A Bioinformatic Pipeline to Identify Biomarkers for Metastasis Formation from RNA Sequencing Data

Deep molecular characterization of tumors is a prerequisite for precision oncology and personalized anticancer treatment. Analyzing the tumor transcriptome by RNA sequencing (RNAseq) allows the quantification of individual isoforms and also the detection of sequence alteration in the expressed genes. This chapter describes an analysis pipeline that focuses both on accurate quantification of transcripts and on the occurrence of cancer-associated mutations. Another section introduces the analysis of differentially expressed genes for biomarker evaluation on the example of comparing metastasized versus non-metastasized colorectal tumors.