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Dataset ID

NHA000196

Type of data
GWAS for the individual Jomon proportions
Access criteria
Unrestricted-access
Total data volume
64.5 MB
File formats
  • DOCX
  • ZIP
Research
hum0197
Date published
2024-10-28
Date modified
2024-10-28
Secondary ID
hum0197.v21.gwas-jomon.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
header_description_hum0197v21gwas-jomonv1.docxDictionary file20.4 KB
hum0197.v21.gwas-jomon.v1.zip64.5 MB

Analysis method

genome wide SNPs

Materials and participants
The first cohort of Biobank Japan (n = 171,287)
  • Subject count
    171,287 (Individual)
  • Cohort
    BioBank Japan
  • Population
    Japanese
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • 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
QC and filtering
Sample QC: We excluded (i) individuals with lower call rates (< 99%), (ii) closely related individuals with genetic relatedness ≥ 0.178 calculated from a genetic related matrix (GRM) by GCTA (version 1.93.3beta2). We included samples of the estimated Japanese ancestry using PCA.
Variant QC: We excluded variants with (i) call rate < 99%, (ii) P value for Hardy-Weinberg equilibrium (HWE) < 1.0 × 10-6, (iii) number of heterozygotes < 5, and (iv) a concordance rate < 99.5% or a non-reference concordance rate between GWAS array and whole genome sequencing.
after association test: Double genomic control correction method using METAL was conducted. Computing Z score for each variant by considering the sign of the beta coefficient and the associated p-value, we left the variants with positive Z score.
Imputation
Eagle, Minimac3
Analysis method
1) GCTA-fastGWA with the adjustment of covariates: age, age2, sex, the top 20 PCs, 45 disease status, geographic regions, and PCA clusters.
2) Fixed-effect meta-analysis of Mainland summary data including individuals from the Mainland and EA_admix clusters (n = 151,075) and of Ryukyu summary data including individuals from the Ryukyu, Ryukyu admix, and Hokkaido_sub clusters (n = 10,080) using METAL.
Variant count
3,454,970 SNPs
Data use policy
NBDC data sharing policy (JGAP000001)