Genomic Analysis of DTCs
by Shawn P. Fahl, PhD
December 10, 2018
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Next-generation deep sequencing is a powerful tool to understand the global genomic mutations and transcriptional alterations associated with complex diseases, such as cancer and autoimmunity. Dissociated tumor cells, or DTCs, are cryopreserved single cell suspensions that consist of the complete cellular composition of the tumor microenvironment. DTCs are amenable to numerous downstream applications. To investigate the utility of DTCs for genomic applications, we performed whole exome sequencing (WES) and whole transcriptome sequencing (RNASeq) on eight DTC samples across four indications. High quality DNA and RNA was isolated from each DTC sample at quantities suitable for downstream WES and RNASeq analysis. Whole exome analysis revealed numerous genomic variants, including previously described pathogenic alleles in clinically-relevant oncogenes. Whole transcriptome analysis revealed differential gene expression across each of the samples, although the samples did cluster based on their tissue of origin. The gene expression data was then further subdivided on specific gene subsets to highlight cellular functionalities such as T cell responsiveness. This study confirms the suitability of cryopreserved tumor derived singlecell suspensions for downstream genomic analysis to identify known and novel genomic alterations and gene expression changes.
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