NBDC Research ID: hum0006.v4

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)

Surgical specimen obtained from 94 patients with gliomas, including primary and matched recurrent samples (total 114 samples) and paired normal blood cells

Data Set ID	Type of Data	Criteria	Release Date
JGAS000004	astrocytoma NGS (Exome)	Controlled Access (Type I)	2014/01/31
JGAS000004 data addition	oligodendroglioma NGS (Exome, RNA-seq), Methylation array	Controlled Access (Type I)	2017/06/05
JGAS000106	gliomas (diffuse cerebellar glioma, cerebral glioblastoma, thalamic glioma) NGS (Exome, RNA-seq), Methylation array	Controlled Access (Type I)	2017/09/01
JGAS000146	gliomas NGS (Exome, RNA-seq), Methylation array	Controlled Access (Type I)	2019/02/13

*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) glioma (ICD10: C71): 12 cases (25 tumor samples, 12 non-tumor samples) 11 pairs of primary-recurrent gliomas and 1 primary glioma
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	JGAD000004 (astrocytoma) JGAD000106 (oligodendroglioma) JGAD000112 (diffuse cerebellar glioma) JGAD000215 (primary grade II/III gliomas and their recurrent tumors; 36 samples, matched normal blood; 16 samples) JGAD000218 (primary grade IV gliomas and their recurrent tumors; 16 samples, matched normal blood; 8 samples)
Total Data Volume	JGAD000004: 375.31 GB (fastq, bam [reference: hg19]) JGAD000106: 885.30 GB (fastq, bam [reference: hg19]) JGAD000112: 506.99 GB (fastq, bam [reference: hg19]) JGAD000215: 1.32 TB (fastq, bam [reference: hg19]) JGAD000218: 552.72 GB (fastq, bam [reference: hg19])
Comments (Policies)	NBDC 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) glioma (ICD10: C71): 24 cases (31 samples) 8 pairs of primary-recurrent gliomas, 8 primary gliomas, and 7 recurrent gliomas
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	JGAD000107 JGAD000113 (diffuse cerebellar glioma, cerebral glioblastoma) JGAD000216 (gliomas including primary grade II/III gliomas and their recurrent tumors; 31 samples) JGAD000219 (recurrent tumors of primary grade IV gliomas; 8 samples)
Total Data Volume	JGAD000107: 239.26 GB (bam, fastq） JGAD000113: 363.23 GB (bam, fastq） JGAD000216: 302.43 GB (bam, fastq） JGAD000219: 96.94 GB (bam, fastq）
Comments (Policies)	NBDC 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) glioma (ICD10: C71): 93 cases (113 samples) 20 pairs of primary-recurrent gliomas, 69 primary gliomas, and 4 recurrent gliomas
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	JGAD000108 JGAD000114 (diffuse cerebellar glioma, thalamic glioma) JGAD000217 (gliomas including primary grade II/III tumors and their recurrent tumors; 113 samples)
Total Data Volume	JGAD000108: 139.75 MB (txt) JGAD000114: 154.82 MB (txt) JGAD000217: 398.82 MB (txt)
Comments (Policies)	NBDC 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):

Name	Title	Project 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	-
Project for Cancer Research and Therapeutic Evolution (P-CREATE)	Analysis of the mechanisms for development of tumor heterogeneity related to treatment resistance of gliomas and discovery of therapeutic strategies	-

PUBLICATIONS

	Title	DOI	Data Set ID
1	Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma	doi:10.1126/science.1239947	JGAD000004
2	Genetic and epigenetic stability of oligodendrogliomas at recurrence	doi: 10.1186/s40478-017-0422-z	JGAD000106-JGAD000108
3	Distinct molecular profile of diffuse cerebellar gliomas	doi: 10.1007/s00401-017-1771-1	JGAD000112-JGAD000113
4	DNA demethylation is associated with malignant progression of lower-grade gliomas	doi: 10.1038/s41598-019-38510-0	JGAD000215-JGAD000219

USERS (Controlled-Access Data)

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