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Aisner DL, Gocke CD, Jones D, Limson M, Morrissette J, Segal JP. The Genomics Organization for Academic Laboratories (GOAL): A vision for a genomics future for academic pathology. Acad Pathol 2023; 10:100090. [PMID: 37583476 PMCID: PMC10424130 DOI: 10.1016/j.acpath.2023.100090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/26/2023] [Accepted: 06/18/2023] [Indexed: 08/17/2023] Open
Abstract
Innovative and self-sustaining clinical genomics laboratories specializing in cutting-edge oncology testing are critical to the success of academic pathology departments and resident and fellow education in molecular pathology. However, the pressures and challenges facing these laboratories are numerous, including the complexities of validating comprehensive cancer next-generation sequencing (NGS) panels, competition from commercial laboratories, and the reimbursement and regulatory hurdles inherent in high-complexity testing. Cross-institutional collaborations, including shared assay content and interpretative frameworks, are a valuable element to academic laboratory success. To address these and other needs, the Genomics Organization for Academic Laboratories (GOAL) was conceived in 2018, incorporated in 2020 and has grown to include 29 participating institutions in 2022. Here, we describe the mission of GOAL, its structure, and the outcomes and projects undertaken in its first years.
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Affiliation(s)
- Dara L. Aisner
- Department of Pathology, University of Colorado, Denver, CO, USA
| | | | - Daniel Jones
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Melvin Limson
- Genomics Organization for Academic Laboratories and the Association of Pathology Chairs, Wilmington, DE, USA
| | - Jennifer Morrissette
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremy P. Segal
- Department of Pathology, University of Chicago, Chicago, IL, USA
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Bessi S, Pepe F, Russo G, Pisapia P, Ottaviantonio M, Biancalani F, Iaccarino A, Russo M, Biancalani M, Troncone G, Malapelle U. Comparison of two next-generation sequencing-based approaches for liquid biopsy analysis in patients with non-small cell lung cancer: a multicentre study. J Clin Pathol 2023; 76:206-210. [PMID: 35701144 DOI: 10.1136/jclinpath-2022-208308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
In the era of personalised medicine, testing for an increasing number of predictive biomarkers is becoming a priority. However, tissue biopsies from these patients are oftentimes insufficient for conventional approaches, a common issue that deprives them of the clinical benefits of biomarker-directed treatments. To tackle this problem, many clinical laboratories are resorting to circulating tumour DNA (ctDNA), which is becoming increasingly appreciated as a valuable source for biomarker testing. In this context, next-generation sequencing (NGS) has become essential. Indeed, different NGS systems are able to detect several clinically relevant low-frequency hot-spot mutations simultaneously in a single run. However, their reproducibility in the analysis of ctDNA has not yet been investigated. The purpose of this study was to evaluate the reproducibility of using Illumina MiSeq and Thermo Fisher Ion S5 Plus platforms to assess pathogenic alterations in non-small cell lung cancer (NSCLC) liquid biopsy specimens. Using the in vitro diagnostic (IVD) NGS panel Myriapod NGS Cancer panel DNA (Diatech Pharmacogenetics) on MiSeq platform (Illumina), we reanalysed ctDNA extracted from a retrospective series of n=40 patients with advanced NSCLC previously tested with a custom NGS panel (SiRe) on Thermo Fisher Ion S5 Plus system. Overall, 13 out of 40 (32.5%) ctDNA samples displayed pathogenic alterations in at least two genes, namely, EGFR and KRAS A concordance rate of 100% was identified between the two methodologies in terms of sample mutational status and total number of detected variables. All NGS platforms featured a high degree of concordance.
