NBDC Research ID: hum0006.v3

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SUMMARY

Aims: The identification of genomic/genetic alterations in brain tumors (gliomas) and analysis of their clinicopathological significance.

Methods: Exome sequencing, RNA sequencing and Methylation array were performed. Matched normal DNA was also used for Exome sequencing.

Participants/Materials:

Surgical specimen obtained from 6 patients with astrocytoma (primary and matched recurrent samples) and paired normal peripheral blood cells (Total: 23 samples).

Surgical specimen obtained from 16 patients with oligodendroglioma (12 primary and matched recurrent samples, 8 samples obtained from 4 patients by multi-sampling)

Surgical specimen obtained from patients with gliomas (17 patients with diffuse cerebellar glioma, 8 patients with cerebral glioblastoma and 14 patients with thalamic glioma)

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000004

astrocytoma

NGS (Exome)

Controlled Access (Type I) 2014/01/31
JGAS00000000004 data addition

oligodendroglioma

NGS (Exome, RNA-seq), Methylation array

Controlled Access (Type I) 2017/06/05
JGAS00000000106

gliomas (diffuse cerebellar glioma, cerebral glioblastoma, thalamic glioma)

NGS (Exome, RNA-seq), Methylation array

Controlled Access (Type I) 2017/09/01

*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

astrocytoma (ICD10: C71): 6 cases (23 samples)

oligodendroglioma (ICD10: C71): 16 cases (48 samples)

diffuse cerebellar glioma (ICD10: C71): 17 cases (34 samples)

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source DNAs extracted from surgical specimen of brain tumors (primary and matched recurrent samples) and paired normal peripheral blood cells.
Cell Lines -
Library Construction (kit name) Agilent SureSelect Human All Exon v.4
Fragmentation Methods Ultrasonic fragmentation (Covaris SS)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Data set ID

JGAD00000000004 (astrocytoma)

JGAD00000000106 (oligodendroglioma)

JGAD00000000112 (diffuse cerebellar glioma)

Total Data Volume 1070 GB (fastq, bam [reference: hg19])
Comments (Policies) NBDC policy & P-DIRECT policy

 

RNA-seq

Participants/Materials

oligodendroglioma (ICD10: C71): 16 cases (27 samples)

diffuse cerebellar glioma (ICD10: C71): 14 cases (14 samples)

cerebral glioblastoma (ICD10: C71): 8 cases (8 samples)

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source RNAs extracted from surgical specimen of brain tumors (primary and matched recurrent samples) and paired normal peripheral blood cells.
Cell Lines -
Library Construction (kit name) TruSeq Stranded Total RNA Library Prep Kit
Fragmentation Methods Alkalization
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Data set ID

JGAD00000000107

JGAD00000000113 (diffuse cerebellar glioma, cerebral glioblastoma)

Total Data Volume 280 GB (bam, fastq)
Comments (Policies) NBDC policy & P-DIRECT policy

 

Methylation array

Participants/Materials

oligodendroglioma (ICD10: C71): 16 cases (30 samples)

diffuse cerebellar glioma (ICD10: C71): 17 cases (17 samples)

thalamic glioma (ICD10: C71): 14 cases (14 samples)

Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina [HumanMethylation 450 BeadChip]
Library Source DNAs extracted from surgical specimen of brain tumors (primary and matched recurrent samples) and paired normal peripheral blood cells.
Cell Lines -
Library Construction (kit name) Illumina HumanMethylation450 BeadChip kit
Algorithms for Calculating Methylation-rate (software) Genome Studio v2010.3
Filtering Methods HumanMethylation450_15017482_v1.1 (bpm)
Probe Number (after QC) 485577 methylation sites
Japanese Genotype-phenotype Archive Data set ID

JGAD00000000108

JGAD00000000114 (diffuse cerebellar glioma, thalamic glioma)

Total Data Volume 149 MB (txt)
Comments (Policies) NBDC policy & P-DIRECT policy

 

DATA PROVIDER

Principal Investigator: Nobuhito Saito

Affiliation: Department of Neurosurgery, The University of Tokyo

Project / Group Name: Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT)

URL: http://p-direct.jfcr.or.jp/english/

Funds / Grants (Research Project Number):

NameTitleProject Number

Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT)

Development of novel therapeutic strategy and biomarker for the treatment of malignant brain tumors

-

 

PUBLICATIONS

TitleDOIData Set ID
1 Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma doi:10.1126/science.1239947 JGAD00000000004
2 Genetic and epigenetic stability of oligodendrogliomas at recurrence doi: 10.1186/s40478-017-0422-z JGAD00000000106-JGAD00000000108
3 Distinct molecular profile of diffuse cerebellar gliomas doi: 10.1007/s00401-017-1771-1 JGAD00000000112-JGAD00000000113

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use