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Dataset ID

NHA000187

Type of data
GWAS for 15 phenotypes
Access criteria
Unrestricted-access
Total data volume
25.2 GB
File formats
  • TXT
  • DOCX
Research
hum0197
Date published
2023-06-06
Date modified
2023-06-06
Secondary ID
hum0197.v16.gwas.v1

Unrestricted-access files linked to this dataset

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41–46 / 46

FileLabelSizeCopy URL
hum0197.v16.SC.2BB.v1.txt.gzDisease name: gastric cancer / Abbreviation: SC / ICD10: C16 / Patients / Controls: 6,798/484,805 (BBJ + UKB)270 MB
hum0197.v16.SC.BBJ.v1.txt.gzDisease name: gastric cancer / Abbreviation: SC / ICD10: C16 / Patients / Controls: 5,775/150,462 (BBJ)664 MB
hum0197.v16.SC.UKB.v1.txt.gzDisease name: gastric cancer / Abbreviation: SC / ICD10: C16 / Patients / Controls: 1,023/334,343 (UKB)864 MB
hum0197.v16.UC.2BB.v1.txt.gzDisease name: endometrial cancer / Abbreviation: UC / ICD10: C54 / Patients / Controls: 2,840/254,142 (BBJ + UKB)274 MB
hum0197.v16.UC.BBJ.v1.txt.gzDisease name: endometrial cancer / Abbreviation: UC / ICD10: C54 / Patients / Controls: 948/70,676 (BBJ)659 MB
hum0197.v16.UC.UKB.v1.txt.gzDisease name: endometrial cancer / Abbreviation: UC / ICD10: C54 / Patients / Controls: 1,892/183,466 (UKB)893 MB

41–46 / 46

Analysis method

genome wide SNPs

Materials and participants
BioBank Japan (n=180,215), UK Biobank (n=377,441)
large-scale meta-analysis including the summary statistics of other cohorts (FinnGen, BCAC, and PRACTICAL) for breast and prostate cancer (n=648,746 and 482,080)
no. Phenotypes: 15
Patients: biliary tract (ICD10: C22.1, 23-24), breast (ICD10: C509), cervical (ICD10: C53), colorectal (ICD10: C18-20), endometrial (ICD10: C54), esophageal (ICD10: C15), gastric (ICD10: C16), hepatocellular (ICD10: C22.0), lung (ICD10: C34), non-Hodgkin's lymphoma (ICD10: C82-83), ovarian (ICD10: C56), pancreatic (ICD10: C25), and prostate (ICD10: C61) cancer
Controls: without cancer individuals
(There is overlap among patients in each disease category)
  • Health status
    Mixed
  • Counted as
    Individual
  • Cohort
    BioBank Japan, FinnGen, UK Biobank
  • Population
    European, Finnish, Japanese
Disease
biliary tract (C221, C23, C24)
breast (C509)
cervical (C53)
colorectal (C18, C19, C20)
endometrial (C54)
esophageal (C15)
gastric (C16)
hepatocellular (C220)
lung (C34)
non-Hodgkin's lymphoma (C82, C83)
ovarian (C56)
pancreatic (C25)
prostate (C61)
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
FinnGen1 ThermoFisher Array
HumanExome BeadChip Kit
HumanOmniExpress BeadChip Kit
HumanOmniExpressExome BeadChip Kit
Infinium OncoArray-500K v1.0 BeadChip Kit
UK BiLEVE Axiom Array
UK Biobank Axiom Array
Platform
Applied Biosystems UK BiLEVE Axiom Array
Applied Biosystems UK Biobank Axiom Array
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Illumina iCOGS
Illumina OncoArray
Thermo Fisher Scientific FinnGen1 ThermoFisher Array
QC and filtering
Sample QC and Variant QC for each dataset: refer to ReadMe file
We excluded the variants with Rsq < 0.7 and MAF < 0.01.
Imputation
BBJ: Eagle, Minimac3
UK Biobank: IMPUTE4
FinnGen: beagle4.1
BCAC: IMPUTE2
PRACTICAL: IMPUTE2
Analysis method
SAIGE software was used with age, sex, and top five principal components as covariates.
RE2C software was used for the multi-trait meta-analysis adjusting for sample overlap between GWAS summary data.
Variant count
BBJ 13MN: 7,398,798
BBJ each cancer: 7,442,557 (Mean)
BBJ each cancer: 7,420,485–7,444,681 (Range)
UK Biobank 13MN: 9,602,853
UK Biobank each cancer: 9,620,786 (Mean)
UK Biobank each cancer: 9,620,343–9,620,935 (Range)
BBJ+UK Biobank 13MN: 5,374,018
BBJ+UK Biobank each cancer: 5,696,155 (Mean)
BBJ+UK Biobank each cancer: 5,677,934–5,698,357 (Range)
BBJ+UK Biobank+FinnGen+BCAC (breast cancer): 5,104,756
BBJ+UK Biobank+FinnGen+PRACTICAL (prostate cancer): 5,105,796
BBJ+UK Biobank+FinnGen+BCAC+PRACTICAL (breast cancer+prostate cancer): 5,100,089
Processed data type
GWAS summary statistics
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)