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Stenzinger A, Vogel A, Lehmann U, Lamarca A, Hofman P, Terracciano L, Normanno N. Molecular profiling in cholangiocarcinoma: A practical guide to next-generation sequencing. Cancer Treat Rev 2024; 122:102649. [PMID: 37984132 DOI: 10.1016/j.ctrv.2023.102649] [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: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Cholangiocarcinomas (CCA) are a heterogeneous group of tumors that are classified as intrahepatic, perihilar, or distal according to the anatomic location within the biliary tract. Each CCA subtype is associated with distinct genomic alterations, including single nucleotide variants, copy number variants, and chromosomal rearrangements or gene fusions, each of which can influence disease prognosis and/or treatment outcomes. Molecular profiling using next-generation sequencing (NGS) is a powerful technique for identifying unique gene variants carried by an individual tumor, which can facilitate their accurate diagnosis as well as promote the optimal selection of gene variant-matched targeted treatments. NGS is particularly useful in patients with CCA because between one-third and one-half of these patients have genomic alterations that can be targeted by drugs that are either approved or in clinical development. NGS can also provide information about disease evolution and secondary resistance alterations that can develop during targeted therapy, and thus facilitate assessment of prognosis and choice of alternative targeted treatments. Pathologists play a critical role in assessing the viability of biopsy samples for NGS, and advising treating clinicians whether NGS can be performed and which of the available platforms should be used to optimize testing outcomes. This review aims to provide clinical pathologists and other healthcare professionals with practical step-by-step guidance on the use of NGS for molecular profiling of patients with CCA, with respect to tumor biopsy techniques, pre-analytic sample preparation, selecting the appropriate NGS panel, and understanding and interpreting results of the NGS test.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology Heidelberg (IPH), Center for Molecular Pathology, University Hospital Heidelberg, In Neuenheimer Feld 224, 69120 Heidelberg, Building 6224, Germany.
| | - Arndt Vogel
- Division of Gastroenterology and Hepatology, Toronto General Hospital Medical Oncology, Princess Margaret Cancer Centre, Schwartz Reisman Liver Research Centre, 200 Elizabeth Street, Office: 9 EB 236 Toronto, ON, M5G 2C4, Canada.
| | - Ulrich Lehmann
- Institute for Pathology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
| | - Angela Lamarca
- Department of Medical Oncology, Oncohealth Institute, Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Fundación Jiménez Díaz University Hospital, Av. de los Reyes Católicos, 2, 28040 Madrid, Spain; Department of Medical Oncology, The Christie NHS Foundation Trust, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, IHU RespirERA, Siège de l'Université: Grand Château, 28 Avenue de Valrose, 06103 Nice CEDEX 2, France.
| | - Luigi Terracciano
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 4, 20072 Pieve Emanuele, Milan, Italy; IRCCS Humanitas Research Hospital, Via Alessandro Manzoni, 56, 20089 Rozzano, Milan, Italy.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
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Betti M, Maria Salzano C, Massacci A, D'Antonio M, Grassucci I, Marcozzi B, Canfora M, Melucci E, Buglioni S, Casini B, Gallo E, Pescarmona E, Ciliberto G, Pallocca M. Development of a Somatic Variant Registry in a National Cancer Center: towards Molecular Real World Data preparedness. J Biomed Inform 2023; 142:104394. [PMID: 37209976 DOI: 10.1016/j.jbi.2023.104394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/21/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023]
Abstract
The Biomedical Research field is currently advancing to develop Clinical Trials and translational projects based on Real World Evidence. To make this transition feasible, clinical centers need to work toward Data Accessibility and Interoperability. This task is particularly challenging when applied to Genomics, that entered in routinary screening in the last years via mostly amplicon-based Next-Generation Sequencing panels. Said experiments produce up to hundreds of features per patient, and their summarized results are often stored in static clinical reports, making critical information inaccessible to automated access and Federated Search consortia. In this study, we present a reanalysis of 4620 solid tumor sequencing samples in five different histology settings. Furthermore, we describe all the Bioinformatics and Data Engineering processes that were put in place in order to create a Somatic Variant Registry able to deal with the large biotechnological variability of routinary Genomics Profiling.
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Affiliation(s)
- Martina Betti
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Chiara Maria Salzano
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Alice Massacci
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Mattia D'Antonio
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Isabella Grassucci
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Benedetta Marcozzi
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Marco Canfora
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Elisa Melucci
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Simonetta Buglioni
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Beatrice Casini
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Enzo Gallo
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Edoardo Pescarmona
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Matteo Pallocca
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
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Caliez O, Pietrasz D, Ksontini F, Doat S, Simon JM, Vaillant JC, Taly V, Laurent-Puig P, Bachet JB. Circulating tumor DNA: a help to guide therapeutic strategy in patients with borderline and locally advanced pancreatic adenocarcinoma? Dig Liver Dis 2022; 54:1428-1436. [PMID: 35120842 DOI: 10.1016/j.dld.2022.01.126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND prognostic biomarkers could be useful to better select patients with borderline resectable (BR) or locally advanced (LA) pancreatic adenocarcinoma (PA) for chemoradiotherapy (CRT) and/or secondary resection. AIMS The main objective of this work was to study characteristics, received treatments and prognostic of patients with BR or LA PA according to their baseline circulating tumor DNA status and, for secondary objective, neutrophil-to-lymphocyte Ratio (NLR). METHODS ctDNA status at baseline was determined using Next Generation Sequencing in a consecutive monocentric cohort of patients with a BR or LA PA. RESULTS 69 patients were included, 31 with BR PA and 38 with LA PA. 14 (20.3%) patients had baseline positive ctDNA. Five (7.8%) patients had NLR> 5. Patients with positive ctDNA had 3.7 months shorter progression free survival (p = 0.006). Patients with positive ctDNA had earlier progression after the beginning of CRT (4.4 vs 7.1 months; p = 0.068) and shorter relapse free survival after secondary resection (9.2 vs 22.9 months; p = 0.016). CONCLUSIONS positive ctDNA at baseline was associated with a worse prognosis in patients with BR or LA PA. These data are exploratory and must be confirmed in further prospective trials.
