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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000385 | Controlled-access (Type I) | 2022/01/14 | |
| JGAS000385 (Data addition) | NGS (Target Capture) | Controlled-access (Type I) | 2022/07/28 |
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MOLECULAR DATA
| 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 |
| 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 | Enzymatic fragmentation |
| 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 |
| 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 |
| 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 fragmentation (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 |
| 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 |
| 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):
| 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 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Integrated analysis of mechanisms of genetic susceptibility and clonal evolution in pediatric cancers | 20H00528 |
PUBLICATIONS
| Title | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data 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 |
