From Complete Catalogs to "Actionable" Shortlists: Integrative Analysis of Next-generation Sequencing Data in Cancer Research



May 28, 2013

Next-generation sequencing has become a revolutionary tool for cancer research. However, there is still a big gap between complete catalogues of genomic alternations identified from NGS studies and “actionable” shortlists for further functional investigation. Using my two recent studies (RNA-seq in gastric cancer and exome-seq in endometrial cancer), I will discuss how to identify “driver” genes underlying the tumorigenesis. In the first study, we performed a comprehensive analysis on the whole-transcriptome of gastric cancer, and developed a multilayer and integrative analytic framework for identifying potential therapeutic targets from RNA-seq data (Kim et al., Cancer Research 2012). In the second study, we developed an integrated systems-biology approach to identifying driver somatic mutations from whole-exome sequencing data, which combines bioinformatics prioritization, a high-throughput approach to generating mutants and high-through cell viability assays (Liang et al., Genome Research 2012).

Drug DiscoveryGenomicsInformatics

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