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Affiliation(s)
- Olivier Caliez
- Department of Gastroenterology, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; French National Institute of Health and Medical Research (INSERM), Centre de Recherche des Cordeliers, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université de Paris, Paris, France; Sorbonne Université, UPMC, Paris 6, France
| | - Daniel Pietrasz
- French National Institute of Health and Medical Research (INSERM), Centre de Recherche des Cordeliers, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université de Paris, Paris, France; Department of Digestive Surgery, Hôpital Paul Brousse, Villejuif, France
| | - Feryel Ksontini
- Department of Oncology, Institute Salah-Azaïz, Tunis, Tunisia
| | - Solène Doat
- Department of Gastroenterology, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jean-Marc Simon
- Department of Radiation Oncology, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jean-Christophe Vaillant
- Department of Digestive Surgery, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Valerie Taly
- French National Institute of Health and Medical Research (INSERM), Centre de Recherche des Cordeliers, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université de Paris, Paris, France
| | - Pierre Laurent-Puig
- French National Institute of Health and Medical Research (INSERM), Centre de Recherche des Cordeliers, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université de Paris, Paris, France
| | - Jean-Baptiste Bachet
- Department of Gastroenterology, La Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; French National Institute of Health and Medical Research (INSERM), Centre de Recherche des Cordeliers, Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université de Paris, Paris, France; Sorbonne Université, UPMC, Paris 6, France.
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Vauchier C, Pluvy J, Theou-Anton N, Soussi G, Poté N, Brosseau S, Gounant V, Zalcman G. Poor performance status patient with long-lasting major response to pembrolizumab in advanced non-small-cell lung cancer with coexisting POLE mutation and deficient mismatch repair pathway. Lung Cancer 2021; 160:28-31. [PMID: 34371300 DOI: 10.1016/j.lungcan.2021.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/13/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Immunotherapy with immune checkpoint inhibitors (ICIs) represents a major breakthrough in lung cancer treatment. For patients with advanced non-small-cell lung cancer (NSCLC) and poor performance status (PS), the availability of sensitivity markers to immune-checkpoint inhibitors (ICI) would be useful for attending physicians and assist them in their decision-making process. Deficient mismatch repair (dMMR) can lead to high microsatellite instability (MSI-H) and coexist with mutations in polymerase proofreading (DNA polymerase Epsilon POLE and delta 1 POLD1) with a specific mutational signature. This would result in high tumor mutational burden and programmed cell death protein ligand 1 (PD-L1) overexpression. We report herein on a NSCLC case with MSI-H and POLE mutation in a patient with inaugural poor general condition, who exhibited prolonged response to anti-programmed cell death protein (PD-1) therapy. Additionally, there was a marked improvement of the patient's performance status, from PS 3 before ICI administration to PS 1 upon ICI therapy.
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Affiliation(s)
- Charles Vauchier
- Department of Thoracic Oncology & CIC1425-CLIP2 Early Phase Cancer Clinical Trials Unit, University Hospital Bichat-Claude Bernard, Université de Paris, Paris, France
| | - Johan Pluvy
- Department of Thoracic Oncology & CIC1425-CLIP2 Early Phase Cancer Clinical Trials Unit, University Hospital Bichat-Claude Bernard, Université de Paris, Paris, France
| | - Nathalie Theou-Anton
- Department of Genetics, University Hospital Bichat-Claude Bernard, Université de Paris, Paris, France
| | - Ghassen Soussi
- Department of Thoracic Oncology & CIC1425-CLIP2 Early Phase Cancer Clinical Trials Unit, University Hospital Bichat-Claude Bernard, Université de Paris, Paris, France
| | - Nicolas Poté
- Department of Pathology, University Hospital Bichat-Claude Bernard, UMR INSERM 1152, Université de Paris, Paris, France
| | - Solenn Brosseau
- Department of Thoracic Oncology & CIC1425-CLIP2 Early Phase Cancer Clinical Trials Unit, University Hospital Bichat-Claude Bernard, Université de Paris, Paris, France; U830 INSERM "Cancer, Heterogeneity, Instability and Plasticity", Institut Curie Research Center, Paris, France
| | - Valérie Gounant
- Department of Thoracic Oncology & CIC1425-CLIP2 Early Phase Cancer Clinical Trials Unit, University Hospital Bichat-Claude Bernard, Université de Paris, Paris, France
| | - Gérard Zalcman
- Department of Thoracic Oncology & CIC1425-CLIP2 Early Phase Cancer Clinical Trials Unit, University Hospital Bichat-Claude Bernard, Université de Paris, Paris, France; U830 INSERM "Cancer, Heterogeneity, Instability and Plasticity", Institut Curie Research Center, Paris, France.
