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Bossé Y, Dasgupta A, Abadier M, Guthrie V, Song F, Saavedra Armero V, Gaudreault N, Orain M, Lamaze FC, Melton C, Nance T, Hung T, Hodgson D, Abbosh C, Joubert P. Prognostic implication of methylation-based circulating tumor DNA detection prior to surgery in stage I non-small cell lung cancer. Cancer Lett 2024; 594:216984. [PMID: 38797230 DOI: 10.1016/j.canlet.2024.216984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) positivity at diagnosis, which is associated with worse outcomes in multiple solid tumors including stage I-III non-small cell lung cancer (NSCLC), may have utility to guide (neo)adjuvant therapy. METHODS In this retrospective study, 260 patients with clinical stage I NSCLC (180 adenocarcinoma, 80 squamous cell carcinoma) were allocated (2:1) to high- and low-risk groups based on relapse versus disease-free status ≤5 years post-surgery. We evaluated the association of preoperative ctDNA detection by a plasma-only targeted methylation-based multi-cancer early detection (MCED) test with NSCLC relapse ≤5 years post-surgery in the overall population, followed by histology-specific subgroup analyses. RESULTS Across clinical stage I patients, preoperative ctDNA detection did not associate with relapse within 5 years post-surgery. Sub-analyses confined to lung adenocarcinoma suggested a histology-specific association between ctDNA detection and outcome. In this group, ctDNA positivity tended to associate with relapse within 2 years, suggesting prognostic implications of MCED test positivity may be histology- and time-dependent in stage I NSCLC. Preoperative ctDNA detection was associated with upstaging of clinical stage I to pathological stage II-III NSCLC. CONCLUSIONS Our findings suggest preoperative ctDNA detection in patients with resectable clinical stage I NSCLC using MCED, a pan-cancer screening test developed for use in an asymptomatic population, has no detectable prognostic value for relapse ≤5 years post-surgery. MCED detection may be associated with early adenocarcinoma relapse and increased pathological upstaging rates in stage I NSCLC. However, given the exploratory nature of these findings, independent validation is required.
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Affiliation(s)
- Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada; Department of Molecular Medicine, Université Laval, Quebec City, Canada.
| | - Abhijit Dasgupta
- Oncology Data Science, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Michael Abadier
- Translational Medicine Early Oncology, AstraZeneca, Waltham, MA, USA
| | - Violeta Guthrie
- Oncology Data Science, Oncology R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Florian Song
- Translational Medicine Early Oncology, AstraZeneca, Munich, Germany
| | - Victoria Saavedra Armero
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Nathalie Gaudreault
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Michèle Orain
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Fabien C Lamaze
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | | | | | | | - Darren Hodgson
- Translational Medicine Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Chris Abbosh
- Translational Medicine Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada; Department of Molecular Biology, Pathology and Medical Biochemistry, Université Laval, Quebec City, Canada
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Blanluet C, Kuo CJ, Bhattacharya A, Santiago JG. Design and Evaluation of a Robust CRISPR Kinetic Assay for Hot-Spot Genotyping. Anal Chem 2024; 96:7444-7451. [PMID: 38684052 DOI: 10.1021/acs.analchem.3c05657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Next-generation sequencing offers highly multiplexed and accurate detection of nucleic acid sequences but at the expense of complex workflows and high input requirements. The ease of use of CRISPR-Cas12 assays is attractive and may enable highly accurate detection of sequences implicated in, for example, cancer pathogenic variants. CRISPR assays often employ end-point measurements of Cas12 trans-cleavage activity after Cas12 activation by the target; however, end point-based methods can be limited in accuracy and robustness by arbitrary experimental choices. To overcome such limitations, we develop and demonstrate here an accurate assay targeting a mutation of the epidermal growth factor gene implicated in lung cancer (exon 19 deletion). The assay is based on characterizing the kinetics of Cas12 trans-cleavage to discriminate the mutant from wild-type targets. We performed extensive experiments (780 reactions) to calibrate key assay design parameters, including the guide RNA sequence, reporter sequence, reporter concentration, enzyme concentration, and DNA target type. Interestingly, we observed a competitive reaction between the target and reporter molecules that has important consequences for the design of CRISPR assays, which use preamplification to improve sensitivity. Finally, we demonstrate the assay on 18 tumor-extracted amplicons and 100 training iterations with 99% accuracy and discuss discrimination parameters and models to improve wild type versus mutant classification.
