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Exploration of the immune cell landscape in brain cancer utilizing gene expression and copy number data

By Yuriy Gusev, Krithika Bhuvaneshwar, Subha Madhavan

Posted 09 Dec 2018
bioRxiv DOI: 10.1101/490599

Brain cancer is a common cancer that affects more than 700,000 people in the US every year. We explore the dynamic changes in the abundance of immune cells based on RNA and DNA samples extracted from a large cohort of brain cancer patients. We used gene expression data and copy number data from a large brain cancer collections - the REMBRANDT project (REpository for Molecular BRAin Neoplasia DaTa) that includes 671 patients. We applied virtual flow cytometry tools CIBERSORT and xCell to estimate the abundance of the immune cells in the RNA of these samples. The immune cell landscape in this dataset is compared with that of the TCGA brain cancer collection, that includes 511 patients with Lower Grade Glioma (TCGA-LGG) and 156 patients with Glioblastoma (TCGA-GBM). We also discuss how well the results align with published literature, and how this computational analysis can help better understand how immune cells affect clinical outcome and survival in brain cancer patients.

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