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Clinical Application of Next-Generation Sequencing of Plasma Cell-Free DNA for Genotyping Untreated Advanced Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13112707. [PMID: 34070940 PMCID: PMC8199488 DOI: 10.3390/cancers13112707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Plasma ctDNA is a material source for molecular analysis particularly useful when tissue is not available or sufficient. NGS-based plasma genotyping should be integrated into the clinical workup of newly diagnosed advanced NSCLC. Abstract Background: Analysis of circulating tumor DNA (ctDNA) has remarkable potential as a non-invasive lung cancer molecular diagnostic method. This prospective study addressed the clinical value of a targeted-gene amplicon-based plasma next-generation sequencing (NGS) assay to detect actionable mutations in ctDNA in patients with newly diagnosed advanced lung adenocarcinoma. Methods: ctDNA test performance and concordance with tissue NGS were determined, and the correlation between ctDNA findings, clinical features, and clinical outcomes was evaluated in 115 patients with paired plasma and tissue samples. Results: Targeted-gene NGS-based ctDNA and NGS-based tissue analysis detected 54 and 63 genomic alterations, respectively; 11 patients presented co-mutations, totalizing 66 hotspot mutations detected, 51 on both tissue and plasma, 12 exclusively on tissue, and 3 exclusively on plasma. NGS-based ctDNA revealed a diagnostic performance with 81.0% sensitivity, 95.3% specificity, 94.4% PPV, 83.6% NPV, test accuracy of 88.2%, and Cohen’s Kappa 0.764. PFS and OS assessed by both assays did not significantly differ. Detection of ctDNA alterations was statistically associated with metastatic disease (p = 0.013), extra-thoracic metastasis (p = 0.004) and the number of organs involved (p = 0.010). Conclusions: This study highlights the potential use of ctDNA for mutation detection in newly diagnosed NSCLC patients due to its high accuracy and correlation with clinical outcomes.
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Fenizia F, Alborelli I, Costa JL, Vollbrecht C, Bellosillo B, Dinjens W, Endris V, Heydt C, Leonards K, Merkelback-Bruse S, Pfarr N, van Marion R, Allen C, Chaudhary R, Gottimukkala R, Hyland F, Wong-Ho E, Jermann P, Machado JC, Hummel M, Stenzinger A, Normanno N. Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis: Results from the Onconetwork Immuno-Oncology Consortium. J Mol Diagn 2021; 23:882-893. [PMID: 33964449 DOI: 10.1016/j.jmoldx.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor mutation burden (TMB) is evaluated as a biomarker of response to immunotherapy. We present the efforts of the Onconetwork Immuno-Oncology Consortium to validate a commercial targeted sequencing test for TMB calculation. A three-phase study was designed to validate the Oncomine Tumor Mutational Load (OTML) assay at nine European laboratories. Phase 1 evaluated reproducibility and accuracy on seven control samples. In phase 2, six formalin-fixed, paraffin-embedded samples tested with FoundationOne were reanalyzed with the OTML panel to evaluate concordance and reproducibility. Phase 3 involved analysis of 90 colorectal cancer samples with known microsatellite instability (MSI) status to evaluate TMB and MSI association. High reproducibility of TMB was demonstrated among the sites in the first and second phases. Strong correlation was also detected between mean and expected TMB in phase 1 (r2 = 0.998) and phase 2 (r2 = 0.96). Detection of actionable mutations was also confirmed. In colorectal cancer samples, the expected pattern of MSI-high/high-TMB and microsatellite stability/low-TMB was present, and gene signatures produced by the panel suggested the presence of a POLE mutation in two samples. The OTML panel demonstrated robustness and reproducibility for TMB evaluation. Results also suggest the possibility of using the panel for mutational signatures and variant detection. Collaborative efforts between academia and companies are crucial to accelerate the translation of new biomarkers into clinical research.
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Affiliation(s)
- Francesca Fenizia
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - Ilaria Alborelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jose Luis Costa
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Claudia Vollbrecht
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | - Winand Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, France
| | - Katharina Leonards
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Nicole Pfarr
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Christopher Allen
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Ruchi Chaudhary
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Rajesh Gottimukkala
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Fiona Hyland
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Elaine Wong-Ho
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Philip Jermann
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jose Carlos Machado
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Michael Hummel
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy.