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Affiliation(s)
- Charles Blanluet
- CentraleSupelec─Universite Paris-Saclay, 91190 Gif-sur-Yvette, France
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Asmita Bhattacharya
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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Fleming KE, Hupel A, Mithoowani H, Lulic-Kuryllo T, Valdes M. Biomarker Turnaround Times and Impact on Treatment Decisions in Patients with Advanced Non-Small Cell Lung Carcinoma at a Large Canadian Community Hospital with an Affiliated Regional Cancer Centre. Curr Oncol 2024; 31:1515-1528. [PMID: 38534948 PMCID: PMC10969576 DOI: 10.3390/curroncol31030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 05/26/2024] Open
Abstract
Background: Timely reporting of molecular biomarkers is critical in guiding optimal treatment decisions in patients with advanced non-small cell lung carcinoma (NSCLC). Any delays along the tissue or treatment pathway may be associated with suboptimal treatment/outcomes and a reduced quality of life. For many centres, biomarkers are tested off-site. Methods: A retrospective chart review of 123 patients with advanced NSCLC seen between 1 June 2021 and 30 June 2022 was conducted. With a focus on core biomarkers (PD L1, EGFR, and ALK), the outcome variables were as follows: total turnaround time (total TAT), divided into pre-laboratory, laboratory, and post-laboratory time intervals, as well as time to treatment decision (TOTD) and time to optimal systemic therapy decision (TOTSD). Results: At first consult, only 20.3% of patients had all core biomarker results available. The median total TAT was significantly longer for non-squamous (non-SCC) than squamous cell carcinoma (SCC) specimens (36.5 versus 22 days, p < 0.001). The median pre-laboratory time for the entire cohort was 5 calendar days. The median laboratory testing time was greater for non-SCC compared to the SCC specimens (23 versus 12 days, p < 0.001). The median time from consult to TOTD was 19 calendar days for the entire cohort. Conclusions: This study emphasizes the need for the expansion of regional resources to meet the clinical needs of advanced NSCLC patients treated at a regional cancer centre which uses an off-site molecular laboratory.
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Affiliation(s)
- Katelyn E. Fleming
- Office of Innovation & Research, Grand River Hospital, Kitchener, ON N2G 1G3, Canada
| | - Ava Hupel
- Office of Innovation & Research, Grand River Hospital, Kitchener, ON N2G 1G3, Canada
| | - Hamid Mithoowani
- Department of Oncology, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Tea Lulic-Kuryllo
- Office of Innovation & Research, Grand River Hospital, Kitchener, ON N2G 1G3, Canada
| | - Mario Valdes
- Department of Oncology, Grand River Regional Cancer Centre, Kitchener, ON N2G 1G3, Canada
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Grafham GK, Craddock KJ, Huang W, Louie AV, Zhang L, Hwang DM, Parmar A. Referred molecular testing as a barrier to optimal treatment decision making in metastatic non-small cell lung cancer: Experience at a tertiary academic institution in Canada. Cancer Med 2024; 13:e6886. [PMID: 38317584 PMCID: PMC10905241 DOI: 10.1002/cam4.6886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/08/2023] [Accepted: 12/16/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Molecular testing is critical to guiding treatment approaches in patients with metastatic non-small cell lung cancer (mNSCLC), with testing delays adversely impacting the timeliness of treatment decisions. Here, we aimed to evaluate the time from initial mNSCLC diagnosis to treatment decision (TTD) following implementation of in-house EGFR, ALK, and PD-L1 testing at our institution. METHODS We conducted a retrospective chart review of 165 patients (send-out testing, n = 92; in-house testing, n = 73) with newly diagnosed mNSCLC treated at our institution. Data were compared during the send-out (March 2017-May 2019) and in-house (July 2019-March 2021) testing periods. We performed a detailed workflow analysis to provide insight on the pre-analytic, analytic, and post-analytic intervals that constituted the total TTD. RESULTS TTD was significantly shorter with in-house testing (10 days vs. 18 days, p < 0.0001), driven largely by decreased internal handling and specimen transit times (2 days vs. 3 days, p < 0.0001) and laboratory turnaround times (TAT, 3 days vs. 8 days, p < 0.0001), with 96% of in-house cases meeting the international guideline of a ≤ 10-day intra-laboratory TAT (vs. 74% send-out, p < 0.001). Eighty-eight percent of patients with in-house testing had results available at their first oncology consultation (vs. 52% send-out, p < 0.0001), and all patients with in-house testing had results available at the time of treatment decision (vs. 86% send-out, p = 0.57). CONCLUSION Our results demonstrate the advantages of in-house biomarker testing for mNSCLC at a tertiary oncology center. Incorporation of in-house testing may reduce barriers to offering personalized medicine by improving the time to optimal systemic therapy decision.
