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Dataset ID

NHA000188

Type of data
GWAS for Hunner-type interstitial cystitis
Access criteria
Unrestricted-access
Total data volume
660 MB
File formats
  • DOCX
  • ZIP
Research
hum0197
Date published
2023-06-27
Date modified
2023-06-27
Secondary ID
hum0197.v17.hic-gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
header_description_hum0197.v17.docxDictionary file20.4 KB
hum0197.v17.hic-gwas.v1.zip660 MB

Analysis method

genome wide SNPs

Materials and participants
Hunner-type interstitial cystitis cases (ICD10: N301): 144
Control participants: 41,516
  • Health status
    Mixed
  • Subject count
    41,660 (Individual)
Disease
Hunner-type interstitial cystitis cases (N301)
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
shapeit4 for haplotype phasing
minimac4 for imputation
Analysis method
GenomeStudio for genotyping
SAIGE
Variant count
7,909,790 variants
Processed data type
GWAS summary statistics
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)