NBDC Research ID: hum0096.v2
SUMMARY
Aims: To explore genetic alteratoins in pediatric T-cell acute lymphoblastic leukemia (T-ALL), we performed genome wide analysis using next generation sequencing methods.
Methods: We performed whole transcriptome sequencing in 123 pediatric T-ALL for detecting gene fusion and analysing expression data. Among them, 79 cases were further analyzed in DNA metylation array.
Participants/Materials: 123 pediatric T-ALL patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000090 | NGS (RNA-seq) | Controlled-access (Type I) | 2017/05/25 |
| JGAS000138 | Methylation array | Controlled-access (Type I) | 2019/11/18 |
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MOLECULAR DATA
| Participants/Materials | pediatric T-ALL patients (ICD10: C91.0): 123 cases |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | total RNAs extracted from bone marrow aspirates, peripheral blood cells, or lymph nodes of pediatric T-ALL patients |
| Cell Lines | - |
| Library Construction (kit name) |
TruSeq RNA Library Prep Kit NEBNext Ultra RNA Library Prep Kit for Illumina |
| Fragmentation Methods | restriction enzyme reaction |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 108 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000090 |
| Total Data Volume | 927 GB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | pediatric T-ALL patients (ICD10: C91.0): 79 cases |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium MethylationEPIC] |
| Library Source | DNAs extracted from bone marrow aspirates, peripheral blood cells, or lymph nodes of pediatric T-ALL patients |
| Cell Lines | - |
| Library Construction (kit name) | EpiTect Fast Bisulfite Conversion Kit, Infinium MethylationEPIC |
| Algorithms for Calculating Methylation-rate (software) | - |
| Probe Number | 866,554 probes (raw data) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000207 |
| Total Data Volume | 2 GB (idat) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Junko Takita
Affiliation: Department of Pediatrics, Graduate School of Medicine, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Development for novel therapeutic stratagies of intractable cancers in children and adolescent and young adult using molecular profilings | JP16cm0106509 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Development for novel therapeutic stratagies of intractable pediatric cancers based on the multi-omics analysis | 17H04224 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Recurrent PU.1 (SPI1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia | doi: 10.1038/ng.3900 | JGAD000090 |
| 2 | DNA methylation-based classification reveals difference between pediatric T-cell acute lymphoblastic leukemia and normal thymocytes | doi: 10.1038/s41375-019-0626-2 | JGAD000207 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Jinyan HUANG | Shanghai Jiao Tong University School of Medicine, State Key Laboratory Of Medical Genomics, Rui-jin Hospital | JGAD000090 | 2017/07/19-2018/04/01 | ||
| BERNARD Olivier | Institut Gustave Roussy | JGAD000090 | 2017/09/14-2019/12/31 | ||
| Jun J Yang | Department of Pharmaceutical Science, St. Jude Children's Hospital | JGAD000090 | 2019/04/11-2019/07/07 | ||
| Charles G. Mullighan | Pathology Department, St. Jude Children's Research Hospital | Genomic analysis for acute lymphoblastic leukemia | JGAD000090 | 2019/10/11-2020/01/17 | |
| Takaomi Sanda | Cancer Science Institute of Singapore, National University of Singapore | Sequencing and Expression Analyses in T-Cell Leukemia Using Publicly-Available Datasets | JGAD000090, JGAD000207 | 2020/07/14-2024/03/31 | |
| Charles de Bock | Children's Cancer Institute, University of New South Wales | Elusidating the role of the TCF7-SPI1 fusion in T cell acute lymphoblastic leukemia | JGAD000090 | 2020/08/17-2021/06/09 | |
| Chengyu Liang | The Wistar institute | Oncogenic mechanism of T-cell lymphoblastic leukemia | JGAD000090, JGAD000207 | 2022/01/07-2024/11/22 | |
| Takahiko Yasuda | Clinical Research Center, Nagoya Medical Center | Basic research aimed at elucidating the molecular pathology and developing effective and safe treatment methods for hematological diseases | JGAD000090 | 2022/01/10-2025/03/31 | |
| Jinyan Huang | School of Medicine, Zhejiang University | Comprehensive analysis of alternative splicing in malignant tumors | JGAD000090, JGAD000207 | 2022/03/07-2024/01/01 | |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000090 | 2022/12/26-2025/03/31 |