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Affiliation(s)
- Grace K. Grafham
- Temerty Faculty of MedicineUniversity of TorontoTorontoOntarioCanada
| | - Kenneth J. Craddock
- Department of Laboratory Medicine and Molecular DiagnosticsSunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Weei‐Yuarn Huang
- Department of Laboratory Medicine and Molecular DiagnosticsSunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Alexander V. Louie
- Temerty Faculty of MedicineUniversity of TorontoTorontoOntarioCanada
- Department of Radiation OncologySunnybrook Health Sciences CentreTorontoOntarioCanada
| | | | - David M. Hwang
- Department of Laboratory Medicine and Molecular DiagnosticsSunnybrook Health Sciences CentreTorontoOntarioCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Ambica Parmar
- Temerty Faculty of MedicineUniversity of TorontoTorontoOntarioCanada
- Division of Hematology and Medical Oncology, Department of MedicineSunnybrook Health Sciences CentreTorontoOntarioCanada
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Ferrara M, Pecorino B, D’Agate MG, Angelico G, Capoluongo ED, Malapelle U, Pepe F, Scollo P, Mereu L. Uterine Tumours Resembling Ovarian Sex-Cord Tumors: A Case Report and Review of the Literature. J Clin Med 2023; 12:7131. [PMID: 38002745 PMCID: PMC10671931 DOI: 10.3390/jcm12227131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Uterine tumors resembling ovarian sex-cord tumors (UTROSCT) are thought to develop from pluripotent uterine mesenchymal cells or endometrial stromal cells with secondary sex-cord differentiation. The patient was a 73-year-old postmenopausal woman who had abnormal vaginal bleeding, and she underwent a laparoscopic hysterectomy with bilateral salpingo-oophorectomy. The diagnosis was a case of UTROSCT. A scoping review of the UTROSCT case report present in the literature has been conducted, and 63 articles were found, of which 45 were considered for the 66 clinical cases examined. At the time of diagnosis, six metastatic localizations were found in 59 patients undergoing demolitive surgery (10.2%). Recurrences were diagnosed in 13/59 (22%) patients with multiple locations. A molecular study was performed in 18/66 cases (27.3%) and genetic alterations were found in 10/18 (55.6%) patients. UTROSCTs are considered rare uterine tumors, typically with a favorable prognosis, and are generally considered to have a good prognosis. But, from the review done, they may already manifest themselves at advanced stages, with the possibility of recurrences even at a distance. It would, therefore, be important to be able to define the most aggressive forms and, perhaps, molecular investigation with sequencing could help identify patients most at risk.
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Affiliation(s)
- Martina Ferrara
- Department of Obstetrics and Gynecology, Cannizzaro Hospital, University of Enna “Kore”, 94100 Enna, Italy; (B.P.); (M.G.D.); (P.S.)
| | - Basilio Pecorino
- Department of Obstetrics and Gynecology, Cannizzaro Hospital, University of Enna “Kore”, 94100 Enna, Italy; (B.P.); (M.G.D.); (P.S.)
| | - Maria Gabriella D’Agate
- Department of Obstetrics and Gynecology, Cannizzaro Hospital, University of Enna “Kore”, 94100 Enna, Italy; (B.P.); (M.G.D.); (P.S.)
| | - Giuseppe Angelico
- Department of Anatomic Pathology and Histology, Cannizzaro Hospital, 95100 Catania, Italy;
| | | | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80126 Naples, Italy; (U.M.); (F.P.)
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, 80126 Naples, Italy; (U.M.); (F.P.)
| | - Paolo Scollo
- Department of Obstetrics and Gynecology, Cannizzaro Hospital, University of Enna “Kore”, 94100 Enna, Italy; (B.P.); (M.G.D.); (P.S.)
