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Dataset ID

NHA000086

Type of data
GWAS for 1221 patients of inflammatory bowel diseases with thiopurine-induced adverse events (leukopenia, alopecia)
Access criteria
Unrestricted-access
Total data volume
289 MB
File formats
  • XLSX
  • ZIP
Research
hum0166
Date published
2019-07-30
Date modified
2019-07-30
Secondary ID
hum0166.v1.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0166.v1.gwas.v1.zip289 MB
hum0166.v1.gwas.v1_header.xlsxDictionary file11.2 KB

Analysis method

Genotyping by array

Materials and participants
inflammatory bowel diseases: 1221 + 2680 cases
Crohn's disease (ICD10: K509): 516 + 1175 cases
Ulcerative Colitis (ICD10: K519): 674 + 1459 cases
Gastrointestinal Behçet's disease (ICD10: M352): 16 >+ 43 cases
other inflammatory bowel diseases (ICD10: K523): 15 + 3 cases
  • Health status
    Affected
  • Subject count
    3901 (Individual)
Disease
Crohn's disease (K509)
Ulcerative Colitis (K519)
Gastrointestinal Behçet's disease (M352)
other inflammatory bowel diseases (K523)
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
Axiom 2.0 Reagent Kit
Platform
Affymetrix Japonica Array
Reference genome
GRCh37
QC and filtering
・SNVs with low imputation quality
(with a posterior genotype probability of < 0.8 for each genotype or with info score < 0.5 for each variant)
・call rate < 0.97
・minor allele frequency (MAF) < 0.01 or 0.05
(0.01 for GWASs of > 50 cases, 0.05 for GWASs of low-frequency adverse events or conditional GWASs on rs116855232)
・Hardy-Weinberg equilibrium (HWE) p < 1 × 10^−6
Imputation
・EAGLE (v 2.4) for prephasing
・IMPUTE4 (v 1.0) ＋ 2KJPN (reference panel)
Analysis method
Affymetrix Power Tools (version 1.16.1, Affymetrix)
Variant count
5,831,032 SNPs
Data use policy
NBDC data sharing policy (JGAP000001)