processed data of JGAD000495 (WGS for 1,964 individuals) by JGA (mitochondrial variant calls)
Access criteria
Controlled-access (Type I)
Total data volume
70.9 MB
File formats
  • VCF
  • IDX
Research
hum0014
Date published
2024-10-18
Date modified
2024-10-18
DDBJ Search
JGAD000893 (opens in a new tab)
JGA Study
JGAS000381 (opens in a new tab)

Analysis method

WGS

Materials and participants
1,765 myocardial infarction patients (ICD10: I21) and 199 dementia patients (ICD10: F00-03)
  • Health status
    Affected
  • Subject count
    1964 (Individual)
  • Cohort
    BioBank Japan
  • Population
    Japanese
Disease
  • myocardial infarction patients
  • dementia patients
Sample description
DNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq DNA PCR-Free Library Prep Kit
Fragmentation
Ultrasonic fragmentation
Platform
Illumina HiSeq X
Read type
Paired-end
Read length
151 bp
Reference genome
GRCh37
Mapping
BWA mem 0.7.12
Read deduplication
Picard 2.10.6
Realignment and base quality recalibration
GATK 3.7
Mapping quality
Reads with MAPQ<20 were excluded at variant calling with GATK 3.7 HaplotypeCaller
QC and filtering
Data with bad base quality and high %GC content were removed.
Aligment:
Data matched for the following condition were removed.
- Low mapping rate
- Different insert size
- Gender information mismatch between meta-data and genotype data
- Suspected sex chromosome aberration
Genotyping:
GATK's best practices includes a variant filtering step following Variant Quality Score Recalibration (VQSR)
- DP/GP (DP < 5, GQ < 20, DP > 60, GQ < 95)
- Heterozygosity (F>=0.05)
- Hardy-Weinberg equilibrium (p < 10^-6)
- Repeat & Low Complexity
Principal Component Analysis (PCA):
PCA was performed with individuals included in the 1000 genomes project and outliers from Japanese cluster were removed.
After these filtering steps, variants located in the regions listed as the HighConfidenceRegion (Genome-In-A-Bottle project) were flagged.
Analysis method
GATK 3.7 HaplotypeCaller
Coverage (depth)
Myocardial infarction: 15x
Dementia: 30x
Variant count
Autosomes: 10,202,908
X chromosome: 410,435
Autosomes: 76,768,387
X chromosome: 2,898,518
Data use policy
NBDC data sharing policy (JGAP000001)