NBDC Research ID: hum0225.v1
SUMMARY
Aims: Estimating the risks of developing adult T-cell leukemia (ATL) through a genetic analysis of human T-cell leukemia virus (HTLV-1)-associated myelopathy (HAM)
Methods: Target capture sequencing by using of NGS technology
Participants/Materials: HAM 21 cases (infected and uninfected cells)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000226 | NGS (Target Capture) | Controlled-access (Type I) | 2020/05/08 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
HAM（ICD-10：A858/B973）： 21 cases (46 samples) infected cells (tumor cells): 23 samples (including post-ATL specimens for 2 cases) uninfected cells (non-tumor cells): 23 samples (including post-ATL specimens for 2 cases) |
| Targets | Target Capture |
| Target Loci for Capture Methods | 280 genes (human) including 50 candidate genes for ATL and whole genome of HTLV-1 provirus |
| Platform | Illumina [HiSeq 2500/3000] |
| Library Source | DNAs extracted from PBMC (infected and uninfected cells) of HAM patients |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT HS Target Enrichment System |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000318 |
| Total Data Volume | 238 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Makoto Yamagishi / Yoshihisa Yamano
Affiliation: Graduate School of Frontier Sciences, The University of Tokyo / Institute of Medical Science, St. Marianna University School of Medicine
Project / Group Name: Laboratory of Tumor Cell Biology / Department of Rare Disases Research
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED) | Development of risk stratification and prevention for HTLV-1-associated diseases based on multi-omics database | JP20fk0108126 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Analysis of genome/epigenome control mechanism that regulates abnormal traits of HTLV-1 infected cells in HAM | 19H03575 |
| Practical Research Project for Rare / Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | The establishment of evidence for clinical guideline development on HAM and HTLV-1-related refractory disease through integration of patient registry | JP19ek0109356 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Mortality and risk of progression to adult T-cell leukemia/lymphoma in patients with HTLV-1-associated myelopathy/tropical spastic paraparesis | doi: 10.1073/pnas.1920346117 | JGAD000318 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Masao Matsuoka | Kumamoto University School of Medicine Hematology, Rheumatology and Infectious Diseases | Japan | Retrospective observational study of characteristics, clinical course and treatment of malignant lymphoma and adult T-cell leukemia/lymphoma with genetic and pathological evaluations | JGAD000318 | 2022/05/16-2030/03/31 |
