NBDC Research ID: hum0029.v2
SUMMARY
Aims: Identification of new susceptibility gene(s) to cole medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN)
Methods: SNP-based and SNV/INDEL/structural variation-based genome-wide association study.
Participants/Materials: Patients with cold medicine-related SJS/TEN and healthy controls
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0029.v1.freq.v1 | GWAS for SJS | Unrestricted-access | 2016/03/09 |
| hum0029.v2.var.v1 | GWAS for SJS/TEN | Unrestricted-access | 2020/12/21 |
*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: | 117 SJS patients and 691 healthy controls |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Axiom Genome-Wide ASI 1 Array] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | AXIOM 2.0 Reagent Kit |
| Genotype Call Methods (software) | Genotyping Console ver. 4.2.0.26 |
| Filtering Methods | Sample Call rate < 0.95, SNP call rate < 0.97, HWE P < 0.001 |
| Marker Number (after QC) | 449,205 SNPs (hg19) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 130 MB |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | 133 SJS/TEN patients (ICD10: L511) and 418 healthy controls |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | TruSeq® DNA PCR-Free Sample Prep Kit |
| Genotype Call Methods (software) | GATK3.8 HaplotypeCaller, MELT 2.1.4, LUMPY 0.2.3, SVTyper 0.6.1 |
| Filtering Methods | variant call rates < 95%, MAF < 1%, or HWE p-value < 1×10^-5 |
| Marker Number (after QC) | 7,173,860 variants (hg19) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 122 MB |
| Comments (Policies) | NBDC policy |
*This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Mayumi Ueta
Affiliation: Kyoto Prefectural University of Medicine
Project / Group Name: Department of Frontier Medical Science and Technology for Ophthalmology
URL: http://frontier-medueta.com/english/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific research (B) | Pioneering research for elucidation of pathogenic mechanism and prediction of onset risk | 22390325 |
| Tailor-made Medical Treatment Program (BioBank Japan: BBJ) | Genetic and Pathogenic studies on cold medicine-related severe drug adverse reactions | - |
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Genome Science | 221S0002 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | IKZF1, a new susceptibility gene for cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis with severe mucosal involvement. | doi: 10.1016/j.jaci.2014.12.1916 | hum0029.v1.freq.v1 |
| 2 | Mapping of susceptible variants for cold medicine-related Stevens-Johnson syndrome by whole-genome resequencing | doi: 10.1038/s41525-021-00171-2 | hum0029.v2.var.v1 |