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8
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Marin E, Reyes R, Arcocha A, Viñolas N, Mezquita L, Gonzalvo E, Saez de Gordoa K, Jares P, Reguart N, Teixido C. Prospective Evaluation of Single Nucleotide Variants by Two Different Technologies in Paraffin Samples of Advanced Non-Small Cell Lung Cancer Patients. Diagnostics (Basel) 2020; 10:E902. [PMID: 33153192 PMCID: PMC7693424 DOI: 10.3390/diagnostics10110902] [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: 10/07/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022] Open
Abstract
Targeted therapies are a new paradigm in lung cancer management. Next-generation sequencing (NGS) techniques have allowed for simultaneous testing of several genes in a rapid and efficient manner; however, there are other molecular diagnostic tools such as the nCounter® Vantage 3D single nucleotide variants (SNVs) solid tumour panel which also offer important benefits regarding sample input and time-to-response, making them very attractive for daily clinical use. This study aimed to test the performance of the Vantage panel in the routine workup of advanced non-squamous non-small cell lung cancer (NSCLC) patients and to validate and compare its outputs with the Oncomine Solid Tumor (OST) panel DNA kit, the standard technique in our institution. Two parallel multiplexed approaches were performed based on DNA NGS and direct digital detection of DNA with nCounter® technology to evaluate SNVs. A total of 42 advanced non-squamous NSCLC patients were prospectively included in the study. Overall, 95% of samples were successfully characterized by both technologies. The Vantage panel accounted for a sensitivity of 95% and a specificity of 82%. In terms of predictive values, the probability of truly presenting the SNV variant when it is detected by the nCounter panel was 82%, whereas the probability of not presenting the SNV variant when it is not detected by the platform was 95%. Finally, Cohen's Kappa coefficient was 0.76, indicating a substantial correlation grade between OST and Vantage panels. Our results make nCounter an analytically sensitive, practical and cost-effective tool.
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Affiliation(s)
- Elba Marin
- Division of Medical Oncology, Hospital Clínic, 08036 Barcelona, Spain; (E.M.); (R.R.); (A.A.); (N.V.); (L.M.); (N.R.)
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi I Sunyer, 08036 Barcelona, Spain
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
| | - Roxana Reyes
- Division of Medical Oncology, Hospital Clínic, 08036 Barcelona, Spain; (E.M.); (R.R.); (A.A.); (N.V.); (L.M.); (N.R.)
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
| | - Ainara Arcocha
- Division of Medical Oncology, Hospital Clínic, 08036 Barcelona, Spain; (E.M.); (R.R.); (A.A.); (N.V.); (L.M.); (N.R.)
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
| | - Nuria Viñolas
- Division of Medical Oncology, Hospital Clínic, 08036 Barcelona, Spain; (E.M.); (R.R.); (A.A.); (N.V.); (L.M.); (N.R.)
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi I Sunyer, 08036 Barcelona, Spain
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
| | - Laura Mezquita
- Division of Medical Oncology, Hospital Clínic, 08036 Barcelona, Spain; (E.M.); (R.R.); (A.A.); (N.V.); (L.M.); (N.R.)
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi I Sunyer, 08036 Barcelona, Spain
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
| | - Elena Gonzalvo
- Division of Pathology, Hospital Clínic, 08036 Barcelona, Spain; (E.G.); (K.S.d.G.)
| | | | - Pedro Jares
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
- Division of Pathology, Hospital Clínic, 08036 Barcelona, Spain; (E.G.); (K.S.d.G.)
- Molecular Biology Core Facility, Hospital Clínic, 08036 Barcelona, Spain
| | - Noemi Reguart
- Division of Medical Oncology, Hospital Clínic, 08036 Barcelona, Spain; (E.M.); (R.R.); (A.A.); (N.V.); (L.M.); (N.R.)
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi I Sunyer, 08036 Barcelona, Spain
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
| | - Cristina Teixido
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi I Sunyer, 08036 Barcelona, Spain
- Unitat funcional de Tumors Toràcics, Hospital Clínic, 08036 Barcelona, Spain;
- Division of Pathology, Hospital Clínic, 08036 Barcelona, Spain; (E.G.); (K.S.d.G.)
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Gao XH, Li J, Gong HF, Yu GY, Liu P, Hao LQ, Liu LJ, Bai CG, Zhang W. Comparison of Fresh Frozen Tissue With Formalin-Fixed Paraffin-Embedded Tissue for Mutation Analysis Using a Multi-Gene Panel in Patients With Colorectal Cancer. Front Oncol 2020; 10:310. [PMID: 32232001 PMCID: PMC7083147 DOI: 10.3389/fonc.2020.00310] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Next generation sequencing (NGS)-based multi-gene panel tests have been performed to predict the treatment response and prognosis in patients with colorectal cancer (CRC). Whether the multi-gene mutation results of formalin-fixed paraffin-embedded (FFPE) tissues are identical to those of fresh frozen tissues remains unknown. Methods: A 22-gene panel with 103 hotspots was used to detect mutations in paired fresh frozen tissue and FFPE tissue from 118 patients with CRC. Results: In our study, 117 patients (99.2%) had one or more variants, with 226 variants in FFPE tissue and 221 in fresh frozen tissue. Of the 129 variants identified in this study, 96 variants were present in both FFPE and fresh frozen tissues; 27 variants were found in FFPE tissues only; 6 variants were found only in fresh frozen tissues. The mutation results demonstrated >94.0% concordance in all variants, with Kappa coefficient >0.500 in 64.3% (83/129) of variants. At the gene level, concordance ranged from 73.8 to 100.0%, with Kappa coefficient >0.500 in 81.3% (13/16) of genes. Conclusions: The results of mutation analysis performed with a multi-gene panel and FFPE and fresh frozen tissue were highly concordant in patients with CRC, at both the variant and gene levels. There were, however, some important differences in mutation results between the two tissue types. Therefore, fresh frozen tissue should not routinely be replaced with FFPE tissue for mutation analysis with a multi-gene panel. Rather, FFPE tissue is a reasonable alternative for fresh frozen tissue when the latter is unavailable.
