NBDC Research ID: hum0348.v1
SUMMARY
Aims: To elucidate the mechanism of the tumorigenic process involving genomic aberrations by CD30 signaling in HTLV-1–infected T-cells
Methods: CD30+ATL cells, CD30-ATL cells, and HTLV-1 uninfected lymphocytes were sorted by FACS AriaIII. DNA was extracted from each sorted cell and used for whole exome sequencing analysis and array-CGH analysis.
Participants/Materials: Adult T-cell leukemia/lymphoma (ATL): 8 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000537 | Controlled-access (Type I) | 2023/05/15 |
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MOLECULAR DATA
| Participants/Materials |
ATL (ICD10: C91.5): 8 cases CD30+ATL cells: 8 samples CD30-ATL cells: 8 samples HTLV-1 uninfected lymphocytes: 8 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from sorted cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Trimmomatic (v.0.38), DRAGEN Bio-IT Platform (v.3.7.5) |
| Mapping Quality | - |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 83.6 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000656 |
| Total Data Volume | 118.1 GB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | ATL (ICD10: C91.5): 8 cases |
| Targets | array-CGH |
| Target Loci for Capture Methods | - |
| Platform | Agilent Technologies [GenetiSure Cancer Research CGH+SNP Microarray 2 x 400K] |
| Source | DNAs extracted from sorted cells |
| Cell Lines | - |
| Reagents (Kit, Version) | SureTag Complete DNA Labeling Kit |
| Genotype Call Methods (software) | Cytogenomics v5.0 |
| Filtering | ADM-2 algorithm, Threshokd value: 5.5 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000656 |
| Total Data Volume | 118.1 GB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Makoto Nakashima
Affiliation: Graduate School of Frontier Sciences, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Analysis of ATL progression by CD30 signaling and its biomarkers | 19K16580 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | The oncogenic driving force of CD30 signaling-induced chromosomal instability in adult T-cell leukemia/lymphoma | 22K15420 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | The oncogenic driving force of CD30 signaling-induced chromosomal instability in adult T-cell leukemia/lymphoma | doi: 10.1111/cas.15706 | JGAD000656 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
