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Khalifa E, Chapusot C, Tournier B, Sentis J, Marion E, Remond A, Aubry M, Pioche C, Bergeron A, Primois C, Blanchard L, Millière A, Boucheix M, Léger Y, Bairrao M, Brouste V, Martin L, Soubeyran I. Idylla EGFR assay on extracted DNA: advantages, limits and place in molecular screening according to the latest guidelines for non-small-cell lung cancer (NSCLC) patients. J Clin Pathol 2023; 76:698-704. [PMID: 35820776 DOI: 10.1136/jcp-2022-208325] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/28/2022] [Indexed: 11/04/2022]
Abstract
AIMS Idylla epidermal growth factor receptor (EGFR) is a fast and fully automated mutation assay that is easy to implement. However, under the Biocartis-recommended technical conditions, tissue sections are directly introduced into the cartridge, at the risk of exhausting the tumour sample. In this study, we evaluate the performance of Idylla EGFR on extracted DNA and discuss its place within the global non-small-cell lung cancer (NSCLC) screening strategy. METHODS 577 comparative tests between Idylla EGFR on extracted DNA and next-generation sequencing (NGS) were performed across two centres. RESULTS Preanalytical thresholds were established (20% tumour cell content, 50 ng DNA input) and challenged prospectively in routine practice. 16.8% of samples referred for screening were considered non eligible for Idylla EGFR testing. Due to discordant by design cases, Idylla EGFR sensitivity was 86.9% for currently actionable EGFR mutations. Idylla EGFR specificity was 100% in first-line screening. NGS was always feasible on the same DNA. CONCLUSION Idylla EGFR on extracted DNA is feasible and enables tumour material to be saved compared with tissue section use. It is not necessary to replace the analytical thresholds of the Biocartis algorithm. Due to both the limits of the mutational repertoire and the high increase of targetable genes in NSCLC, the use of Idylla EGFR should be restricted to clinical emergency situations accompanied by NGS.
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Affiliation(s)
| | - Caroline Chapusot
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Benjamin Tournier
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Julie Sentis
- Biopathology, Institut Bergonié, Bordeaux, France
| | | | - Alicia Remond
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Manon Aubry
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Célia Pioche
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Anthony Bergeron
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | | | | - Alice Millière
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | | | | | | - Véronique Brouste
- Research and Clinical Epidemiology Unit - Biostatistics, Institut Bergonié, Bordeaux, France
| | - Laurent Martin
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
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Auzanneau C, Bacq D, Bellera C, Blons H, Boland A, Boucheix M, Bourdon A, Chollet E, Chomienne C, Deleuze JF, Delmas C, Dinart D, Espérou H, Geillon F, Geneste D, Italiano A, Jean D, Khalifa E, Laizet Y, Laurent-Puig P, Lethimonnier F, Lévy-Marchal C, Lucchesi C, Malle C, Mancini P, Mathoulin-Pélissier S, Meyer V, Marie-Ange P, Perkins G, Sellan-Albert S, Soubeyran I, Wallet C. Feasibility of high-throughput sequencing in clinical routine cancer care: lessons from the cancer pilot project of the France Genomic Medicine 2025 plan. ESMO Open 2021; 5:S2059-7029(20)32644-2. [PMID: 32713836 PMCID: PMC7383956 DOI: 10.1136/esmoopen-2020-000744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/02/2022] Open
Abstract
Background Whole exome sequencing and RNA sequencing (WES/RNASeq) should now be implemented in the clinical practice in order to increase access to optimal care for cancer patients. Providing results to Tumour Boards in a relevant time frame—that is, compatible with the clinical pathway—is crucial. Assessing the feasibility of this implementation in the French care system is the primary objective of the Multipli study, as one of the four pilot projects of the national France Genomic Medicine 2025 (FGM 2025) plan. The Multipli study encompasses two innovative trials which will be driven in around 2400 patients suffering from a soft-tissue sarcoma (Multisarc) or a metastatic colorectal carcinoma (Acompli). Methods Prior to launching the FGM 2025 cancer pilot study itself, the performance of the Multipli genomic workflow has been evaluated through each step, from the samples collection to the Molecular Tumour Board (MTB) report. Two Multipli-assigned INCa-labelled molecular genetics centres, the CEA-CNRGH sequencing platform and the Institut Bergonié’s Bioinformatics Platform were involved in a multicentric study. The duration of each step of the genomic workflow was monitored and bottlenecks were identified. Results Thirty barriers which could affect the quality of the samples, sequencing results and the duration of each step of the genomic pathway were identified and mastered. The global turnaround time from the sample reception to the MTB report was of 44 calendar days. Conclusion Our results demonstrate the feasibility of tumour genomic analysis by WES/RNASeq within a time frame compatible with the current cancer patient care. Lessons learnt from the Multipli WES/RNASeq Platforms Workflow Study will constitute guidelines for the forthcoming Multipli study and more broadly for the future clinical routine practice in the first two France Genomic Medicine 2025 platforms.
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Affiliation(s)
| | - Céline Auzanneau
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France.,U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Delphine Bacq
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Carine Bellera
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Hélène Blons
- Service de pharmacogénétique et d'oncologie moléculaire, Hopital Europeen Georges Pompidou, Paris, France.,U1147, Centre universitaire des Saint-Pères, Institut national de la santé et de la recherche médicale, Paris, France
| | - Anne Boland
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Marlène Boucheix
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France
| | - Aurélien Bourdon
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Emmanuelle Chollet
- ITMO Cancer, Alliance nationale pour les sciences de la vie et de la santé, Paris, France
| | - Christine Chomienne
- ITMO Cancer, Alliance nationale pour les sciences de la vie et de la santé, Paris, France .,Institut National du Cancer, Boulogne-Billancourt, France
| | - Jean-François Deleuze
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France.,Centre de référence, d'innovation et d'expertise, US39, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Christelle Delmas
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Derek Dinart
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Hélène Espérou
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Flore Geillon
- Fédération francophone de cancérologie digestive, Dijon, France
| | - Damien Geneste
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Antoine Italiano
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unités Essais cliniques de phase précoce et Sarcomes, Institut Bergonié, Bordeaux, France
| | - Delphine Jean
- CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Emmanuel Khalifa
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France.,U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Yec'han Laizet
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Pierre Laurent-Puig
- U1147, Centre universitaire des Saint-Pères, Institut national de la santé et de la recherche médicale, Paris, France.,Service de génétique médicale et clinique, Hopital Europeen Georges Pompidou, Paris, France
| | - Franck Lethimonnier
- ITMO Technologies pour la santé, Alliance nationale pour les sciences de la vie et de la santé, Paris, France
| | - Claire Lévy-Marchal
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Carlo Lucchesi
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Carine Malle
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Pierre Mancini
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Simone Mathoulin-Pélissier
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Vincent Meyer
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Palomares Marie-Ange
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Géraldine Perkins
- U1147, Centre universitaire des Saint-Pères, Institut national de la santé et de la recherche médicale, Paris, France.,Service de génétique médicale et clinique, HEGP, Paris, Île-de-France, France
| | - Sabrina Sellan-Albert
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Isabelle Soubeyran
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France.,U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Cédric Wallet
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
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