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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
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Dataset ID

NHA000189

Type of data
GWAS for peptic ulcers
Access criteria
Unrestricted-access
Total data volume
10.4 GB
File formats
  • TXT
  • TSV
  • DOCX
Research
hum0311
Date published
2023-07-27
Date modified
2023-07-27
Secondary ID
hum0311.v5.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
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FileLabelSizeCopy URL
hum0311.v5.peptic ulcer.BBJ1-180K.txt.gzGroup: BBJ1-180K / Disease name: peptic ulcer disease / Patients / Controls: 19,713 / 153,178 / Marker number: 12,013,066581 MB
hum0311.v5.peptic ulcer.BBJ2-42K.txt.gzGroup: BBJ2-42K / Disease name: peptic ulcer disease / Patients / Controls: 3,637 / 34,647 / Marker number: 11,504,022559 MB

21–22 / 22

Analysis method

Genotyping by array (GWAS)

Materials and participants
peptic ulcer (ICD10: K27.9), duodenal ulcer (ICD10: K26.9), gastric ulcer (ICD10: K25.9)
- BBJ1-180K: ulcers (n = 19,713), control (n = 153,178)
- BBJ1-12K: ulcers (n = 1,001), control (n = 8,617)
- BBJ2-42K: ulcers (n = 3,637), control (n = 34,647)
- EAS meta-analysis: ulcers (n = 29,739), control (n = 240,675)
(BBJ180K, BBJ1-12K, BBJ2-42k, and TMM-50K)
- Cross-ancestry meta-analysis (EAS and EUR): ulcers (n = 52,032), control (n = 905,344)
(BBJ180K, BBJ1-12K, BBJ2-42k, TMM-50K, FinnGen, and UKB)
* Detailed information on participants
  • Health status
    Mixed
  • Subject count
    957,376 (Individual)
  • Cohort
    BioBank Japan, FinnGen, Tohoku Medical Megabank, UK Biobank
  • Population
    East Asian, European
Disease
peptic ulcer (K279)
duodenal ulcer (K269)
gastric ulcer (K259)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Experimental method
Genotyping by array
Reagent kit
FinnGen1 ThermoFisher Array
HumanExome BeadChip Kit
HumanOmniExpress BeadChip Kit
HumanOmniExpressExome BeadChip Kit
Infinium Asian Screening Array Kit
UK BiLEVE Axiom Array
UK Biobank Axiom Array
Axiom 2.0 Reagent Kit
Platform
Affymetrix Japonica Array
Applied Biosystems UK BiLEVE Axiom Array
Applied Biosystems UK Biobank Axiom Array
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Illumina Infinium Asian Screening Array
Thermo Fisher Scientific FinnGen1 ThermoFisher Array
QC and filtering
Variants with imputation quality (Rsq) < 0.3 or MAC < 20 were excluded
*Sample QC and Variant QC were described in the Dictionary file
Imputation
Pre-phasing: eagle2
Imputation: minimac4 [reference: 1KGP p3v5 ALL]
Analysis method
Genotype Call: GenomeStudio
Variant count
BBJ1-180K GWAS: 12,013,066 variants (Approx.)
BBJ1-12K GWAS: 10,836,527 variants (Approx.)
BBJ2-42K GWAS: 11,504,022 variants (Approx.)
EAS-specific meta-analysis: 13,846,852 variants (Approx.)
Cross-ancestry meta-analysis: 19,078,654 variants (Approx.)
Data use policy
NBDC data sharing policy (JGAP000001)