NBDC Research ID: hum0251.v1

 

SUMMARY

Aims: Elucidation of molecular pathology for B-cell acute lymphocytic leukemia (B-ALL) by genomic analysis

Methods: RNA Sequencing and target capture sequencing analyses

Participants/Materials: Philadelphia chromosome-negative (Ph-negative) B-ALL

 

Dataset IDType of DataCriteriaRelease Date
JGAS000278 NGS (RNA-seq, Target Capture) Controlled-access (Type I) 2022/10/25

*Release Note

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MOLECULAR DATA

RNA-seq

Participants/Materials Ph-negative B-ALL (ICD10: C91.0): 122 cases
Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNA extracted from leukemia cells
Cell Lines -
Library Construction (kit name) NEBNext Ultra Directional RNA Library Prep Kit
Fragmentation Methods Heat treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 125 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000384
Total Data Volume 681.6 GB (fastq)
Comments (Policies) NBDC policy

 

Target Capture

Participants/Materials Ph-negative B-ALL (ICD10: C91.0): 148 cases
Targets Target Capture
Target Loci for Capture Methods 110 genes
Platform Illumina [HiSeq 2500]
Library Source DNA extracted from leukemia cells
Cell Lines -
Library Construction (kit name) SureSelect XT Low Input
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 125 bp
Mapping Methods bwa
Mapping Quality > 20
Reference Genome Sequence hg19
Coverage (Depth) 570
Japanese Genotype-phenotype Archive Dataset ID JGAD000384
Total Data Volume 681.6 GB (bam)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Yoshihiro Hatta

Affiliation: Division of Hematology and Rheumatology, Nihon University School of Medicine

Project / Group Name: JALSG Ph(-)B-ALL213

Funds / Grants (Research Project Number):

NameTitleProject Number
Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) Treatment with a pediatric protocols and stritified strateiesy by gene panel testing for adolescents and young adults with acute lymphoblastic leukemia JP19ck0106331

 

PUBLICATIONS

TitleDOIDataset ID
1 Two novel high-risk adult B-cell acute lymphoblastic leukemia subtypes with high expression of CDX2 and IDH1/2 mutations doi: 10.1182/blood.2021011921 JGAD000384
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use