Research ID
hum0006-v3Release info
This page is a past version (v3). The latest version is v6.
Latest version (v6)Research title
Genomic and Genetic Analysis of Brain Tumors and Analysis of Their Clinicopathological Significance
Research overview
- Aims
- The identification of genomic/genetic alterations in brain tumors (gliomas) and analysis of their clinicopathological significance.
Brain tumors are diseases with a very poor prognosis and recurrence is almost inevitable even with multidisciplinary treatment. Therefore, it is important to elucidate genetic aberrations associated with the development or malignant transformation of brain tumors. In this study, we will comprehensively analyze molecular landscapes in brain tumors. We will also investigate how these are involved in the response to various therapies to establish new molecular therapies for brain tumors. In addition, we will develop new diagnostic methods and biomarkers by comparing clinicopathological information with molecular profiles and analyze the relationship between diagnosis, prognosis prediction, and therapeutic response prediction using bioinformatics and artificial intelligence. - Methods
- Exome sequencing, RNA sequencing and Methylation array were performed. Matched normal DNA was also used for Exome sequencing.
Targeted DNA sequencing for vascular malformation samples was conducted to investigate somatic mutations.
FLeCS-seq, SMART-seq, RNA-seq, short-read WGS, and ultralong-read WGS analyses for normal left frontal lobe tissues were performed. - 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
Twelve cerebral cavernous malformations, 1 vertebral hemangioma, 3 orbital cavernous malformations, and respective paired peripheral blood samples
Normal left frontal lobe tissues from a patient with glioma - URL
- N/A
Datasets
The list is the one this version published; each dataset's content is shown as it is now.
| Cart | Dataset ID | Type of data | Analysis method | Access criteria | Date published |
|---|---|---|---|---|---|
| JGAD000004 | astrocytoma NGS (Exome) |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000106 | oligodendroglioma NGS (Exome, RNA-seq), Methylation array |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000112 | gliomas (diffuse cerebellar glioma, cerebral glioblastoma, thalamic glioma) NGS (Exome, RNA-seq), Methylation array |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000107 | oligodendroglioma NGS (Exome, RNA-seq), Methylation array |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000113 | gliomas (diffuse cerebellar glioma, cerebral glioblastoma, thalamic glioma) NGS (Exome, RNA-seq), Methylation array |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000108 | oligodendroglioma NGS (Exome, RNA-seq), Methylation array |
| Controlled-access (Type I) | 2020-09-28 | |
| JGAD000114 | gliomas (diffuse cerebellar glioma, cerebral glioblastoma, thalamic glioma) NGS (Exome, RNA-seq), Methylation array |
| Controlled-access (Type I) | 2020-09-28 |
Data provider
- Principal investigator
- Nobuhito Saito
- Affiliation
- Department of Neurosurgery, The University of Tokyo
Research projects
| Name | URL |
|---|---|
Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT) | N/A |
Grants
| Name | Title | Project number |
|---|---|---|
KAKENHI Grant-in-Aid for Scientific Research (B) | Analysis of novel vascular malformation causative gene |
|
Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT), Japan Agency for Medical Research and Development (AMED) | Development of novel therapeutic strategy and biomarker for the treatment of malignant brain tumors | N/A |
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Analysis of the mechanisms for development of tumor heterogeneity related to treatment resistance of gliomas and discovery of therapeutic strategies | N/A |
Related publications
| Title | DOI | Dataset ID |
|---|---|---|
Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma | ||
Genetic and epigenetic stability of oligodendrogliomas at recurrence | ||
Distinct molecular profile of diffuse cerebellar gliomas | ||
DNA demethylation is associated with malignant progression of lower-grade gliomas | ||
Somatic GJA4 gain-of-function mutation in orbital cavernous venous malformations |
Controlled access users
| Principal investigator | Affiliation | Country/Region | Research title | Period of data use | Dataset ID |
|---|---|---|---|---|---|
| Nehemiah Alvarez | De Novo Genomics Corporation | Kansas, United States | Evolutionary conservation of gene expression and epigenetic analysis of trophoblast stem cells | 2018-01-15 – 2021-03-19 | |
| Michiaki Hamada | Hamada Laboratory, Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | 2023-01-05 – 2027-10-31 | |
| Frank Attenello | Department of Neurological Surgery, USC Keck School of Medicine | United States | Examining the role of a novel long noncoding RNA, linc02454, in resistance of glioblastoma to temozolomide | 2023-04-06 – 2026-01-31 |