NBDC Research ID: hum0017.v1
SUMMARY
Aims: Primary central nervous system lymphoma (PCNSL) is a rare type lymphoma confined to the central nervous system. Effective therapies against PCNSL are severely limited. By conducting whole exome sequencing of PCNSL specimens, we aimed to reveal molecular mechanism underlying PCNSL carcinogenesis.
Methods: Genomic DNA was extracted from surgically resected PCNSL tissues and paired peripheral blood, and subjected to Exome analysis. RNA extracted from surgically resected PCNSL tissues was subjected to RNA-seq analysis.
Participants/Materials: Forty-one cases diagnosed to have PCNSL
URL: https://www.ncc.go.jp/en/ri/division/genetics/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000021 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2016/02/22 |
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MOLECULAR DATA
| Participants/Materials | 41 PCNSL cases |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | Genomic DNA extracted from surgically resected PCNSL tissues and paired peripheral blood cells (41 pairs) |
| Cell Lines | - |
| Library Construction (kit name) |
SureSelect Kit ver. 5 NEBNext Ultra DNA Library Prep Kit for Illumina |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris LE220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100-105 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000021 |
| Total Data Volume | 1.65 TB (bam file, reference : hg19) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 30 PCNSL cases |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | RNA extracted from surgically resected PCNSL tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra Directional RNA Library Prep Kit for Illumina（New England BioLabs） |
| Fragmentation Methods | RNA Seq Fragmentation Mix in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000021 |
| Total Data Volume | 350 GB (fastq file) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroyuki Mano
Affiliation: Division of Cellular Signaling, National Cancer Center Research Institute
Project / Group Name: PCNSL Genomic Analysis
URL： https://www.ncc.go.jp/en/ri/division/genetics/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Leading Advanced Projects for medical innovation, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-LEAP) | Project for novel therapeutic targets in cancer | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genomic characterization of primary central nervous system lymphoma | doi: 10.1007/s00401-016-1536-2 | JGAD000021 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Li WEI | National Key Laboratory of Birth Defects and Reproductive Health, Chongqing Institute of Population and Family Planning | JGAD000021 | 2016/11/25-2020/10/05 | ||
| Mosquera Orgueira, Adrian | Institute for Research in Health at Santiago de Compostela (IDIS) | JGAD000021 | 2017/04/04-2019/03/06 | ||
| Margaret A. Shipp | Dana-Farber Cancer Institute | JGAD000021 | 2017/11/29-2019/12/31 | ||
| Keiichiro Hattori | Department of Hematology, University of Tsukuba | Indentification of neuroinflammatory cells supporting the development of primary central nervous system lymphoma | JGAD000021 | 2019/02/22-2021/12/19 | |
| Seishi Ogawa | Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University | Comprehensive analysis of genetic alterations in hematological malignancies. | JGAD000021 | 2020/01/09-2024/03/31 | |
| Jessica Okosun | Barts Cancer Institute, Queen Mary University of London | Dissecting the molecular heterogeneity and evolution of central nervous system lymphomas | JGAD000021 | 2021/11/02-2024/08/01 | |
| Wei Hua | Huashan Hospital, Fudan University Neurosurgery | China | Genomic and molecular characterization of primary central nervous system lymphoma | JGAD000021 | 2022/06/13-2023/05/04 |
| Ryuta Saito | Department of Neurosurgery, Nagoya University Graduate School of Medicine | Japan | Genetic analysis during the progression of brain tumors and its impact on tumor microenvironment formation | JGAD000021 | 2022/10/06-2024/03/31 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000021 | 2022/12/26-2025/03/31 |
| Shinsuke Iida | Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences | Japan | Whole Exome Sequencing Analysis of Diffuse Large B-Cell Lymphoma That Progressed to Central Nervous System | JGAD000021 | 2024/03/05-2025/08/05 |