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Affiliation(s)
- Silvia Bessi
- Departmental Structure of Oncological Molecular Pathology, Azienda USL Toscana Centro, Prato, Italy
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Marco Ottaviantonio
- Departmental Structure of Oncological Molecular Pathology, Azienda USL Toscana Centro, Prato, Italy
| | | | | | - Maria Russo
- Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Biancalani
- Morphological Diagnostic and Biomolecular Characterization Area, Complex Unit of Pathological Anatomy, Azienda USL Toscana Centro, Prato, Italy
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Malapelle U, Pepe F, Pisapia P, Sgariglia R, Nacchio M, Barberis M, Bilh M, Bubendorf L, Büttner R, Cabibi D, Castiglia M, De Andrea CE, de Biase D, Dumur CI, Fontanini G, Freire J, Gristina V, Hofman P, Ilie M, Lozano MD, Merkelbach-Bruse S, Pappesch R, Pelusi N, Roma G, Russo A, Savic S, Siemanowski J, Tallini G, Tischler V, Vander Borght S, Weynand B, Xu T, Troncone G. TargetPlex FFPE-Direct DNA Library Preparation Kit for SiRe NGS panel: an international performance evaluation study. J Clin Pathol 2022; 75:416-421. [PMID: 33766954 DOI: 10.1136/jclinpath-2021-207450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 02/05/2023]
Abstract
AIM Next generation sequencing (NGS) represents a key diagnostic tool to identify clinically relevant gene alterations for treatment-decision making in cancer care. However, the complex manual workflow required for NGS has limited its implementation in routine clinical practice. In this worldwide study, we validated the clinical performance of the TargetPlex FFPE-Direct DNA Library Preparation Kit for NGS analysis. Impressively, this new assay obviates the need for separate, labour intensive and time-consuming pre-analytical steps of DNA extraction, purification and isolation from formalin-fixed paraffin embedded (FFPE) specimens in the NGS workflow. METHODS The TargetPlex FFPE-Direct DNA Library Preparation Kit, which enables NGS analysis directly from FFPE, was specifically developed for this study by TargetPlex Genomics Pleasanton, California. Eleven institutions agreed to take part in the study coordinated by the Molecular Cytopathology Meeting Group (University of Naples Federico II, Naples, Italy). All participating institutions received a specific Library Preparation Kit to test eight FFPE samples previously assessed with standard protocols. The analytical parameters and mutations detected in each sample were then compared with those previously obtained with standard protocols. RESULTS Overall, 92.8% of the samples were successfully analysed with the TargetPlex FFPE-Direct DNA Library Preparation Kit on Thermo Fisher Scientific and Illumina platforms. Altogether, in comparison with the standard workflow, the TargetPlex FFPE-Direct DNA Library Preparation Kit was able to detect 90.5% of the variants. CONCLUSION The TargetPlex FFPE-Direct DNA Library Preparation Kit combined with the SiRe panel constitutes a convenient, practical and robust cost-saving solution for FFPE NGS analysis in routine practice.
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Affiliation(s)
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | | | - Massimo Barberis
- Clinic Unit of Histopathology and Molecular Diagnostics, Istituto Europeo di Oncologia, Milano, Italy
| | - Michel Bilh
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Reinhard Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Daniela Cabibi
- Health Promotion Sciences, Maternal and Infantile Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Marta Castiglia
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Dario de Biase
- Medicine (DIMES)a Hospital, Anatomic Pathology Unit, University of Bologna, Bologna, Italy
| | - Catherine I Dumur
- Molecular Diagnostic Department, Aurora Diagnostics, Jacksonville, Florida, USA
| | - Gabriella Fontanini
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Javier Freire
- Pathology, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Valerio Gristina
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Marius Ilie
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Nice, France
| | - Maria Dolores Lozano
- Pathology, Universidad de Navarra-Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Roberto Pappesch
- Department of Pathology, University of Cologne, Cologne, Germany
| | | | - Gianluca Roma
- R&D Department, TargetPlex Genomics, Belmont, California, USA
| | - Antonio Russo
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Spasenija Savic
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | | | | | | | - Sara Vander Borght
- Department of Pathology, Katholieke Universiteit Leuven UZ Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Pathology, Katholieke Universiteit Leuven UZ Leuven, Leuven, Belgium
| | - Tom Xu
- R&D Department, SenseCare Medicals, Inc, Pleasanton, California, USA
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Malapelle U, De Luca C, Iaccarino A, Pepe F, Pisapia P, Russo M, Sgariglia R, Nacchio M, Vigliar E, Bellevicine C, Schmitt FC, Troncone G. Predictive molecular pathology in the time of COVID-19. J Clin Pathol 2021; 74:234-237. [PMID: 32434770 PMCID: PMC7242869 DOI: 10.1136/jclinpath-2020-206711] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 12/22/2022]
Abstract
AIMS In the time of COVID-19, predictive molecular pathology laboratories must still timely select oncological patients for targeted treatments. However, the need to respect social distancing measures may delay results generated by laboratory-developed tests based on sequential steps a long hands-on time. Laboratory workflows should now be simplified. METHODS The organisation of the University of Naples Federico II predictive pathology laboratory was assessed before (March-April 2019) and during (March-April 2020) the Italian lockdown. RESULTS The number of patients undergoing single or multiple biomarker testing was similar in 2019 (n=43) and in 2020 (n=45). Considering adequate samples for molecular testing, before the outbreak, next-generation sequencing was mostly used (35/42, 83.3%). Testing six genes had a reagent cost of €98/patient. Conversely, in 2020, almost all cases (38/41, 92.7%) were analysed by automated testing. This latter had for any single assay/gene a significant reagent cost (€95-€136) and a faster mean turnaround time (5.3 vs 7.9 working days). CONCLUSION In the times of coronavirus, laboratory fully automated platforms simplify predictive molecular testing. Laboratory staff may be more safely and cost-effectively managed.
