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 IDType of DataCriteriaRelease Date
JGAS000147

NGS (RNA-seq)

Methylation array

SNP array

Controlled-access (Type I) 2020/01/10

*Release Note

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

RNA-seq

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

 

Methylation array

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

 

SNP array

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):

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 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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