NBDC Research ID: hum0405.v2
SUMMARY
Aims: In recent years, "cancer stem cells" have been reported to exist in many cancers. Many reports have shown that they are the main cause of cancer recurrence. The aim of this study is to test whether cancer stem cells can be identified using patient samples. We will perform omics analysis of rare pediatric cancers by integrating genomics, transcriptomics, proteomics and metabolomics, including somatic and germline mutations, to deepen our understanding of the biological characteristics of the target disease. Based on the knowledge gained and clinical information from patients, we will conduct preclinical pharmacological studies using mouse models and in vitro models to investigate the therapeutic effects of novel therapeutic agents and novel therapeutic strategies such as cellular therapies.
Methods: WES, RNA-seq and Small RNA-seq
Participants/Materials:
Pediatric B-cell precursor acute lymphocytic leukemia: 69 cases
Pediatric acute myeloid leukemia: 9 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000623 | Controlled-access (Type I) | 2023/12/25 | |
| JGAS000631 | Controlled-access (Type I) | 2025/07/16 |
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MOLECULAR DATA
| Participants/Materials |
Pediatric B-cell precursor acute lymphocytic leukemia (ICD10: C910): 64 cases leukemia cells from peripheral blood or bone marrow fluid: 64 samples Pediatric acute myeloid leukemia (ICD10: C920): 3 cases whole blood or bone marrow aspirates at the time of remission or relapse: 6 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400RS] |
| Library Source | DNAs extracted from leukemia cells |
| Cell Lines | - |
| Library Construction (kit name) | Lotus DNA Library Prep Kit, xGen Exome Research Panel |
| Fragmentation Methods | Restriction enzyme reaction |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Genomon v2.6.2 |
| Mapping Quality | Reads and variants with MAPQ< 20 or base call quality< 15 were excluded. |
| Reference Genome Sequence | GRCh37 |
| Coverage (Depth) | 129 |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000752: Pediatric B-cell precursor acute lymphocytic leukemia JGAD000761: Pediatric acute myeloid leukemia |
| Total Data Volume |
JGAD000752: 935.2 GB (fastq) JGAD000761: 180.6 GB (bam, bai) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric B-cell precursor acute lymphocytic leukemia (ICD10: C910): 69 cases leukemia cells from peripheral blood or bone marrow fluid: 69 samples Pediatric acute myeloid leukemia (ICD10: C920): 9 cases (5 cases revealed pediatric B-cell precursor acute lymphocytic leukemia at onset and Pediatric acute myeloid leukemia at relapse） whole blood or bone marrow aspirates at disease onset or relapse: 15 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X] |
| Library Source | RNAs extracted from leukemia cells |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II Directional RNA Library Prep Kit for Illumina |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Genomon v2.6.2 |
| Mapping Quality | unmapped reads < 5% |
| Reference Genome Sequence | GRCh37 |
| Coverage (Depth) | Uniquely mapped reads >90% |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000752: Pediatric B-cell precursor acute lymphocytic leukemia JGAD000761: Pediatric acute myeloid leukemia |
| Total Data Volume |
JGAD000752: 935.2 GB (fastq) JGAD000761: 180.6 GB (bam, bai) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric B-cell precursor acute lymphocytic leukemia (ICD10: C910): 69 cases leukemia cells from peripheral blood or bone marrow fluid: 69 samples |
| Targets | small RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 550] |
| Library Source | RNAs extracted from leukemia cells |
| Cell Lines | - |
| Library Construction (kit name) | NEXTflex Small RNA Sequencing kit v3 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD00752 |
| Total Data Volume | 935.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Junko Takita
Affiliation: Department of Pediatrics, Graduate School of Medicine, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Study of spatiotemporal variety of intractable pediatric cancers and development of new drugs | JP22ama221505 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Development of novel therapeutic strategies for intractable pediatric cancers based on the multi-omics information | 17H04224 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Integrated analysis of mechanisms of genetic susceptibility to cancer and clonal evolution in pediatric cancer | 20H00528 |
| KAKENHI Grant-in-Aid for Challenging Research (Exploratory) | Development of novel therapeutic strategies for pediatric solid tumor based on non-driver gene targeted approaches | 21K19405 |
| KAKENHI Grant-in-Aid for Challenging Research (Exploratory) | Elucidation of crosstalk between neurodevelopmental disorders and tumorigenesis and development of novel therapeutic drugs | 23K18264 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | RNA-seq-based miRNA signature as an independent predictor of relapse in pediatric B-cell acute lymphoblastic leukemia | doi: 10.1182/bloodadvances.2023011583 | JGAD000752 |
| 2 | Multi-omics analysis identifies an M-MDSC-like immunosuppressive phenotype in lineage-switched AML with KMT2A rearrangement | JGAD000761 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
