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Dataset ID

NHA000204

Type of data
GWAS for loss of the Y chromosome
Access criteria
Unrestricted-access
Total data volume
192 MB
File formats
  • TXT
  • DOCX
Research
hum0197
Date published
2025-12-02
Date modified
2025-12-02
Secondary ID
hum0197.v27.LOY-meta.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Dictionary_LOY_meta.docxDictionary file18.5 KB
LOY_GWAS.txt.gz192 MB

Analysis method

genome wide SNPs

Materials and participants
161,026 Japanese males
BioBank Japan (BBJ): 120,522
Japan COVID-19 Task Force (JCTF): 3,161
Tohoku Medical Megabank (TMM): 26,544
Cohort of COVID-19 vaccine recipients (COVC)*1: 888
Hospital-based Epidemiologic Research Program at Aichi Cancer Center (HERPACC): 6,636
The Japan Public Health Center-based Prospective Study for the Next Generation (JPHC): 3,275
  • Subject count
    161,026 (Individual)
  • Cohort
    BioBank Japan, Tohoku Medical Megabank
  • Population
    Japanese
  • Sex
    Male
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
Affymetrix Japonica Array
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Illumina Infinium Asian Screening Array
QC and filtering
Sample QC: We excluded individuals with a low call rate (< 0.95) and outliers from the PCA-based East Asian cluster.
Variant QC: Quality control of the variants was conducted using the following criteria: (i) with a low call rate (< 0.99); (ii) with low minor allele counts (< 5); and (iii) with Hardy-Weinberg equilibrium test P value < 1.0 × 10−10.
Post-imputation QC: Variants with imputation quality Rsq < 0.3 or minor allele frequency (MAF) < 0.005 were excluded.
Imputation
BBJ: Eagle, Minimac3
JCTF, COVC, HERPACC, JPHC: SHAPEIT4, Minimac4
TMM: SHAPEIT2, IMPUTE4
Analysis method
BBJ: SAIGE
JCTF, COVC, HERPACC, JPHC: SAIGE
TMM: regenie
meta-analysis: METAL
Variant count
9,062,001 variant (reference: In-house Japanese-specific reference panel composed of n = 11,754 whole-genome sequence data)
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)