| | - Liliana Mereu
- Department of Obstetrics and Gynecology, Policlinico G Rodolico, CHIRMED, University of Catania, 95124 Catania, Italy
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Normanno N, Machado JC, Pescarmona E, Buglioni S, Navarro L, Esposito Abate R, Ferro A, Mensink R, Lambiase M, Lespinet-Fabre V, Calgua B, Jermann PM, Ilié M, Hofman P. European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors. Int J Mol Sci 2023; 24:13788. [PMID: 37762091 PMCID: PMC10531166 DOI: 10.3390/ijms241813788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. This multicenter study evaluated the performance of a CE in vitro diagnostic (IVD) assay, the Oncomine Dx Express Test, on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. Eighty-two archived formalin-fixed paraffin embedded (FFPE) tissue samples from lung, colorectal, central nervous system, melanoma, breast, gastric, thyroid, and soft tissue cancers were used to assess the presence of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variations (CNVs), gene fusions, and splice variants. These clinical samples were previously characterized at the various academic centers using orthogonal methods. The Oncomine Dx Express Test showed high performance with 100% concordance with previous characterization for SNVs, indels, CNVs, gene fusions, and splice variants. SNVs and indels with allele frequencies as low as 5% were correctly identified. The test detected all the expected ALK, RET, NTRK1, and ROS1 fusion isoforms and MET exon 14-skipping splice variants. The average TAT from extracted nucleic acids to the final variant report was 18.3 h. The Oncomine Dx Express Test in combination with the Ion Torrent Genexus System is a CE-IVD-compliant, performant, and multicenter reproducible method for NGS detection of actionable biomarkers from a range of tumor samples, providing results in a short TAT that could support timely decision- making for targeted therapeutic interventions.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (N.N.); (R.E.A.)
| | - José Carlos Machado
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal; (J.C.M.); (A.F.); (R.M.)
- Institute of Molecular Pathology and Immunology, University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Edoardo Pescarmona
- I.R.C.C.S. Regina Elena National Cancer Institute, 00144 Rome, Italy; (E.P.); (S.B.)
| | - Simonetta Buglioni
- I.R.C.C.S. Regina Elena National Cancer Institute, 00144 Rome, Italy; (E.P.); (S.B.)
| | - Lara Navarro
- Consorcio Hospital General de Valencia, 46014 Valencia, Spain;
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (N.N.); (R.E.A.)
| | - Anabela Ferro
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal; (J.C.M.); (A.F.); (R.M.)
- Institute of Molecular Pathology and Immunology, University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Rob Mensink
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal; (J.C.M.); (A.F.); (R.M.)
- Institute of Molecular Pathology and Immunology, University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Matilde Lambiase
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (N.N.); (R.E.A.)
| | - Virginie Lespinet-Fabre
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, France; (V.L.-F.); (M.I.)
| | - Byron Calgua
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland; (B.C.); (P.M.J.)
| | - Philip M. Jermann
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland; (B.C.); (P.M.J.)
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, France; (V.L.-F.); (M.I.)
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, France; (V.L.-F.); (M.I.)
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Dagogo-Jack I, Manoogian A, Jessop N, Georgantas NZ, Fintelmann FJ, Farahani A, Digumarthy SR, Price MC, Folch EE, Keyes CM, Do A, Peterson JL, Mino-Kenudson M, Pitman M, Rivera M, Nardi V, Dias-Santagata D, Le LP, Iafrate AJ, Heist RS, Ritterhouse LR, Lennerz JK. Integrated Radiology, Pathology, and Pharmacy Program to Accelerate Access to Osimertinib. JCO Oncol Pract 2023; 19:786-792. [PMID: 37437226 PMCID: PMC10538938 DOI: 10.1200/op.23.00031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/18/2023] [Accepted: 05/30/2023] [Indexed: 07/14/2023] Open
Abstract
PURPOSE Targeted therapy yields superior outcomes relative to genotype-agnostic therapy for patients with epidermal growth factor receptor (EGFR)-mutant lung cancer. Workflows that facilitate timely detection of EGFR mutations and early dispensation of osimertinib can improve management of this disease. METHODS We developed an Integrated Radiology, Pathology, and Pharmacy Program to minimize delays in initiating osimertinib. The intervention consisted of parallel workflows coupling interventional radiology, surgical pathology, and analysis of nucleic acids from frozen tissue with early pharmacy engagement. We compared time to EGFR testing results and time to treatment for participating patients with those of historical cohorts. RESULTS Between January 2020 and December 2021, 222 patients participated in the intervention. The median turnaround time from biopsy to EGFR results was 1 workday. Forty-nine (22%) tumors harbored EGFR exon 19 deletions or EGFR L858R. Thirty-one (63%) patients were prescribed osimertinib via the intervention. The median interval between osimertinib prescription and osimertinib dispensation was 3 days; dispensation occurred within 48 hours for 42% of patients. The median interval between biopsy and osimertinib dispensation was 5 days. Three patients received osimertinib within 24 hours of EGFR results. Compared with patients with EGFR-mutant non-small-cell lung cancer who were diagnosed through routine workflows, the intervention led to a significant reduction in median time between biopsy and EGFR results (1 v 7 days; P < .01) and median time to treatment initiation (5 v 23 days; P < .01). CONCLUSION Combining radiology and pathology workflows with early parallel pharmacy engagement leads to a significant reduction in time to initiating osimertinib. Multidisciplinary integration programs are essential to maximize clinical utility of rapid testing.
