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De Falco V, Poliero L, Vitello PP, Ciardiello D, Vitale P, Zanaletti N, Giunta EF, Terminiello M, Caputo V, Carlino F, Di Liello R, Ventriglia A, Famiglietti V, Martinelli E, Morgillo F, Orditura M, De Vita F, Fasano M, Napolitano S, Martini G, Della Corte CM, Franco R, Altucci L, Ciardiello F, Troiani T. Feasibility of next-generation sequencing in clinical practice: results of a pilot study in the Department of Precision Medicine at the University of Campania 'Luigi Vanvitelli'. ESMO Open 2021; 5:S2059-7029(20)30067-3. [PMID: 32234730 PMCID: PMC7174013 DOI: 10.1136/esmoopen-2020-000675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/28/2022] Open
Abstract
Background The emerging role of next-generation sequencing (NGS) targeted panels is revolutionising our approach to cancer patients, providing information on gene alterations helpful for diagnosis and clinical decision, in a short time and with acceptable costs. Materials and methods In this work, we evaluated the clinical application of FoundationOne CDx test, a hybrid capture-based NGS. This test identifies alterations in 324 genes, tumour mutational burden and genomic signatures as microsatellite instability. The decision to obtain the NGS assay for a particular patient was done according to investigator’s choice. Results Overall, 122 tumour specimens were analysed, of which 84 (68.85%) succeeded. The success rate was influenced by type of specimen formalin-fixed paraffin embedded (FFPE block vs FFPE slides), by origin of the sample (surgery vs biopsy) and by time of fixation (<5 years vs ≥5 years). The most frequent subgroups of effective reports derived from colorectal cancer (25 samples), non-small-cell lung cancer (16 samples), ovarian cancer (10 samples), biliary tract cancer (9 samples), breast cancer (7 samples), gastric cancer (7 samples). The most frequent alterations found in whole population referred to TP53 (45.9%), KRAS (19.6%) and APC (13.9%). Furthermore, we performed an analysis of patients in whom this comprehensive genomic profiling (CGP) had a relevance for the patient’s disease. Conclusions On our opinion, CGP could be proposed in clinical practice in order to select patients that could most benefit from the analysis proposed, like patients with good performance status without any available treatments or with unexpected resistance to a therapy.
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Affiliation(s)
- Vincenzo De Falco
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Luca Poliero
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Pietro Paolo Vitello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Davide Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Pasquale Vitale
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Nicoletta Zanaletti
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Emilio Francesco Giunta
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Marinella Terminiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Vincenza Caputo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Francesca Carlino
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Raimondo Di Liello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Anna Ventriglia
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Vincenzo Famiglietti
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Erika Martinelli
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Floriana Morgillo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Michele Orditura
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Ferdinando De Vita
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Morena Fasano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Stefania Napolitano
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Giulia Martini
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Carminia Maria Della Corte
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Renato Franco
- Department of Mental, Physical Health and Preventive Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Lucia Altucci
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Fortunato Ciardiello
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Teresa Troiani
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
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Papadopoulou E, Tsoulos N, Tsantikidi K, Metaxa-Mariatou V, Stamou PE, Kladi-Skandali A, Kapeni E, Tsaousis G, Pentheroudakis G, Petrakis D, Lampropoulou DI, Aravantinos G, Varthalitis I, Kesisis G, Boukovinas I, Papakotoulas P, Katirtzoglou N, Athanasiadis E, Stavridi F, Christodoulou C, Koumarianou A, Eralp Y, Nasioulas G. Clinical feasibility of NGS liquid biopsy analysis in NSCLC patients. PLoS One 2019; 14:e0226853. [PMID: 31860648 PMCID: PMC6924668 DOI: 10.1371/journal.pone.0226853] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Background Analysis of circulating tumor nucleic acids in plasma of Non-Small Cell Lung Cancer (NSCLC) patients is the most widespread and documented form of "liquid biopsy" and provides real-time information on the molecular profile of the tumor without an invasive tissue biopsy. Methods Liquid biopsy analysis was requested by the referral physician in 121 NSCLC patients at diagnosis and was performed using a sensitive Next Generation Sequencing assay. Additionally, a comparative analysis of NSCLC patients at relapse following EGFR Tyrosine Kinase Inhibitor (TKIs) treatment was performed in 50 patients by both the cobas and NGS platforms. Results At least one mutation was identified in almost 49% of the cases by the NGS approach in NSCLC patients analyzed at diagnosis. In 36 cases with paired tissue available a high concordance of 86.11% was observed for clinically relevant mutations, with a Positive Predictive Value (PPV) of 88.89%. Furthermore, a concordance rate of 82% between cobas and the NGS approach for the EGFR sensitizing mutations (in exons 18, 19, 21) was observed in patients with acquired resistance to EGFR TKIs, while this concordance was 94% for the p.T790M mutation, with NGS being able to detect this mutation in three 3 additional patients. Conclusions This study indicates the feasibility of circulating tumor nucleic acids (ctNA) analysis as a tumor biopsy surrogate in clinical practice for NSCLC personalized treatment decision making. The use of new sensitive NGS techniques can reliably detect tumor-derived mutations in liquid biopsy and provide clinically relevant information both before and after targeted treatment in patients with NSCLC. Thus, it could aid physicians in treatment decision making in clinical practice.
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Affiliation(s)
| | | | | | | | | | | | | | | | - George Pentheroudakis
- Department of Medical Oncology, School of Medicine, Ioannina, Greece
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Dimitrios Petrakis
- Department of Medical Oncology, School of Medicine, Ioannina, Greece
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | | | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | - George Kesisis
- Oncology Department, Saint Luke Private Hospital, Thessaloniki, Greece
| | | | - Pavlos Papakotoulas
- First Department of Clinical Oncology, Theagenio Hospital, Thessaloniki, Greece
| | | | | | - Flora Stavridi
- Fourth Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | | | - Anna Koumarianou
- Hematology Oncology Unit, Fourth Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | - Yeşim Eralp
- Department of Medical Oncology, Istanbul University School of Medicine, İstanbul, Turkey
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