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Affiliation(s)
- Xian Hua Gao
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Juan Li
- Department of Nephrology, Changhai Hospital, Shanghai, China
| | - Hai Feng Gong
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Guan Yu Yu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Peng Liu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Li Qiang Hao
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Lian Jie Liu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Chen Guang Bai
- Department of Pathology, Changhai Hospital, Shanghai, China
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
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Papachristos A, Kemos P, Katsila T, Panoilia E, Patrinos GP, Kalofonos H, Sivolapenko GB. VEGF-A and ICAM-1 Gene Polymorphisms as Predictors of Clinical Outcome to First-Line Bevacizumab-Based Treatment in Metastatic Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20225791. [PMID: 31752122 PMCID: PMC6888109 DOI: 10.3390/ijms20225791] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/10/2019] [Accepted: 11/13/2019] [Indexed: 12/11/2022] Open
Abstract
Bevacizumab is used to treat metastatic colorectal cancer (mCRC). However, there are still no available predictors of clinical outcomes. We investigated selected single nucleotide polymorphisms (SNPs) in the genes involved in VEGF-dependent and -independent angiogenesis pathways and other major intracellular signaling pathways involved in the pathogenesis of mCRC as an attempt to find predictors of clinical outcome. Forty-six patients treated with first-line bevacizumab-based chemotherapy were included in this study with a 5 year follow up. Genomic DNA was isolated from whole blood for the analysis of VEGF-A (rs2010963, 1570360, rs699947), ICAM-1 (rs5498, rs1799969) SNPs and from tumor tissue for the detection of genomic variants in KRAS, NRAS, BRAF genes. PCR and next generation sequencing were used for the analysis. The endpoints of the study were progression-free survival (PFS) and overall survival (OS). The VEGF-A rs699947 A/A allele was associated with increased PFS (p = 0.006) and OS (p = 0.043). The ICAM-1 rs1799969 G/A allele was associated with prolonged OS (p = 0.036). Finally, BRAF wild type was associated with increased OS (p = 0.027). We identified VEGF-A and ICAM-1 variants in angiogenesis and other major intracellular signaling pathways, such as BRAF, that can predict clinical outcome upon bevacizumab administration. These identified biomarkers could be used to select patients with mCRC who may achieve long-term responses and benefit from bevacizumab-based therapies.
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Affiliation(s)
- Apostolos Papachristos
- Laboratory of Pharmacokinetics, Department of Pharmacy, School of Health Sciences, University of Patras, Patra 26504, Greece; (A.P.); (E.P.)
- Division of Cancer, University College London Hospital NHS Foundation Trust, London NW12BU, UK
| | - Polychronis Kemos
- Centre for Immunobiology, Blizard institute, Queen Mary University of London, London E12AT, UK;
| | - Theodora Katsila
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patra 26504, Greece; (T.K.); (G.P.P.)
- Institute of Chemical Biology, National Hellenic Research Centre, Athens 11635, Greece
| | - Eirini Panoilia
- Laboratory of Pharmacokinetics, Department of Pharmacy, School of Health Sciences, University of Patras, Patra 26504, Greece; (A.P.); (E.P.)
| | - George P. Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patra 26504, Greece; (T.K.); (G.P.P.)
| | - Haralabos Kalofonos
- Division of Medical Oncology, University Hospital of Patras, Patra 26504, Greece;
| | - Gregory B. Sivolapenko
- Laboratory of Pharmacokinetics, Department of Pharmacy, School of Health Sciences, University of Patras, Patra 26504, Greece; (A.P.); (E.P.)
- Correspondence: ; Tel.: +30-26-1096-2324
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11
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Targeted Gene Next-Generation Sequencing Panel in Patients with Advanced Lung Adenocarcinoma: Paving the Way for Clinical Implementation. Cancers (Basel) 2019; 11:cancers11091229. [PMID: 31443496 PMCID: PMC6770536 DOI: 10.3390/cancers11091229] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/04/2019] [Accepted: 08/15/2019] [Indexed: 12/24/2022] Open
Abstract
Identification of targetable molecular changes is essential for selecting appropriate treatment in patients with advanced lung adenocarcinoma. Methods: In this study, a Sanger sequencing plus Fluorescence In Situ Hybridization (FISH) sequential approach was compared with a Next-Generation Sequencing (NGS)-based approach for the detection of actionable genomic mutations in an experimental cohort (EC) of 117 patients with advanced lung adenocarcinoma. Its applicability was assessed in small biopsies and cytology specimens previously tested for epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutational status, comparing the molecular changes identified and the impact on clinical outcomes. Subsequently, an NGS-based approach was applied and tested in an implementation cohort (IC) in clinical practice. Using Sanger and FISH, patients were classified as EGFR-mutated (n = 22, 18.8%), ALK-mutated (n = 9, 7.7%), and unclassifiable (UC) (n = 86, 73.5%). Retesting the EC with NGS led to the identification of at least one gene variant in 56 (47.9%) patients, totaling 68 variants among all samples. Still, in the EC, combining NGS plus FISH for ALK, patients were classified as 23 (19.7%) EGFR; 20 (17.1%) KRAS; five (4.3%) B-Raf proto-oncogene (BRAF); one (0.9%) Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2); one (0.9%) STK11; one (0.9%) TP53, and nine (7.7%) ALK mutated. Only 57 (48.7%) remained genomically UC, reducing the UC rate by 24.8%. Fourteen (12.0%) patients presented synchronous alterations. Concordance between NGS and Sanger for EGFR status was very high (κ = 0.972; 99.1%). In the IC, a combined DNA and RNA NGS panel was used in 123 patients. Genomic variants were found in 79 (64.2%). In addition, eight (6.3%) EML4-ALK, four (3.1%), KIF5B-RET, four (3.1%) CD74-ROS1, one (0.8%) TPM3-NTRK translocations and three (2.4%) exon 14 skipping MET Proto-Oncogene (MET) mutations were detected, and 36% were treatable alterations. Conclusions: This study supports the use of NGS as the first-line test for genomic profiling of patients with advanced lung adenocarcinoma.