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Affiliation(s)
- Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | | | - Nicholas Jessop
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - N. Zeke Georgantas
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Florian J. Fintelmann
- Harvard Medical School, Boston, MA
- Department of Radiology, Massachusetts General Hospital, Boston, MA
| | - Alexander Farahani
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Subba R. Digumarthy
- Harvard Medical School, Boston, MA
- Department of Radiology, Massachusetts General Hospital, Boston, MA
| | - Melissa C. Price
- Harvard Medical School, Boston, MA
- Department of Radiology, Massachusetts General Hospital, Boston, MA
| | - Erik E. Folch
- Harvard Medical School, Boston, MA
- Interventional Pulmonology, Massachusetts General Hospital, Boston, MA
| | - Colleen M. Keyes
- Harvard Medical School, Boston, MA
- Interventional Pulmonology, Massachusetts General Hospital, Boston, MA
| | - Andrew Do
- Massachusetts General Hospital Cancer Center, Boston, MA
| | | | - Mari Mino-Kenudson
- Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Martha Pitman
- Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Miguel Rivera
- Harvard Medical School, Boston, MA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Valentina Nardi
- Harvard Medical School, Boston, MA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Dora Dias-Santagata
- Harvard Medical School, Boston, MA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Long P. Le
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Anthony John Iafrate
- Harvard Medical School, Boston, MA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Rebecca S. Heist
- Massachusetts General Hospital Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Lauren R. Ritterhouse
- Harvard Medical School, Boston, MA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | - Jochen K. Lennerz
- Harvard Medical School, Boston, MA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
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8
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Silas U, Blüher M, Bosworth Smith A, Saunders R. Fast In-House Next-Generation Sequencing in the Diagnosis of Metastatic Non-small Cell Lung Cancer: A Hospital Budget Impact Analysis. JOURNAL OF HEALTH ECONOMICS AND OUTCOMES RESEARCH 2023; 10:111-118. [PMID: 37389301 PMCID: PMC10306161 DOI: 10.36469/001c.77686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
Background: Targeted therapy for cancer is becoming more frequent as the understanding of the molecular pathogenesis increases. Molecular testing must be done to use targeted therapy. Unfortunately, the testing turnaround time can delay the initiation of targeted therapy. Objective: To investigate the impact of a next-generation sequencing (NGS) machine in the hospital that would allow for in-house NGS testing of metastatic non-small cell lung cancer (mNSCLC) in a US setting. Methods: The differences between 2 hospital pathways were established with a cohort-level decision tree that feeds into a Markov model. A pathway that used in-house NGS (75%) and the use of external laboratories (so-called send-out NGS) (25%), was compared with the standard of exclusively send-out NGS. The model was from the perspective of a US hospital over a 5-year time horizon. All cost input data were in or inflated to 2021 USD. Scenario analysis was done on key variables. Results: In a hospital with 500 mNSCLC patients, the implementation of in-house NGS was estimated to increase the testing costs and the revenue of the hospital. The model predicted a $710 060 increase in testing costs, a $1 732 506 increase in revenue, and a $1 022 446 return on investment over 5 years. The payback period was 15 months with in-house NGS. The number of patients on targeted therapy increased by 3.38%, and the average turnaround time decreased by 10 days when in-house NGS was used. Discussion: Reducing testing turnaround time is a benefit of in-house NGS. It could contribute to fewer mNSCLC patients lost to second opinion and an increased number of patients on targeted therapy. The model outcomes predicted that, over a 5-year period, there would be a positive return on investment for a US hospital. The model reflects a proposed scenario. The heterogeneity of hospital inputs and the cost of send-out NGS means context-specific inputs are needed. Conclusion: Using in-house NGS testing could reduce the testing turnaround time and increase the number of patients on targeted therapy. Additional benefits for the hospital are that fewer patients will be lost to second opinion and that in-house NGS could generate additional revenue.
