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 |