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: http://mano-lab.umin.jp/english/index.html

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000021 NGS (Exome, RNA-seq) Controlled Access (Type I) 2016/02/22

*Release Note

* Data users need to apply the Form 2 (Application Form 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)

Agilent SureSelect Kit ver. 5

NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolab)

Fragmentation Methods Covaris (LE220)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100-105 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000021
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 Data set ID JGAD00000000021
Total Data Volume 350 GB (fastq file)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Hiroyuki Mano

Affiliation: Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo

Project / Group Name: PCNSL Genomic Analysis

URL: http://mano-lab.umin.jp/english/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

TitleDOIData Set ID
1 Genomic characterization of primary central nervous system lymphoma doi: 10.1007/s00401-016-1536-2 JGAD00000000021

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Li WEI National Key Laboratory of Birth Defects and Reproductive Health, Chongqing Institute of Population and Family Planning JGAD00000000021 2016/11/25-2020/10/05
Mosquera Orgueira, Adrian Institute for Research in Health at Santiago de Compostela (IDIS) JGAD00000000021 2017/04/04-2019/03/06
Margaret A. Shipp Dana-Farber Cancer Institute JGAD00000000021 2017/11/29-2019/12/31