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Affiliation(s)
- Ubong Silas
- Coreva Scientific GmbH & Co. KG, Königswinter, Germany
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9
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Yang S, Kim SH, Kang M, Joo JY. Harnessing deep learning into hidden mutations of neurological disorders for therapeutic challenges. Arch Pharm Res 2023:10.1007/s12272-023-01450-5. [PMID: 37261600 DOI: 10.1007/s12272-023-01450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
The relevant study of transcriptome-wide variations and neurological disorders in the evolved field of genomic data science is on the rise. Deep learning has been highlighted utilizing algorithms on massive amounts of data in a human-like manner, and is expected to predict the dependency or druggability of hidden mutations within the genome. Enormous mutational variants in coding and noncoding transcripts have been discovered along the genome by far, despite of the fine-tuned genetic proofreading machinery. These variants could be capable of inducing various pathological conditions, including neurological disorders, which require lifelong care. Several limitations and questions emerge, including the use of conventional processes via limited patient-driven sequence acquisitions and decoding-based inferences as well as how rare variants can be deduced as a population-specific etiology. These puzzles require harnessing of advanced systems for precise disease prediction, drug development and drug applications. In this review, we summarize the pathophysiological discoveries of pathogenic variants in both coding and noncoding transcripts in neurological disorders, and the current advantage of deep learning applications. In addition, we discuss the challenges encountered and how to outperform them with advancing interpretation.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea.
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10
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Sande CM, Wu R, Yang G, Sussman RT, Bigdeli A, Rushton C, Chitturi A, Patel J, Szankasi P, Morrissette JJD, Lim MS, Elenitoba-Johnson KSJ. Rapid and Automated Semiconductor-Based Next-Generation Sequencing for Simultaneous Detection of Somatic DNA and RNA Aberrations in Myeloid Neoplasms. J Mol Diagn 2023; 25:87-93. [PMID: 36503148 DOI: 10.1016/j.jmoldx.2022.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/17/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Evaluation of suspected myeloid neoplasms involves testing for recurrent, diagnostically and therapeutically relevant genetic alterations. Current molecular testing requires multiple technologies, different domains of expertise, and unconnected workflows, resulting in variable, lengthy turnaround times that can delay treatment. To address this unmet clinical need, we evaluated the Oncomine Myeloid Assay GX panel on the Ion Torrent Genexus platform, a rapid, integrated nucleic acid to report next-generation sequencing platform for detecting clinically relevant genetic aberrations in myeloid disorders. Specimens included synthetic DNA (101 targets) and RNA (9 targets) controls and real-world nucleic acid material derived from bone marrow or peripheral blood samples (40 patients). Ion Torrent Genexus results and performance indices were compared with those obtained from clinically validated genomic testing workflows in 2 separate clinical laboratories. The Ion Torrent Genexus identified 100% of DNA and RNA control variants. For primary patient specimens, the Ion Torrent Genexus reported 82 of 107 DNA variants and 19 of 19 RNA gene fusions identified on clinically validated assays, yielding an 80% overall detection rate. Reanalysis of exported, unfiltered Ion Torrent Genexus data revealed 15 DNA variants not called by the filtered on-board bioinformatics pipeline, yielding a 92% potential detection rate. These results hold promise for the implementation of an integrated next-generation sequencing system to rapidly detect genetic aberrations, facilitating accurate, genomics-based diagnoses and accelerated time to precision therapies in myeloid neoplasms.
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Affiliation(s)
- Christopher M Sande
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rui Wu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Guang Yang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robyn T Sussman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ashkan Bigdeli
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chase Rushton
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Akshay Chitturi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jay Patel
- ARUP Laboratories, Salt Lake City, Utah
| | | | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Megan S Lim
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kojo S J Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
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11
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Trapani D, Crimini E, Sandoval J, Curigliano G. Next-Generation Sequencing for Advanced Breast Cancer: What the Way to Go? Cancer Treat Res 2023; 188:343-351. [PMID: 38175352 DOI: 10.1007/978-3-031-33602-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The rapid implementation of precision medicine tools in diagnosing and treating breast cancer (BC) has widened the potential therapeutic options for patients. The applications of gene sequencing, including next-generation gene sequencing (NGS), have led to numerous questions on how to validate, implement, interpret, prioritize and operationalize precision medicine tools to deliver meaningful and impactful interventions. Limited benefit has been portended with earlier experiences of NGS-driven treatment, in BC. However, the development and use of frameworks of clinical actionability of genomic alterations, for example, detected with NGS, has resulted in better patient selection, and potentially higher therapeutic value. The European Society for Medical Oncology Scale for Clinical Actionability of molecular Targets (ESCAT) is a framework that includes five tiers of clinical actionability, with tier 1 reserved for approved drugs with demonstrated benefits for targetable genomic alterations. The re-analysis of clinical studies by grouping the genomic alterations and matched drugs with ESCAT, in high vs lower tiers has demonstrated a significant benefit portended by high tiers alterations, with the availability of efficacious treatments. As a result, frameworks for actionability, like ESCAT, should be fundamental in developing and implementing NGS-driven, and broadly, precision medicine research and treatments.
