NBDC Research ID: hum0315.v2

 

SUMMARY

Aims: To explore genetic alteratoins in KMT2A-rearranged infant acute lymphoblastic leukemia, we performed genome wide analyses using next generation sequencing technologies.

Methods: A total of 84 infants with KMT2A-r ALL were characterized by RNA sequencing, methylation array, and whole exome and targeted deep sequencing. Single-cell RNA sequencing analysis was performed in two cases. ChIP-seq and RNA sequencing were performed in three cell lines derived from infants with KMT2A-r ALL.

Participants/Materials: 84 infants with KMT2A-rearranged acute lymphoblastic leukemia, and 3 cell lines derived from infants with KMT2A-rearranged acute lymphoblastic leukemia

 

Dataset IDType of DataCriteriaRelease Date
JGAS000385

NGS (Exome)

NGS (RNA-seq)

NGS (scRNA-seq)

NGS (ChIP-seq)

Methylation array

Controlled-access (Type I) 2022/01/14
JGAS000385 (Data addition) NGS (Target Capture) Controlled-access (Type I) 2022/07/28

*Release Note

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

 

MOLECULAR DATA

Exome

Participants/Materials

infants with KMT2A-rearranged acute lymphoblastic leukemia (ICD10: C91.0): 31 cases

    leukemia cells and matched normal blood cells: total 62 samples

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source DNAs extracted from leukemia cells and normal blood cells of patients
Cell Lines -
Library Construction (kit name) SureSelect XT Human All Exon V5+lncRNA
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000500
Total Data Volume 1.2 TB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

infants with KMT2A-rearranged acute lymphoblastic leukemia (ICD10: C91.0): 61 cases

cell lines derived from infants with KMT2A-rearranged acute lymphoblastic leukemia: 3 samples

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source RNAs extracted from leukemia cells of patients and cell lines
Cell Lines -
Library Construction (kit name)

Illumina TruSeq RNA Library Prep Kit

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) 100-150 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000500
Total Data Volume 1.2 TB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

scRNA-seq

Participants/Materials infants with KMT2A-rearranged acute lymphoblastic leukemia (ICD10: C91.0): 2 cases
Targets scRNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq X Ten]
Library Source RNAs extracted from leukemia cells of patients
Cell Lines -
Library Construction (kit name) BD Rhapsody WTA Amplification Kit
Fragmentation Methods -
Spot Type -
Read Length (without Barcodes, Adaptors, Primers, and Linkers) -
Japanese Genotype-phenotype Archive Dataset ID JGAD000500
Total Data Volume 1.2 TB (csv)
Comments (Policies) NBDC policy

 

ChIP-seq

Participants/Materials cell lines derived from infants with KMT2A-rearranged acute lymphoblastic leukemia: 3 samples
Targets ChIP-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2500]
Library Source DNAs extracted from cell lines, immunoprecipitated with an anti-histone antibody (H3K27Ac or H3K4me3) or anti-RNA Polymerase II antibody or anti-KMT2A antibody
Cell Lines -
Library Construction (kit name) Illumina TruSeq ChIP Sample Prep Kit
Fragmentation Methods Enzymatic reaction (MNase)
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 50 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000500
Total Data Volume 1.2 TB (bam [ref: hg19], bw)
Comments (Policies) NBDC policy

 

Methylation array

Participants/Materials

infants with KMT2A-rearranged acute lymphoblastic leukemia (ICD10: C91.0): 84 cases

    EPIC: 25 cases

    450K: 59 cases

Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina [Infinium MethylationEPIC BeadChip, Infinium Human Methylation 450K BeadChip]
Library Source DNAs extracted from leukemia cells of patients
Cell Lines -
Library Construction (kit name)

EPIC: Infinium MethylationEPIC BeadChip Kit

450K: Infinium HumanMethylation450 BeadChip Kit

Probe Number

EPIC: 866,836 probes

450K: 485,577 probes

Japanese Genotype-phenotype Archive Dataset ID JGAD000500
Total Data Volume 1.2 TB (idat)
Comments (Policies) NBDC policy

 

Target Capture

Participants/Materials infants with KMT2A-rearranged acute lymphoblastic leukemia (ICD10: C91.0): 72 cases
Targets Target Capture
Target Loci for Capture Methods ARHGAP32, CDKN2A, CDKN2B, CHD4, CHD7, COL24A1, DDX10, DNHD1, FGF5, FLT3, IGSF9, JAG1, KRAS, MED12, NEB, NF1, NRAS, PAX5, PCDH19, PDGFRB, PICALM, PIK3CA, PIK3R1, PLXNA2, PTPN11, TP53, TTLL4, TUBGCP6, XBP1, XPO1
Platform Illumina [HiSeq X Ten]
Library Source DNAs extracted from leukemia cells of patients
Cell Lines -
Library Construction (kit name) Agilent SureSelect-XT Low Input Reagent Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000500
Total Data Volume 48.5 GB (bam [ref: GRCh37])
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):

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
KAKENHI Grant-in-Aid for Scientific Research (A) Integrated analysis of mechanisms of genetic susceptibility and clonal evolution in pediatric cancers 20H00528

 

PUBLICATIONS

TitleDOIDataset ID
1 Multi-omics analysis defines highly refractory RAS burdened immature subgroup of infant acute lymphoblastic leukemia doi: 10.1038/s41467-022-32266-4 JGAD000500
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Michiaki Hamada Faculty of Science and Engineering, Waseda University Japan Construction of RNA-targeted Drug Discovery Database JGAD000500 2022/12/26-2025/03/31