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 IDType of DataCriteriaRelease Date
JGAS000021 NGS (Exome, RNA-seq) Controlled-access (Type I) 2016/02/22

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

Exome

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

 

RNA-seq

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):

NameTitleProject 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

TitleDOIDataset ID
1 Genomic characterization of primary central nervous system lymphoma doi: 10.1007/s00401-016-1536-2 JGAD000021

 

USERS (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData 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