NBDC Research ID: hum0166.v2



Aims: Discovery of genetic factors associated with thiopurine-induced severe adverse events

Methods: Genome-wide association study

Participants/Materials: Patients with inflammatory bowel diseases (Crohn's disease, Ulcerative Colitis, Gastrointestinal Behçet's disease)


Dataset IDType of DataCriteriaRelease Date
hum0166.v1.gwas.v1 GWAS for 1221 patients of inflammatory bowel diseases with thiopurine-induced adverse events (leukopenia, alopecia) Unrestricted-access 2019/07/30
JGAS000661 SNP array data of 2680 patients with inflammatory bowel diseases Controlled-access (Type I) 2024/01/25

*Release Note

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*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more



hum0166.v1.gwas.v1 / JGAS000661


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

Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix [Japonica Array v1]
Library Source DNAs extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Axiom 2.0 Reagent Kit
Genotype Call Methods (software) Affymetrix Power Tools (version 1.16.1, Affymetrix)
Imputation Methods

・EAGLE (v 2.4) for prephasing

・IMPUTE4 (v 1.0) + 2KJPN (reference panel)

Filtering Methods

・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

Marker Number (after QC) 5,831,032 SNPs (hg19)
NBDC Dataset ID


(Click the Dataset ID to download the file)

Dictionary file

Japanese Genotype-phenotype Archive Dataset ID JGAD000791
Total Data Volume

hum0166.v1.gwas.v1: 282 MB (csv)

JGAD000791: 76.8 GB (CEL)

Comments (Policies) NBDC policy



Principal Investigator: Yoichi Kakuta

Affiliation: Tohoku University Hospital, Department of Gastroenterology

Project / Group Name: MENDEL study group

Funds / Grants (Research Project Number):

NameTitleProject Number
Program for Promoting Platform of Genomics based Drug Discovery, Japan Agency for Medical Research and Development (AMED) Framework development for genomic medicine in inflammatory bowel disease based on the NUDT15 R139C genotyping kit to find the patients intolerant to thiopurines. JP18kk0305002



TitleDOIDataset ID
1 NUDT15 codon 139 is the best pharmacogenetic marker for predicting thiopurine-induced severe adverse events in Japanese patients with inflammatory bowel disease: a multicenter study. doi: 10.1007/s00535-018-1486-7



2 Genetic Analysis of Ulcerative Colitis in Japanese Individuals Using Population-specific SNP Array doi: 10.1093/ibd/izaa033 JGAD000791
3 Genetic Background of Mesalamine-induced Fever and Diarrhea in Japanese Patients with Inflammatory Bowel Disease. doi: 10.1093/ibd/izab004 JGAD000791


USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use