NBDC Research ID: hum0382.v1
SUMMARY
Aims: We collect tumor cells from patients with hematopoietic diseases, analyze genetic abnormalities and epigenetic abnormalities through genomic analyses, and integrate them with cell biological experiments and clinical information to understand the onset, progression, and maintenance of the disease. Specifically, what kind of genetic and epigenetic abnormalities stack up to cause hematopoietic diseases, what kind of cells are the origin of hematopoietic diseases, what kind of abnormalities lead to hematopoietic diseases, and what abnormalities influence clinical prognosis?
Methods: DNAs extracted from bone marrow mononuclear cells purified by ficoll-paque (GE HealthCare, Chicago, IL) and oral mucosa cells were used for whole-genome sequencing analysis.
Participants/Materials: A patient who was initially diagnosed with myelodysplastic syndrome (MDS) and had a fusion FUS gene with ERG (FUS-ERG), and relapsed acute myeloid leukemia (AML) with FUS-ERG
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000587 | NGS (WGS) | Controlled-access (Type I) | 2023/01/19 |
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MOLECULAR DATA
| Participants/Materials |
AML with FUS-ERG (ICD10: C92.0): 1 case 1. bone marrow cells at the first visit for MDS: 1 sample 2. bone marrow cells at that time for AML (relapse): 1 sample 3. oral swab specimen: 1 sample |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from bone marrow mononuclear cells and oral mucosa cells |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | DRAGEN DNA Pipeline |
| Mapping Quality |
1. Mapped reads: 83.26%, Unique reads: 77.34% 2. Mapped reads: 94.94%, Unique reads: 89.15% 3. Mapped reads: 95.09%, Unique reads: 85.93% |
| Reference Genome Sequence | hg19 |
| Coverage (Depth) |
1. Mean depth: 27.96 (Pct > 0.2*mean: 97.61) 2. Mean depth: 54.68 (Pct > 0.2*mean: 97.66) 3. Mean depth: 65.07 (Pct > 0.2*mean: 97.62) |
| Detecting Methods for Variation | DRAGEN DNA Pipeline (Somatic Mode [tumor-normal pipeline]) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000714 |
| Total Data Volume | 488.1 GB (fastq, bam, txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masahiro Kawahara
Affiliation: Department of Hematology, Shiga University of Medical Science
Project / Group Name: Analysis of genetic and epigenetic abnormalities in hematopoietic diseases
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Chugai pharmaceutical Co., Ltd | - | - |
| Kyowa Kirin Co., Ltd | - | - |
| Sanofi K.K. | - | - |
| MSD K.K. | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | FUS-ERG induces late-onset azacitidine resistance in acute myeloid leukaemia cells | doi: 10.1038/s41598-023-41230-1 | JGAD000714 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