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Affiliation(s)
- Dario Trapani
- Division of New Drug Development for innovative therapies, European Institute of Oncology IRCCS, Milan, Italy.
| | - Edoardo Crimini
- Division of New Drug Development for innovative therapies, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hematology, University of Milan, Milan, Italy
| | - José Sandoval
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Unit of Population Epidemiology, Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Giuseppe Curigliano
- Division of New Drug Development for innovative therapies, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hematology, University of Milan, Milan, Italy
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12
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Zhou Y, Koutsilieri S, Eliasson E, Lauschke VM. A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing. Basic Clin Pharmacol Toxicol 2022; 131:452-464. [PMID: 35971800 PMCID: PMC9805052 DOI: 10.1111/bcpt.13779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 01/09/2023]
Abstract
Genetic factors have long been recognized as important determinants of interindividual variability in drug efficacy and toxicity. However, despite the increasing number of established gene-drug associations, candidate polymorphisms can only explain a fraction of the genetically encoded functional variability in drug disposition. Advancements in genetic profiling methods now allow to analyse the landscape of human pharmacogenetic variations comprehensively, which opens new opportunities to identify novel factors that could explain the "missing heritability." Here, we provide an updated overview of the landscape of pharmacogenomic variability based on recent analyses of population-scale sequencing projects. We then summarize the current state-of-the-art how the functional consequences of variants with unknown effects can be quantitatively estimated while discussing challenges and peculiarities that are specific to pharmacogenes. In the last sections, we discuss the importance of considering ethnogeographic diversity to provide equitable benefits of pharmacogenomics and summarize current roadblocks for the implementation of sequencing-based guidance of clinical decision-making. Based on the current state of the field, we conclude that testing is likely to gradually shift from the interrogation of selected candidate polymorphisms to comprehensive sequencing, which allows to consider the full spectrum of pharmacogenomic variations for a true personalization of genomic prescribing.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and PharmacologyKarolinska InstitutetStockholmSweden,Department of Laboratory MedicineKarolinska InstitutetStockholmSweden
| | | | - Erik Eliasson
- Department of Laboratory MedicineKarolinska InstitutetStockholmSweden
| | - Volker M. Lauschke
- Department of Physiology and PharmacologyKarolinska InstitutetStockholmSweden,Dr Margarete Fischer‐Bosch Institute of Clinical PharmacologyStuttgartGermany,University of TübingenTübingenGermany
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13
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Yu IS, Aubin F, Goodwin R, Loree JM, Mather C, Sheffield BS, Snow S, Gill S. Tumor Biomarker Testing for Metastatic Colorectal Cancer: a Canadian Consensus Practice Guideline. Ther Adv Med Oncol 2022; 14:17588359221111705. [PMID: 35898967 PMCID: PMC9310231 DOI: 10.1177/17588359221111705] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
The systemic therapy management of metastatic colorectal cancer (mCRC) has evolved from primarily cytotoxic chemotherapies to now include targeted agents given alone or in combination with chemotherapy, and immune checkpoint inhibitors. A better understanding of the pathogenesis and molecular drivers of colorectal cancer not only aided the development of novel targeted therapies but led to the discovery of tumor mutations which act as predictive biomarkers for therapeutic response. Mutational status of the KRAS gene became the first genomic biomarker to be established as part of standard of care molecular testing, where KRAS mutations within exons 2, 3, and 4 predict a lack of response to anti- epidermal growth factor receptor therapies. Since then, several other biomarkers have become relevant to inform mCRC treatment; however, there are no published Canadian guidelines which reflect the current standards for biomarker testing. This guideline was developed by a pan-Canadian advisory group to provide contemporary, evidence-based recommendations on the minimum acceptable standards for biomarker testing in mCRC, and to describe additional biomarkers for consideration.
