NBDC Research ID: hum0225.v2
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, RNA-seq, ATAC-seq, single-cell Multiome (scRNA-seq, scATAC-seq)
Participants/Materials:
Target capture: HAM 21 cases (infected and uninfected cells)
RNA-seq: HAM 13 cases (infected cells)
ATAC-seq: HAM 2 cases (infected cells)
scMultiome: HAM 2 cases, asymptomatic HTLV-1 carriers 3 individuals
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000226 | NGS (Target Capture) | Controlled-access (Type I) | 2020/05/08 |
| JGAS000835 | NGS (RNA-seq, ATAC-seq, scMultiome) | Controlled-access (Type I) | 2025/09/24 |
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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 |
| Participants/Materials | HAM（ICD-10：A858/B973）： 13 cases |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from HTLV-1-infected T cells sorted using anti-CD4, anti-CADM1, and anti-CD7 antibodies |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext rRNA Depletion Kit |
| Fragmentation Methods | chemical fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000977 |
| Total Data Volume | 583.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | HAM（ICD-10：A858/B973）： 2 cases |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from HTLV-1–infected T cells sorted using anti-CD4, anti-CADM1, and anti-CD7 antibodies |
| Cell Lines | - |
| Library Construction (kit name) | Standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000977 |
| Total Data Volume | 583.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
HAM（ICD-10：A858/B973）： 2 cases HTLV-1-infected asymptomatic individuals: 3 cases |
| Targets | scRNA-seq, scATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs/RNAs extracted from peripheral blood mononuclear cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell Multiome ATAC + Gene Expression |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
scRNA-seq: 118 bp scATAC-seq: 99 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000977 |
| Total Data Volume | 583.2 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 Viral Oncology and Genomics / 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 |
| Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED) | Comprehensive study on elucidation of pathogenesis of HTLV-1 infection based on genome information and development of risk prediction algorithm | JP25fk0108672 |
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 |