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Affiliation(s)
| | | | | | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Maria Russo
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | - Elena Vigliar
- Public Health, University of Naples Federico II, Naples, Italy
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Vigliar E, Iaccarino A, Sciortino M, De Luca C, Malapelle U, Bellevicine C, Troncone G. Molecular predictive testing in precision oncology: The Italian experience. Cancer Cytopathol 2021; 128:622-628. [PMID: 32885914 DOI: 10.1002/cncy.22290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 12/24/2022]
Abstract
In this review, we describe molecular pathology testing to predict response to targeted treatment of solid tumors, focusing on Italian routine clinical practice. The combination of the universal health care system organized at national, regional, and local levels has led a decentralized model, with a large number of local laboratories performing in-house molecular testing following guidelines issued and external quality assessment organized by the Italian Society of Pathology and Cytopathology-Italian Division of the International Academy of Pathology. In this framework, in the early days of predictive testing, sponsored informatics platforms support to set up national programs that aimed to integrate the activity of oncologists and pathologists to test cancer patients for druggable alterations. More recently, reimbursement for molecular testing is being covered completely by the Italian National Health Service. In the near future, considering the development of complex technologies, we expect that outsourcing samples to next-generation sequencing referral laboratories will take place.
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Affiliation(s)
- Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Concomitant Rare KRAS and BRAF Mutations in Lung Adenocarcinoma: A Case Report. JOURNAL OF MOLECULAR PATHOLOGY 2020. [DOI: 10.3390/jmp1010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In July 2020, an active smoker, 63-year old man was admitted to the oncology unit of A.O.R.N. Sant’Anna e San Sebastiano (Caserta, Italy). Chest radiology highlighted right pleural effusion. Total-body CT scanning revealed a solid lesion with lobulated contours in the apical segment of the upper right lobe. The patient’s oncologist requested a molecular assessment of EGFR, ALK, ROS1, BRAF, and KRAS, as well as an evaluation of PD-L1 expression level. To this end, we carried out NGS analysis, on DNA extracted from cytospins, by adopting a custom-designed NGS panel (SiRe®). Overall, no actionable mutations in the tested genes were identified. Conversely, concomitant BRAF exon 11 p.G469A and a KRAS exon 4 p.A146T mutations were detected. Owing to the limited data on the presence of KRAS exon 4 p.A146T point mutation in lung adenocarcinoma patients, a further molecular confirmatory analysis was carried out with a dedicated KRAS cartridge on a fully automated real time polymerase chain reaction. When DNA was extracted from the TTF-1 positive tumor cell slide, the same KRAS alteration was observed. Unfortunately, the patient died in August 2020 before having the chance to start any type of treatment.
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Troncone G, Hofman P. Pathologists and the coronavirus distraction effect. J Clin Pathol 2020; 74:205-206. [PMID: 32499225 DOI: 10.1136/jclinpath-2020-206807] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/03/2022]
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de Biase D, Acquaviva G, Visani M, Sanza V, Argento CM, De Leo A, Maloberti T, Pession A, Tallini G. Molecular Diagnostic of Solid Tumor Using a Next Generation Sequencing Custom-Designed Multi-Gene Panel. Diagnostics (Basel) 2020; 10:diagnostics10040250. [PMID: 32340363 PMCID: PMC7236002 DOI: 10.3390/diagnostics10040250] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 02/05/2023] Open
Abstract
Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid lesions. We report a custom-designed 128 multi-gene panel engineered to cover the relevant targets in 22 oncogene/oncosuppressor genes for the analysis of the solid tumors most frequently subjected to routine genotyping. A total of 1695 solid tumors were analyzed for panel validation. The analytical sensitivity is 5%. Analytical validation: (i) Accuracy: sequencing results obtained using the multi-gene panel are concordant using two different NGS platforms and single-gene approach sequencing (100% of 83 cases); (ii) Precision: consistent results are obtained in the samples analyzed twice with the same platform (100% of 20 cases). Clinical validation: the frequency of mutations identified in different tumor types is consistent with the published literature. This custom-designed multi-gene panel allows to analyze with high sensitivity and throughput 22 oncogenes/oncosuppressor genes involved in diagnostic/prognostic/predictive characterization of central nervous system tumors, non-small-cell lung carcinomas, colorectal carcinomas, thyroid nodules, pancreatic lesions, melanoma, oral squamous carcinomas and gastrointestinal stromal tumors.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
- Correspondence: ; Tel.: +39-051-2144717; Fax: +39-051-6363689
| | - Viviana Sanza
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Chiara M. Argento
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Antonio De Leo
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Thais Maloberti
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
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