NBDC Research ID: hum0116.v1
SUMMARY
Aims: Identification of somatic mutations associated with acute myeloid leukemia (AML) pathogenesis.
Methods: Target Capture sequencing (Acute Myeloid Leukemia Cancer Panel and 41 genes)
Participants/Materials: Leukemia stem cells from AML patients or humanized mice with leukemia derived from immune deficiency mice which were infused with human leukemia stem cells
URL: http://www.riken.jp/en/research/labs/ims/hum_dis_model/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000122 | Controlled-access (Type I) | 2020/11/20 |
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MOLECULAR DATA
Target Capture: AML cancer panel
| Participants/Materials |
AML (ICD10: C920): 19 cases Leukemia stem cell: 33 samples, Pre-leukemia stem cell: 2 samples, T-cell: 6 samples, B-cell: 2 samples (total 43 samples) 37 human leukemia stem cell samples from 37 humanized mice with leukemia derived from immune deficiency mice which were infused with human leukemia stem cell from 12 patients with AML |
| Targets | Target Capture |
| Target Loci for Capture Methods | xGen® Acute Myeloid Leukemia Cancer Panel |
| Platform | Illumina [HiSeq 1500] |
| Library Source |
DNAs extracted from leukemia stem cells, pre-leukemia stem cells, T-cell and B-cells DNAs extracted from leukemia stem cells from humanized mice with leukemia derived from immune deficiency mice which were infused with human leukemia stem cells |
| Cell Lines | - |
| Library Construction (kit name) |
KAPA Hyper Prep kit xGen@ Acute Myeloid Leukemia Cancer Panel |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 50 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000133 |
| Total Data Volume | 423 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
AML (ICD10: C920): 106 cases 1) peripheral blood: 45 samples 2) bone marrow aspirate: 19 samples 3) human leukemia cells from spleen of humanized mice with leukemia derived from immune deficiency mice which were infused with peripheral blood, bone marrow aspirate or samples from patients with AML: 6 samples 4) human leukemia cells from bone marrow aspirate of humanized mice with leukemia derived from immune deficiency mice which were infused with peripheral blood, bone marrow aspirate or samples from patients with AML: 36 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | Coding region of 41 genes (NRAS, KRAS, FLT3, TP53, NPM1, KIT, IDH1, IDH2, SF3B1, U2AF1, TET2, DNMT3A, ASXL1, ASXL2, BCOR, RUNX1, KMT2A(MLL), WT1(WT-1), GATA2, STAG2, RAD21, SMC1A, SMC3, MPL, NF1, PTPN11, CSF3R, CBL, CEBPA, SRSF2, DHX15, ZRSR2, EZH2, SETBP1, KDM6A, ETV6, CUX1, PHF6, MGA, ZBTB7A, PPM1D) |
| Platform | Illumina [HiSeq 2500] |
| Library Source |
DNAs extracted from peripheral blood and bone marrow aspirate DNAs extracted from human leukemia cells from spleen and bone marrow aspirate of humanized mice with leukemia derived from immune deficiency mice which were infused with peripheral blood, bone marrow aspirate or samples from patients with AML |
| Cell Lines | - |
| Library Construction (kit name) | multiplex PCR + 2nd PCR |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000355 |
| Total Data Volume | 23 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Fumihiko Ishikawa
Affiliation: Laboratory for Human Disease Models, Riken Center for Integrative Medical Sciences
Project / Group Name: Target AML project
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Overcoming mutational complexity in acute myeloid leukemia by inhibition of critical pathways | doi: 10.1126/scitranslmed.aao1214 | JGAD000133 |
| 2 | Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive Acute Myeloid Leukemia | doi: 10.1038/s43018-021-00177-w | JGAD000355 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
