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Kastrisiou M, Zarkavelis G, Kougioumtzi A, Sakaloglou P, Kostoulas C, Georgiou I, Batistatou A, Pentheroudakis G, Magklara A. Development and Validation of a Targeted ‘Liquid’ NGS Panel for Treatment Customization in Patients with Metastatic Colorectal Cancer. Diagnostics (Basel) 2021; 11:diagnostics11122375. [PMID: 34943612 PMCID: PMC8700616 DOI: 10.3390/diagnostics11122375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023] Open
Abstract
The detection of actionable mutations in tumor tissue is a prerequisite for treatment customization in patients with metastatic colorectal cancer (mCRC). Analysis of circulating tumor DNA (ctDNA) for the identification of such mutations in patients’ plasma is an attractive alternative to invasive tissue biopsies. Despite having the high analytical sensitivity required for ctDNA analysis, digital polymerase chain reaction (dPCR) technologies can only detect a very limited number of hotspot mutations, whilst a broader mutation panel is currently needed for clinical decision making. Recent advances in next-generation sequencing (NGS) have led to high-sensitivity platforms that allow screening of multiple genes at a single assay. Our goal was to develop a small, cost- and time-effective NGS gene panel that could be easily integrated in the day-to-day clinical routine in the management of patients with mCRC. We designed a targeted panel comprising hotspots in six clinically relevant genes (KRAS, NRAS, MET, BRAF, ERBB2 and EGFR) and validated it in a total of 68 samples from 30 patients at diagnosis, first and second disease progression. Results from our NGS panel were compared against plasma testing with BEAMing dPCR regarding the RAS gene status. The overall percent of agreement was 83.6%, with a positive and negative percent agreement of 74.3% and 96.2%, respectively. Further comparison of plasma NGS with standard tissue testing used in the clinic showed an overall percent agreement of 86.7% for RAS status, with a positive and negative percent agreement of 81.2% and 92.8%, respectively. Thus, our study strongly supports the validity and efficiency of an affordable targeted NGS panel for the detection of clinically relevant mutations in patients with mCRC.
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Affiliation(s)
- Myrto Kastrisiou
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (M.K.); (A.K.)
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece;
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece
| | - George Zarkavelis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece;
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece
| | - Anastasia Kougioumtzi
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (M.K.); (A.K.)
| | - Prodromos Sakaloglou
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (P.S.); (C.K.); (I.G.)
| | - Charilaos Kostoulas
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (P.S.); (C.K.); (I.G.)
| | - Ioannis Georgiou
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (P.S.); (C.K.); (I.G.)
| | - Anna Batistatou
- Department of Pathology, Faculty of Medicine, University of Ioannina, 45500 Ioannina, Greece;
| | - George Pentheroudakis
- Department of Medical Oncology, University General Hospital of Ioannina, 45500 Ioannina, Greece;
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), 45444 Ioannina, Greece
- Correspondence: (G.P.); (A.M.)
| | - Angeliki Magklara
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (M.K.); (A.K.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 45110 Ioannina, Greece
- Institute of Biosciences, University Research Center of Ioannina (URCI), 45110 Ioannina, Greece
- Correspondence: (G.P.); (A.M.)
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