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12
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Barman-Aksözen J, Suter L, Wegmann F, Meienberg J, Minder AE, Beer M, Komminoth P, Minder EI, Schneider-Yin X. A next-generation-sequencing panel for mutational analysis of dominant acute hepatic porphyrias. Scandinavian Journal of Clinical and Laboratory Investigation 2019; 79:305-313. [PMID: 31154864 DOI: 10.1080/00365513.2019.1622030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Molecular diagnosis of autosomal dominant acute hepatic porphyrias (AHPs) plays an important role in the management of these disorders. To introduce next generation sequencing (NGS) to the porphyria diagnosis, we designed a panel that contained four genes, ALAS1, HMBS, CPOX and PPOX for mutational analysis of acute intermittent porphyria (AIP), hereditary coproporphyria (HCP) and variegate porphyria (VP). To validate the AHP panel, 30 samples with known pathogenic variants as determined by Sanger sequencing, were analyzed using the Ion PGM™. Among them, nine have so far not been reported. The pathogenic variants were identified and annotated manually in IGV by three individuals who were blinded to the Sanger results. The AHP panel consists of 95 amplicons that covers 92% of the coding region of the four genes. Of the 95 amplicons, 93 had an average read-depth of >500 reads. In 29 of the 30 tested samples, pathogenic variants were correctly identified and annotated. The number of reads from the mutated alleles were approximately 50% of the total. The annotation of a 22-bp duplication with NGS differed from that of Sanger by one nucleotide. NGS showed an advantage in allelic discrimination over Sanger sequencing and was also able to detect a known somatic variant in the HMBS gene. The AHP panel will be applied in the initial diagnosis of new patients. Any sequence variations with a frequency of ≥10% will be confirmed by Sanger sequencing. The cost-effectiveness of a NGS approach for AHP in a diagnostic laboratory needs to be further assessed.
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Affiliation(s)
| | - Lukas Suter
- a Institute of Laboratory Medicine, Triemli Hospital , Zurich , Switzerland
| | - Franziska Wegmann
- a Institute of Laboratory Medicine, Triemli Hospital , Zurich , Switzerland
| | - Janine Meienberg
- b Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases , Schlieren-Zurich , Switzerland
| | - Anna Elisabeth Minder
- c Division of Endocrinology, Department of Internal Medicine, Triemli Hospital , Zurich , Switzerland
| | - Marc Beer
- d Institute of Pathology, Triemli Hospital , Zurich , Switzerland
| | - Paul Komminoth
- d Institute of Pathology, Triemli Hospital , Zurich , Switzerland
| | - Elisabeth I Minder
- c Division of Endocrinology, Department of Internal Medicine, Triemli Hospital , Zurich , Switzerland
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13
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Kiniwa Y, Yasuda J, Saito S, Saito R, Motoike IN, Danjoh I, Kinoshita K, Fuse N, Yamamoto M, Okuyama R. Identification of genetic alterations in extramammary Paget disease using whole exome analysis. J Dermatol Sci 2019; 94:229-235. [DOI: 10.1016/j.jdermsci.2019.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
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14
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Rachiglio AM, Fenizia F, Piccirillo MC, Galetta D, Crinò L, Vincenzi B, Barletta E, Pinto C, Ferraù F, Lambiase M, Montanino A, Roma C, Ludovini V, Montagna ES, De Luca A, Rocco G, Botti G, Perrone F, Morabito A, Normanno N. The Presence of Concomitant Mutations Affects the Activity of EGFR Tyrosine Kinase Inhibitors in EGFR-Mutant Non-Small Cell Lung Cancer (NSCLC) Patients. Cancers (Basel) 2019; 11:E341. [PMID: 30857358 PMCID: PMC6468673 DOI: 10.3390/cancers11030341] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
Recent findings suggest that a fraction of EGFR-mutant non-small-cell lung cancers (NSCLC) carry additional driver mutations that could potentially affect the activity of EGFR tyrosine kinase inhibitors (TKIs). We investigated the role of concomitant KRAS, NRAS, BRAF, PIK3CA, MET and ERBB2 mutations (other mutations) on the outcome of 133 EGFR mutant patients, who received first-line therapy with EGFR TKIs between June 2008 and December 2014. Analysis of genomic DNA by Next Generation Sequencing (NGS) revealed the presence of hotspot mutations in genes other than the EGFR, including KRAS, NRAS, BRAF, ERBB2, PIK3CA, or MET, in 29/133 cases (21.8%). A p.T790M mutation was found in 9/133 tumour samples (6.8%). The progression free survival (PFS) of patients without other mutations was 11.3 months vs. 7 months in patients with other mutations (log-rank test univariate: p = 0.047). In a multivariate Cox regression model including the presence of other mutations, age, performance status, smoking status, and the presence of p.T790M mutations, the presence of other mutations was the only factor significantly associated with PFS (Hazard Ratio 1.63, 95% CI 1.04⁻2.58; p = 0.035). In contrast, no correlation was found between TP53 mutations and patients' outcome. These data suggest that a subgroup of EGFR mutant tumours have concomitant driver mutations that might affect the activity of first-line EGFR TKIs.
