NBDC Research ID: hum0144.v1
SUMMARY
Aims: To explore genetic alteratoins in pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrome
Methods: SNP array, whole transcriptome sequencing, and DNA methylation array were performed in cases of pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrome
Participants/Materials: 43 pediatric B-cell precursor acute lymphoblastic leukemia cases in Down syndrome
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000147 | Controlled-access (Type I) | 2020/01/10 |
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MOLECULAR DATA
| Participants/Materials | pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrome (ICD10: C91.0): 25 cases |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | RNAs extracted from bone marrow aspirates of pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrom patients |
| Cell Lines | - |
| Library Construction (kit name) | NEB 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) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000221 |
| Total Data Volume | 189 GB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrome (ICD10: C91.0): 36 cases |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium MethylationEPIC BeadChip, Infinium HumanMethylation450 BeadChip] |
| Library Source | DNAs extracted from bone marrow aspirates of pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrom patients |
| Cell Lines | - |
| Library Construction (kit name) | EpiTect Fast Bisulfite Conversion Kit, Infinium MethylationEPIC |
| Algorithms for Calculating Methylation-rate (software) | iScan system and GenomeStudio Software (Illumina) |
| Probe Number | 450k/850k |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000221 |
| Total Data Volume | 189 GB (idat) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrome (ICD10: C91.0): 36 cases |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | |
| Platform | Affymetrix [GeneChip Human Mapping 250k Nsp, Cytoscan HD] |
| Source | DNAs extracted from bone marrow aspirates of pediatric B-cell precursor acute lymphoblastic leukemia in Down syndrom patients |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix Cytoscan HD kit |
| Genotype Call Methods (software) | Genotyping Console ver. 4.2.0.26 |
| Marker number | 750k/250k SNPs |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000221 |
| Total Data Volume | 189 GB (CEL) |
| 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: Comprehensive analysis of genetic aberrations in hematologic malignancies
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 | Integrated genetic and epigenetic analysis revealed heterogeneity of acute lymphoblastic leukemia in Down syndrome | doi: 10.1111/cas.14160 | JGAD000221 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Jinyan Huang | School of Medicine, Zhejiang University | Comprehensive analysis of alternative splicing in malignant tumors | JGAD000221 | 2022/03/07-2024/01/01 | |
| Ching Lau | Pediatric Oncology, The Jackson Laboratory for Genomic Medicine | United States of America | AML in Down's Syndrome | JGAD000221 | 2022/08/15-2024/02/15 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000221 | 2022/12/26-2025/03/31 |
