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 IDType of DataCriteriaRelease Date
JGAS000090 NGS (RNA-seq) Controlled-access (Type I) 2017/05/25
JGAS000138 Methylation array Controlled-access (Type I) 2019/11/18

*Release Note

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MOLECULAR DATA

JGAS000090

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

 

JGAS000138

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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