Dataset ID
JGAD000495
- Type of data
- WGS for 1,765 myocardial infarction patients and 199 dementia patients
- Access criteria
- Controlled-access (Type I)
- Total data volume
- 91.2 TB
- File formats
- FASTQ
- Research
- hum0014
- Date published
- 2022-01-27
- Date modified
- 2022-01-27
- DDBJ Search
- JGAD000495 (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 statusAffected
- Subject count1964 (Individual)
- CohortBioBank Japan
- PopulationJapanese
- Disease
- myocardial infarction patients
- dementia patients
- Sample description
- DNA extracted from peripheral blood cells
- TissuePeripheral blood
- 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 - Processed data type
- Alignment
Variant calls - Data use policy
- NBDC data sharing policy (JGAP000001)
WGS imputation panel (autosomes + X)
- Materials and participants
- [JGAD000867]
- WGS data (JGAD000220) of the biobank Japan project (N=1,026)
[JGAD000868]
- WGS data (JGAD000495) of the biobank Japan project (N=1,964) - Subject count2990 (Individual)
- CohortBioBank Japan
- PopulationJapanese
- Experimental method
- WGS
- Target
- N/A
- Reference genome
- GRCh38
- Mapping
- bwa mem (version 0.7.15)
- Read deduplication
- GATK MarkDuplicates (version 4.1.0.0)
- Realignment and base quality recalibration
- N/A
- Mapping quality
- N/A
- QC and filtering
- Germline whole genome sequencing data were processed, and the aggregate VCF was calculated. Variants were then filtered based on the following conditions:
(1) Variants that did not pass the VQSR filter were excluded
(2) Multi-allelic sites were excluded
(3) Variants with a call rate below 95% were excluded
(4) Variants deviating from Hardy-Weinberg equilibrium (P < 1e-10) were excluded
(5) Variants with a minor allele count (MAC) less than 2 were excluded - Analysis method
- GATK HaplotypeCaller -ERC GVCF (version 4.1.0.0)
The ploidy for variant call was set as follows:
Autosomes and pseudoautosomal regions (PARs): ploidy=2
Non-PARs on the X chromosome: ploidy=2 (female) and ploidy=1 (male)
Non-PARs on the Y chromosome: ploidy=1 (male) - Processed data type
- Reference panel
Variant calls - Dataset ID of processed data
- JGAD000867
JGAD000868 - Processing method
- List of processed data (Imputation reference)
- Data use policy
- NBDC data sharing policy (JGAP000001)