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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

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FileLabelSizeCopy URL
ReadMe_hum0311.v5.docxDictionary file31.1 KB
hum0311.v5.both ulcers.BBJ1-12K.txt.gzGroup: BBJ1-12K / Disease name: both ulcers / Patients / Controls: 102 / 8,617 / Marker number: 10,761,349517 MB
hum0311.v5.both ulcers.BBJ1-180K.txt.gzGroup: BBJ1-180K / Disease name: both ulcers / Patients / Controls: 1,867 / 153,178 / Marker number: 11,997,806582 MB
hum0311.v5.both ulcers.BBJ2-42K.txt.gzGroup: BBJ2-42K / Disease name: both ulcers / Patients / Controls: 387 / 34,647 / Marker number: 11,483,634558 MB
hum0311.v5.both ulcers.EAS.tsv.gzGroup: East Asian meta-analysis (EAS) / Disease name: both ulcers / Patients / Controls: 3,197 / 240,675 / Marker number: 13,806,061332 MB
hum0311.v5.duodenal ulcers only.BBJ1-180K.txt.gzGroup: BBJ1-180K / Disease name: duodenal ulcers only / Patients / Controls: 5,300 / 153,178 / Marker number: 12,000,909581 MB
hum0311.v5.duodenal ulcers.BBJ1-12K.txt.gzGroup: BBJ1-12K / Disease name: duodenal ulcers / Patients / Controls: 383 / 8,617 / Marker number: 10,785,946507 MB
hum0311.v5.duodenal ulcers.BBJ1-180K.txt.gzGroup: BBJ1-180K / Disease name: duodenal ulcers / Patients / Controls: 7,167 / 153,178 / Marker number: 12,002,536581 MB
hum0311.v5.duodenal ulcers.BBJ2-42K.txt.gzGroup: BBJ2-42K / Disease name: duodenal ulcers / Patients / Controls: 1,488 / 34,647 / Marker number: 11,490,965559 MB
hum0311.v5.duodenal ulcers.EAS.tsv.gzGroup: East Asian meta-analysis (EAS) / Disease name: duodenal ulcers / Patients / Controls: 11,964 / 240,675 / Marker number: 13,821,513322 MB
hum0311.v5.duodenal ulcers.EAS_EUR.tsv.gzGroup: Cross-ancestry meta-analysis (EAS and EUR) / Disease name: duodenal ulcers / Patients / Controls: 17,117 / 867,208 / Marker number: 19,009,727419 MB
hum0311.v5.gastric ulcers only.BBJ1-180K.txt.gzGroup: BBJ1-180K / Disease name: gastric ulcers only / Patients / Controls: 12,546 / 153,178 / Marker number: 12,007,257581 MB
hum0311.v5.gastric ulcers.BBJ1-12K.txt.gzGroup: BBJ1-12K / Disease name: gastric ulcers / Patients / Controls: 720 / 8,617 / Marker number: 10,814,879522 MB
hum0311.v5.gastric ulcers.BBJ1-180K.txt.gzGroup: BBJ1-180K / Disease name: gastric ulcers / Patients / Controls: 14,413 / 153,178 / Marker number: 12,008,854581 MB
hum0311.v5.gastric ulcers.BBJ2-42K.txt.gzGroup: BBJ2-42K / Disease name: gastric ulcers / Patients / Controls: 2,536 / 34,647 / Marker number: 11,497,440559 MB
hum0311.v5.gastric ulcers.EAS.tsv.gzGroup: East Asian meta-analysis (EAS) / Disease name: gastric ulcers / Patients / Controls: 20,972 / 240,675 / Marker number: 13,833,037326 MB
hum0311.v5.gastric ulcers.EAS_EUR.tsv.gzGroup: Cross-ancestry meta-analysis (EAS and EUR) / Disease name: gastric ulcers / Patients / Controls: 28,682 / 867,208 / Marker number: 19,018,413418 MB
hum0311.v5.peptic ulcer disease.EAS.tsv.gzGroup: East Asian meta-analysis (EAS) / Disease name: peptic ulcer disease / Patients / Controls: 29,739 / 240,675 / Marker number: 13,846,852325 MB
hum0311.v5.peptic ulcer disease.EAS_EUR.tsv.gzGroup: Cross-ancestry meta-analysis (EAS and EUR) / Disease name: peptic ulcer disease / Patients / Controls: 52,032 / 905,344 / Marker number: 19,078,654419 MB
hum0311.v5.peptic ulcer.BBJ1-12K.txt.gzGroup: BBJ1-12K / Disease name: peptic ulcer disease / Patients / Controls: 1,001 / 8,617 / Marker number: 10,836,527523 MB
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

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)