Analysis of a gene panel for targeted sequencing of colorectal cancer samples

// Klaus Hojgaard Jensen 1, 2, * , Jose M.G. Izarzugaza 1, * , Agnieszka Sierakowska Juncker 1, * , Rasmus Borup Hansen 2 , Torben Frostrup Hansen 3 , Pascal Timshel 1 , Thorarinn Blondal 4 , Thomas Skot Jensen 2 , Eske Rygaard-Hjalsted 2 , Peter Mouritzen 4 , Michael Thorsen 4 , Rasmus Wernersson 2 , Henrik Bjorn Nielsen 1 , Anders Jakobsen 3, * , Soren Brunak 1, 5, * and Flemming Brandt Sorensen 3, 6, * 1 Department of Bio and Health Informatics, Technical University of Denmark, Kgs, Lyngby 2800, Denmark 2 Intomics A/S, Kgs, Lyngby 2800, Denmark 3 Oncology Department, Vejle Hospital, Vejle 7100, Denmark 4 Exiqon A/S, Vedbaek 2950, Denmark 5 Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark 6 Patologisk Institut, Aarhus Universitetshospital, Aarhus 8200, Denmark * These authors contributed equally to this work Correspondence to: Anders Jakobsen, email: Anders.Jakobsen@rsyd.dk Soren Brunak, email: soren.brunak@cpr.ku.dk Flemming Brandt Sorensen, email: flsoer@rm.dk Keywords: colorectal cancer; biomarker discovery; NGS; precision medicine Received: July 14, 2017      Accepted: December 30, 2017      Published: January 10, 2018 ABSTRACT Colorectal cancer (CRC) is a leading cause of death worldwide. Surgical intervention is a successful treatment for stage I patients, whereas other more advanced cases may require adjuvant chemotherapy. The selection of effective adjuvant treatments remains, however, challenging. Accurate patient stratification is necessary for the identification of the subset of patients likely responding to treatment, while sparing others from pernicious treatment. Targeted sequencing approaches may help in this regard, enabling rapid genetic investigation, and at the same time easily applicable in routine diagnosis. We propose a set of guidelines for the identification, including variant calling and filtering, of somatic mutations driving tumorigenesis in the absence of matched healthy tissue. We also discuss the inclusion criteria for the generation of our gene panel. Furthermore, we evaluate the prognostic impact of individual genes, using Cox regression models in the context of overall survival and disease-free survival. These analyses confirmed the role of commonly used biomarkers, and shed light on controversial genes such as CYP2C8 . Applying those guidelines, we created a novel gene panel to investigate the onset and progression of CRC in 273 patients. Our comprehensive biomarker set includes 266 genes that may play a role in the progression through the different stages of the disease. Tracing the developmental state of the tumour, and its resistances, is instrumental in patient stratification and reliable decision making in precision clinical practice.