NBDC Research ID: hum0359.v1
SUMMARY
Aims: The pathogenesis of T/NK cell lymphoma is heterogeneous and complex, and optimal treatment has not been established, partly because the disease is relatively rare. Comprehensive analysis of genomic, epigenomic, and gene expression abnormalities occurring in T/NK cell lymphomas may not only clarify the pathogenesis of the disease, but also identify distinctive disease units, new molecular targets, and prognostic factors. In this study, we will comprehensively analyze the genome, epigenome, and gene expression of T/NK cell lymphoma, and clarify the molecular pathogenesis of the disease by examining the relationship with histopathology, disease type, and prognosis.
Methods: Targeted DNA sequencing of tumor (lymphoma) tissues
Participants/Materials: Extranodal NK/T-cell lymphoma, nasal type
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000548 | NGS (Target Capture) | Controlled-access (Type I) | 2022/07/01 |
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| Participants/Materials | Extranodal NK/T-cell lymphoma, nasal type (ICD10: C86.0): 67 cases |
| Targets | Target Capture |
| Target Loci for Capture Methods | ARID1A, ASXL3, BCOR, CDKN2A, DDX3X, DNMT3A, ECSIT, EP300, FAT4, HDAC9, IDH1, IDH2, JAK1, JAK2, JAK3, KMT2C, KMT2D, MGA, MSN, NRAS, STAT1, STAT3, STAT5A, STAT5B, STAT6, TET1, TET2, TET3, TP53 |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | xGen Prism DNA Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris M220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 142 bp |
| Mapping Methods | CLC Genomics Workbench version 21 |
| Mapping Quality | - |
| Reference Genome Sequence | hg19 |
| Coverage (Depth) | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000668 |
| Total Data Volume | 10.6 GB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Naoki Oishi
Affiliation: Department of Pathology, University of Yamanashi
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Histopathologic Features Associated with Molecular Subtypes of Extranodal NK/T Cell Lymphoma | 21K06883 |
| Kurozumi Medical Foundation | Development of Molecular-based Pathologic Prognostic Stratification for Extranodal NK/T cell lymphoma, Nasal Type | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genetic and immunohistochemical profiling of NK/T-cell Lymphomas reveals prognostically relevant BCOR-MYC association | doi: 10.1182/bloodadvances.2022007541 | JGAD000668 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
