Comprehensive RNA-seq transcriptomic profiling in the malignant progression of gliomas

Abstract

Gliomas are the most common and lethal intracranial tumours. RNA sequencing technologies and advanced data analyses recently enabled the characterization of transcriptomic information, including protein-coding gene expression, non-coding gene expression, alternative splicing, and fusion gene detection, to facilitate detection of diseases and altered phenotypes. As a part of the Chinese Glioma Genome Atlas (CGGA) project, our aim was to delineate comprehensive transcriptome profiling in the malignant progression of human gliomas. Three hundred twenty five gliomas with different grades were collected over the past twelve years. Using the Illumina HiSeq 2,000 system, over 92 million high quality 101-bp paired-end reads were generated per sample, yielding a total of 30 billion reads. This comprehensive dataset will be useful to deepen the comprehensive understanding of gliomas, providing an opportunity to generate new therapies, diagnoses, and preventive strategies.

Combinations of four or more CpGs methylation present equivalent predictive value for MGMT expression and temozolomide therapeutic prognosis in gliomas

“…Sequencing reads were excluded when any one of the following parameters fitted: (a) the read is aligned to adaptor or primer with no more than two mismatches; (b) the read contains over 10% unknown bases; and (c) the read includes more than 50% of low‐quality bases (quality value ≤5). The detailed information of the quality control for the whole RNA sequencing database had been described in our previous study …”

“…The detailed information of the quality control for the whole RNA sequencing database had been described in our previous study. 29 The MGMT mRNA expression level was calculated following the The ROC analysis was also used to evaluate the predictive value of MGMT promotor methylation status for patients' survival. The median OS was used to stratified the patients.…”

ISG20 promotes local tumor immunity and contributes to poor survival in human glioma

“…In the CGGA dataset, there were 325 samples, including 144 GBM and 181 LGG samples. 63 In the TCGA dataset, 150 GBM and 457 LGG samples were available. Information on age, gender, diagnosis, WHO grade, chemo-and radiation therapy regimen, molecular data, and patient prognoses was also collected.…”

Prognostic significance of age related genes in patients with lower grade glioma

“…Molecular profiles, like gene expression portraits, DNA mutation signatures and DNA methylation Ivyspring International Publisher characteristics are quite associated with the clinical overall survival of tumor patients [15][16][17][18][19]. Similar dataset is established in the Chinese Glioma Genome Atlas (CGGA) to provide massive amounts of data for basic and clinical research of glioma [20][21][22]. With the available TCGA, CGGA and Gene Expression Omnibus (GEO) datasets, here, we systematically define the molecular characteristics of age related genes and reveal their prognostic effects in determining the clinical overall survival of tumor patients, particularly LGG patients.…”