NBDC Research ID: hum0166.v2
SUMMARY
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 ID | Type of Data | Criteria | Release 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 |
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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
MOLECULAR DATA
hum0166.v1.gwas.v1 / JGAS000661
| Participants/Materials |
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) |
| 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 |
DATA PROVIDER
Principal Investigator: Yoichi Kakuta
Affiliation: Tohoku University Hospital, Department of Gastroenterology
Project / Group Name: MENDEL study group
Funds / Grants (Research Project Number):
| Name | Title | Project 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 |
PUBLICATIONS
| Title | DOI | Dataset 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 |
hum0166.v1.gwas.v1 JGAD000791 |
| 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 Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
