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Dataset ID

NHA000192

Type of data
GWAS for recurrent pregnancy loss
Access criteria
Unrestricted-access
Total data volume
437 MB
File formats
  • DOCX
  • ZIP
Research
hum0197
Date published
2024-05-30
Date modified
2024-05-30
Secondary ID
hum0197.v20.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Description_GWASsummary_RPL_Japanese_SoneharaNatCommun2024.docxDictionary file21.0 KB
hum0197.v20.gwas.v1.zip437 MB

Analysis method

genome wide SNPs

Materials and participants
Recurrent pregnancy loss cases (ICD10: N96): 1,728
Control participants: 24,315
  • Health status
    Mixed
  • Subject count
    26,043 (Individual)
Disease
Recurrent pregnancy loss cases (N96)
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
Infinium Asian Screening Array Kit
Platform
Illumina Infinium Asian Screening Array
Reference genome
GRCh37
QC and filtering
Sample QC: We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Japanese ancestry using PCA.
Variant QC: We excluded variants with (1) genotyping call rate < 99%, (2) minor allele count < 5, (3) P-value for Hardy-Weinberg equilibrium < 1.0 × 10^−10, and (4) > 5% allele frequency difference compared with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project.
Post-imputation QC: We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 0.5%.
Imputation
Haplotype phasing: shapeit4
Imputation: minimac4
Analysis method
Genotyping: GenomeStudio
SAIGE
Variant count
8,717,430 variants
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)