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Affiliation(s)
- Irene S. Yu
- Department of Medical Oncology, BC Cancer
Surrey, Surrey, BC, Canada
| | - Francine Aubin
- Division of Hematology and Oncology, Department
of Medicine, Centre Hospitalier de l’Université de Montréal, Montreal, QC,
Canada
| | - Rachel Goodwin
- Division of Medical Oncology, Department of
Medicine, Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
| | - Jonathan M. Loree
- Department of Medical Oncology, BC Cancer
Agency - Vancouver Centre, Vancouver, BC, Canada
| | - Cheryl Mather
- Department of Laboratory Medicine and
Pathology, University of Alberta, Edmonton, AB, Canada
| | - Brandon S. Sheffield
- Division of Advanced Diagnostics, William Osler
Health System, Brampton, ON, Canada
| | - Stephanie Snow
- Department of Medicine, Queen Elizabeth II
Health Sciences Centre, Halifax, NS, Canada
| | - Sharlene Gill
- Department of Medical Oncology, BC Cancer
Agency – Vancouver Centre, 600 W 10th Ave, Vancouver, BC, V5Z 4E6,
Canada
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14
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Durães C, Pereira Gomes C, Costa JL, Quagliata L. Demystifying the Discussion of Sequencing Panel Size in Oncology Genetic Testing. EUROPEAN MEDICAL JOURNAL 2022. [DOI: 10.33590/emj/22c9259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Clinical laboratories worldwide are implementing next-generation sequencing (NGS) to identify cancer genomic variants and ultimately improve patient outcomes. The ability to massively sequence the entire genome or exome of tumour cells has been critical to elucidating many complex biological questions. However, the depth of information obtained by these methods is strenuous to process in the clinical setting, making them currently unfeasible for broader adoption. Instead, targeted sequencing, usually on a selection of clinically relevant genes, represents the predominant approach that best balances accurate identification of genomic variants with high sensitivity and a good cost-effectiveness ratio. The information obtained from targeted sequencing can support diagnostic classification, guide therapeutic decisions, and provide prognostic insights. The use of targeted gene panels expedites sample processing, including data analysis, results interpretation, and medical reports generation, directly affecting patient management. The key decision factors for selecting sequencing methods and panel size in routine testing should include diagnostic yield and clinical utility, sample availability, and processing turnaround time.
Profiling by default all patients with late-stage cancer with large panels is not affordable for most healthcare systems and does not provide substantial clinical benefit at present. Balancing between understanding cancer biology, including patients in clinical trials, maximising testing, and ensuring a sustainable financial burden for society requires thorough consideration. This review provides an overview of the advantages and drawbacks of different sizes NGS panels for tumour molecular profiling and their clinical applicability.
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Affiliation(s)
- Cecília Durães
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
| | | | - Jose Luis Costa
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
| | - Luca Quagliata
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
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15
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Ilié M, Hofman V, Bontoux C, Heeke S, Lespinet-Fabre V, Bordone O, Lassalle S, Lalvée S, Tanga V, Allegra M, Salah M, Bohly D, Benzaquen J, Marquette CH, Long-Mira E, Hofman P. Setting Up an Ultra-Fast Next-Generation Sequencing Approach as Reflex Testing at Diagnosis of Non-Squamous Non-Small Cell Lung Cancer; Experience of a Single Center (LPCE, Nice, France). Cancers (Basel) 2022; 14:2258. [PMID: 35565387 PMCID: PMC9104603 DOI: 10.3390/cancers14092258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
The number of genomic alterations required for targeted therapy of non-squamous non-small cell lung cancer (NS-NSCLC) patients has increased and become more complex these last few years. These molecular abnormalities lead to treatment that provides improvement in overall survival for certain patients. However, these treated tumors inexorably develop mechanisms of resistance, some of which can be targeted with new therapies. The characterization of the genomic alterations needs to be performed in a short turnaround time (TAT), as indicated by the international guidelines. The origin of the tissue biopsies used for the analyses is diverse, but their size is progressively decreasing due to the development of less invasive methods. In this respect, the pathologists are facing a number of different challenges requiring them to set up efficient molecular technologies while maintaining a strategy that allows rapid diagnosis. We report here our experience concerning the development of an optimal workflow for genomic alteration assessment as reflex testing in routine clinical practice at diagnosis for NS-NSCLC patients by using an ultra-fast-next generation sequencing approach (Ion Torrent Genexus Sequencer, Thermo Fisher Scientific). We show that the molecular targets currently available to personalized medicine in thoracic oncology can be identified using this system in an appropriate TAT, notably when only a small amount of nucleic acids is available. We discuss the new challenges and the perspectives of using such an ultra-fast NGS in daily practice.
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Affiliation(s)
- Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Virginie Lespinet-Fabre
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
| | - Olivier Bordone
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Salomé Lalvée
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
| | - Virginie Tanga
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Maryline Allegra
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Myriam Salah
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Doriane Bohly
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Jonathan Benzaquen
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Pasteur Hospital, 06000 Nice, France
| | - Charles-Hugo Marquette
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Pasteur Hospital, 06000 Nice, France
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
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