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)
| Dataset 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 |
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MOLECULAR DATA
| 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 Dataset ID |
JGAD000004 (astrocytoma) JGAD000106 (oligodendroglioma) JGAD000112 (diffuse cerebellar glioma) |
| Total Data Volume | 1070 GB (fastq, bam [reference: hg19]) |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID |
JGAD000113 (diffuse cerebellar glioma, cerebral glioblastoma) |
| Total Data Volume | 280 GB (bam, fastq） |
| Comments (Policies) | NBDC policy |
| 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 Dataset ID |
JGAD000114 (diffuse cerebellar glioma, thalamic glioma) |
| Total Data Volume | 149 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 |
- |
PUBLICATIONS
| Title | DOI | Dataset 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 |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
