Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data for Chinese Glioma Patients

Abstract

1Gliomas are the most common and malignant intracranial tumours in adults. Recent studies have 2 shown that functional genomics greatly aids in the understanding of the pathophysiology and 3 therapy of glioma. However, comprehensive genomic data and analysis platforms are relatively 4 limited. In this study, we developed the Chinese Glioma Genome Atlas (CGGA, 5 http://www.cgga.org.cn), a user-friendly data portal for storage and interactive exploration of multi-6 dimensional functional genomic data that includes nearly 2,000 primary and recurrent glioma 7 samples from Chinese cohorts. CGGA currently provides access to whole-exome sequencing (286 8 samples), messenger RNA sequencing (1,018 samples) and microarray (301 samples), DNA 9 methylation microarray (159 samples), and microRNA microarray (198 samples) data, as well as 10 detailed clinical data (e.g., WHO grade, histological type, critical molecular genetic information, 11 age, sex, chemoradiotherapy status and survival data). In addition, we developed an analysis tool to 12 allow users to browse mutational, mRNA/microRNA expression, and DNA methylation profiles and 13 perform survival and correlation analyses of specific glioma subtypes. CGGA greatly reduces the 14 barriers between complex functional genomic data and glioma researchers who seek rapid, intuitive, 15 and high-quality access to data resources and enables researchers to use these immeasurable data 16 sources for biological research and clinical application. Importantly, the free provision of data will 17 allow researchers to quickly generate and provide data to the research community. 18 19

Hypoxia-induced release, nuclear translocation, and signaling activity of a DLK1 intracellular fragment in glioma

“…1c-h). Analysis of DLK1 expression in the Cancer Genome Atlas (TCGA [21]), in the Chinese Glioma Genome Atlas (CGGA [22]) datasets and evaluation of DLK1 stainings in low-vs high-grade murine tumors revealed higher DLK1 expression in high-grade gliomas, that typically have hypoxic areas ( Fig. 1i and Supplementary Fig.…”

CENPN Acts as a Novel Biomarker that Correlates With the Malignant Phenotypes of Glioma Cells

“…Next-generation sequencing data (HTSeq-FPKM) and clinical variables were obtained from TCGA ( Wang et al, 2016 ). In addition, data for 1,018 glioma cases generated with the Illumina HiSeq platform were obtained from the CGGA ( Zhao et al, 2021 ). Apart from that, a total of 112 glioma cases enrolled from the Department of Neurosurgery (Huanhu Hospital, Tianjin, China) were used for validation.…”

Nidogen-1 expression is associated with overall survival and temozolomide sensitivity in low-grade glioma patients

“…Chinese Glioma Genome Atlas (CGGA) ( http://www.cgga.org.cn/ ) is a user-friendly database with functional genomic data for approximately 2,000 primary and recurrent glioma samples from Chinese cohorts. The analysis tools in the CGGA database allow access to gene mutational data, mRNA and microRNA expression data, DNA methylation profiles, as well as survival and correlation analysis of specific glioma types [ 72 ]. We used the CGG database to analyze NID1 expression levels in different glioma grades.…”