NBDC Research ID: hum0209.v1
SUMMARY
Aims: To develop genetic and clinical prediction models for the efficacy and hepatotoxicity of methotrexate (MTX) in patients with rheumatoid arthritis (RA).
Methods: Among RA patients treated with MTX, 1,966 polymorphisms of 246 enzymes/transporters relevant to pharmacokinetics and pharmacodynamics were detected by the Drug Metabolism Enzymes and Transporters (DMET) microarray and direct sequencing, and clinical variables at baseline were collected. For efficacy, response criteria of the European League Against Rheumatism were used to classify patients as responders or non-responders. Hepatotoxicity was defined as elevations of aspartate aminotransferase or alanine aminotransferase equal to or greater than 1.5 times the reference range upper limit. Genetic and clinical prediction models for the efficacy and hepatotoxicity of MTX were developed in patients with RA.
Participants/Materials: 166 RA patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0209.v1.var.v1 | Genotype frequencies for variants detected by the DMET and direct sequencing | Unrestricted-access | 2019/12/13 |
*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
| Participants/Materials | RA (ICD10: M06.9): 166 cases |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform |
Array: GeneChip® Scanner 3000 7G (Thermo Fisher Scientific) Direct sequencing: Veriti 96-Well Thermal Cycler and 3730XL DNA Analyzer (Applied Biosystems) |
| Library Source | DNA extracted from peripheral blood cells of RA patients treated with MTX |
| Cell Lines | - |
| Reagents (Kit, Version) |
Array: the DMET Plus Premier pack kits (Thermo Fisher Scientific) Direct sequencing: the BigDye Terminator v3.1 Cycle Sequencing Kit and the BigDye XTerminator Purification Kit (Applied Biosystems) |
| Genotype Call Methods (software) |
Array: the Affymetrix DMET Console Software Direct sequencing: The 3730xl DNA Analyzer Software |
| Filtering Methods | SNP loci with copy number variation and loci on the sex chromosome were excluded from the analyses. |
| Marker Number (after QC) | 1916 variants |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 164 KB (csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shunichi Kumagai
Affiliation: Center for Rheumatic Diseases, Shinko Hospital
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genetic and clinical prediction models for the efficacy and hepatotoxicity of methotrexate in patients with rheumatoid arthritis: a multicenter cohort study | doi: 10.1038/s41397-019-0134-9 | hum0209.v1.var.v1 |
| 2 |
