Clinical application of targeted next-generation sequencing for colorectal cancer patients: a multicentric Belgian experience
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Nicky D’Haene1, Quitterie Fontanges1, Nancy De Nève1, Oriane Blanchard1, Barbara Melendez1, Monique Delos2, Marie-Françoise Dehou3, Calliope Maris1,4, Nathalie Nagy5, Emmanuel Rousseau6, Josse Vandenhove7, André Gilles8, Carine De Prez9, Laurine Verset1,10, Marie-Paule Van Craynest11, Pieter Demetter1, Jean-Luc Van Laethem12, Isabelle Salmon1 and Marie Le Mercier1
1Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
2Department of Pathology, CHU UCL Namur, Yvoir, Belgium
3CMP Pathology Laboratory, Brussels, Belgium
4Department of Pathology, Braine l´Alleud Waterloo Hospital, Braine l´Alleud, Belgium
5Department of Pathology, Charleroi University Hospital, Charleroi, Belgium
6Department of Pathology, Mouscron Hospital, Mouscron, Belgium
7Department of Pathology, Sint Maria Hospital, Halle, Belgium
8Department of Pathology, EPICURA Hospital, Frameries, Belgium
9Department of Pathology, Brugmann University Hospital, Brussels, Belgium
10CurePath, Jumet, Belgium
11New LabPatho, Braine l´Alleud, Belgium
12Department of Oncology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
Nicky D’Haene, email: firstname.lastname@example.org
Keywords: colorectal cancer; next-generation sequencing
Abbreviations: CRC: Colorectal Cancer; NGS: Next-generation sequencing; FFPE: formalin-fixed paraffin-embedded; TAT: turnaround time
Received: December 12, 2017 Accepted: March 17, 2018 Published: April 17, 2018
International guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-EGFR agents for metastatic colorectal cancer (CRC) patients. Daily, new data emerges on the theranostic and prognostic role of molecular biomarkers; this is a strong incentive for a validated, sensitive, and broadly available molecular screening test. Next-generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. We report here our 2 years of clinical practice using NGS results to guide therapeutic decisions.
The Ion Torrent AmpliSeq colon/lung cancer panel, which allows mutation detection in 22 cancer-related genes, was prospectively used in clinical practice (BELAC ISO 15189 accredited method). The DNA of 741 formalin-fixed paraffin-embedded CRC tissues, including primary tumors and metastasis, was obtained from 14 different Belgian institutions and subjected to targeted NGS.
Of the tumors tested, 98% (727) were successfully sequenced and 89% (650) harbored at least one mutation. KRAS, BRAF and NRAS mutations were found in 335 (46%), 78 (11%) and 32 (4%) samples, respectively. These mutation frequencies were consistent with those reported in public databases. Moreover, mutations and amplifications in potentially actionable genes were identified in 464 samples (64%), including mutations in PIK3CA (14%), ERBB2 (0.4%), AKT1 (0.6%), and MAP2K1 (0.1%), as well as amplifications of ERBB2 (0.3%) and EGFR (0.3%). The median turnaround time between reception of the sample in the laboratory and report release was 8 calendar days.
Overall, the AmpliSeq colon/lung cancer panel was successfully applied in daily practice and provided reliable clinically relevant information for CRC patients.
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