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Affiliation(s)
- Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Francesca Fenizia
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Maria Carmela Piccirillo
- Clinical Trials Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Domenico Galetta
- Medical Oncology, National Cancer Research Center "Giovanni Paolo II", 70126 Bari, Italy.
| | - Lucio Crinò
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy.
| | - Bruno Vincenzi
- Medical Oncology, Campus Bio-Medico University of Rome, 00128 Rome, Italy.
| | | | - Carmine Pinto
- Medical Oncology, S. Maria Nuova Hospital-IRCCS Reggio Emilia, 42122 Reggio Emilia, Italy.
| | - Francesco Ferraù
- Medical Oncology, "S. Vincenzo" Hospital, 98039 Taormina (ME), Italy.
| | - Matilde Lambiase
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Agnese Montanino
- Medical Oncology, Thoraco-Pulmonary Department, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Vienna Ludovini
- Department of Medical Oncology, Santa Maria della Misericordia Hospital, 06129 Perugia, Italy.
| | | | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Gaetano Rocco
- Thoracic Surgery, Thoraco-Pulmonary Department, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Gerardo Botti
- Surgical Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Francesco Perrone
- Clinical Trials Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Alessandro Morabito
- Medical Oncology, Thoraco-Pulmonary Department, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy.
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15
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Kandhavelu J, Subramanian K, Khan A, Omar A, Ruff P, Penny C. Computational Analysis of miRNA and their Gene Targets Significantly Involved in Colorectal Cancer Progression. Microrna 2019; 8:68-75. [PMID: 30073936 DOI: 10.2174/2211536607666180803100246] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/05/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Globally, colorectal cancer (CRC) is the third most common cancer in women and the fourth most common cancer in men. Dysregulation of small non-coding miRNAs have been correlated with colon cancer progression. Since there are increasing reports of candidate miRNAs as potential biomarkers for CRC, this makes it important to explore common miRNA biomarkers for colon cancer. As computational prediction of miRNA targets is a critical initial step in identifying miRNA: mRNA target interactions for validation, we aim here to construct a potential miRNA network and its gene targets for colon cancer from previously reported candidate miRNAs, inclusive of 10 up- and 9 down-regulated miRNAs from tissues; and 10 circulatory miRNAs. METHODS The gene targets were predicted using DIANA-microT-CDS and TarBaseV7.0 databases. Each miRNA and its targets were analyzed further for colon cancer hotspot genes, whereupon DAVID analysis and mirPath were used for KEGG pathway analysis. RESULTS We have predicted 874 and 157 gene targets for tissue and serum specific miRNA candidates, respectively. The enrichment of miRNA revealed that particularly hsa-miR-424-5p, hsa-miR-96-5p, hsa-miR-1290, hsa-miR-224, hsa-miR-133a and has-miR-363-3p present possible targets for colon cancer hallmark genes, including BRAF, KRAS, EGFR, APC, amongst others. DAVID analysis of miRNA and associated gene targets revealed the KEGG pathways most related to cancer and colon cancer. Similar results were observed in mirPath analysis. A new insight gained in the colon cancer network pathway was the association of hsa-mir-133a and hsa-mir-96-5p with the PI3K-AKT signaling pathway. In the present study, target prediction shows that while hsa-mir-424-5p has an association with mostly 10 colon cancer hallmark genes, only their associations with MAP2 and CCND1 have been experimentally validated. CONCLUSION These miRNAs and their targets require further evaluation for a better understanding of their associations, ultimately with the potential to develop novel therapeutic targets.
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Affiliation(s)
- Jeyalakshmi Kandhavelu
- Oncology Division, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa
| | - Kumar Subramanian
- Oncology Division, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa
| | - Amber Khan
- Oncology Division, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa
| | - Aadilah Omar
- Oncology Division, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa
| | - Paul Ruff
- Oncology Division, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa
| | - Clement Penny
- Oncology Division, Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa
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16
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Clinical significance of multiple gene detection with a 22-gene panel in formalin-fixed paraffin-embedded specimens of 207 colorectal cancer patients. Int J Clin Oncol 2019; 24:141-152. [PMID: 30612269 DOI: 10.1007/s10147-018-1377-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 12/02/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Simultaneous detection of multiple molecular biomarkers is helpful in the prediction of treatment response and prognosis for colorectal cancer (CRC) patients. METHODS A 22-gene panel consisting of 103 hotspot regions was utilized in the formalin-fixed paraffin-embedded (FFPE) tissue samples of 207 CRC patients, using the next-generation sequencing (NGS)-based multiplex PCR technique. Those 22 genes included AKT1, ALK, BRAF, CTNNB1, DDR2, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, KRAS, MAP2K1, MET, NOTCH1, NRAS, PIK3CA, PTEN, SMAD4, STK11, and TP53. RESULTS Of the 207 patients, 193 had one or more variants, with 170, 20, and 3 having one, two, and three mutated genes, respectively. Of the total 414 variants identified in this study, 384, 25, and 5 were single-nucleotide variants, deletion, and insertion. The top four frequently mutated genes were TP53, KRAS, PIK3CA, and FBXW7. There was high consistency between the results of NGS-PCR technique and routine ARMS-PCR in KRAS and BRAF mutation detection. Univariate and multivariate analyses demonstrated that advanced TNM stage, elevated serum CEA, total variants number ≥ 2, AKT1 and PTEN mutation were independent predictors of shorter DFS; poor differentiation, advanced TNM stage, total variants number ≥ 2, BRAF, CTNNB1 and NRAS mutation were independent predictors of shorter OS. CONCLUSIONS It is feasible to detect multiple gene mutations with a 22-gene panel in FFPE CRC specimens. TNM stage and total variants number ≥ 2 were independent predictors of DFS and OS. Detection of multiple gene mutations may provide additional prognostic information to TNM stage in CRC patients.
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17
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Pinto C, Normanno N, Orlandi A, Fenizia F, Damato A, Maiello E, Tamburini E, Di Costanzo F, Tonini G, Bilancia D, Corsi D, Pisconti S, Ferrau F, Gori S, Daniele B, Zaniboni A, Soto Parra H, Frassinetti GL, Iaffaioli RV, Cassata A, Zampino MG, Repetto L, Calegari MA, Barone C. Phase III study with FOLFIRI + cetuximab versus FOLFIRI + cetuximab followed by cetuximab alone in RAS and BRAF WT mCRC. Future Oncol 2018; 14:1339-1346. [PMID: 29846100 DOI: 10.2217/fon-2017-0592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The optimal duration and intensity of first-line therapy in metastatic colorectal cancer patients once they have achieved an objective response is controversial. In a molecularly selected RAS and BRAF wild-type (wt) population, this concern is amplified. Once disease control has been achieved with a combination therapy including an anti-EGFR antibody, further exposure both to cytotoxic drugs and targeted therapy might result only in increased toxicity. In unresectable metastatic RAS and BRAF wt colorectal cancer patients, a deintensified therapy could represent a valuable option that might preserve quality of life. We designed a study to compare FOLFIRI/cetuximab to FOLFIRI/cetuximab for eight cycles followed by cetuximab alone in first-line treatment of RAS and BRAF (wt) metastatic colorectal cancer patients.
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Affiliation(s)
- Carmine Pinto
- Medical Oncology, Clinical Cancer Center, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Nicola Normanno
- Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Campania, Italy
| | - Armando Orlandi
- Oncology Unit, Fondazione Policlinico Universitario "A Gemelli", Roma, Lazio, Italy
| | - Francesca Fenizia
- Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Campania, Italy
| | - Angela Damato
- Medical Oncology, Clinical Cancer Center, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Evaristo Maiello
- Oncology Unit, Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Puglia, Italy
| | - Emiliano Tamburini
- Oncology Unit Azienda Unita Sanitaria Locale della Romagna, Rimini, Emilia-Romagna, Italy
| | | | - Giuseppe Tonini
- Oncology Unit, Università Campus Bio-Medico di Roma, Roma, Lazio, Italy
| | | | - Domenico Corsi
- Oncology Unit, San Giovanni Calabita Hospital, Roma, Lazio, Italy
| | | | | | - Stefania Gori
- Medical Oncology, Clinical Cancer Center, Ospedale Sacro Cuore Don Calabria, Negrar, Veneto, Italy
| | - Bruno Daniele
- Oncology Unit, Azienda Ospedaliera Gaetano Rummo, Benevento, Campania, Italy
| | - Alberto Zaniboni
- Oncology Unit, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, Lombardia, Italy
| | - Héctor Soto Parra
- Oncology Unit, Università degli Studi di Catania Scuola di Facoltà di Medicina, Catania, Sicilia, Italy
| | - Giovanni Luca Frassinetti
- Oncology Unit, IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori Meldola, Emilia-Romagna, Italy
| | - Rosario Vincenzo Iaffaioli
- Oncologia Clinica Sperimentale Addome, Instituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Campania, Italy
| | - Antonio Cassata
- Oncologia Clinica Sperimentale Addome, Instituto Nazionale Tumori IRCCS Fondazione Pascale, Napoli, Campania, Italy
| | | | - Lazzaro Repetto
- Oncology Unit, Ospedale Civile "G Borea", Sanremo, Liguria, Italy
| | | | - Carlo Barone
- Oncology Unit, Fondazione Policlinico Universitario "A Gemelli", Roma, Lazio, Italy
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Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? Acad Pathol 2018; 5:2374289518766521. [PMID: 29761157 PMCID: PMC5944141 DOI: 10.1177/2374289518766521] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.
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Affiliation(s)
- Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Roghayeh Fazeli
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shi Yang
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Raveen Basran
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas Maher
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Daniel Remick
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
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19
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Simultaneous identification of clinically relevant single nucleotide variants, copy number alterations and gene fusions in solid tumors by targeted next-generation sequencing. Oncotarget 2018; 9:22749-22768. [PMID: 29854313 PMCID: PMC5978263 DOI: 10.18632/oncotarget.25229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/05/2018] [Indexed: 01/19/2023] Open
Abstract
In this study, we have set-up a routine pipeline to evaluate the clinical application of Oncomine™ Focus Assay, a panel that allows the simultaneous detection of single nucleotide hotspot mutations in 35 genes, copy number alterations (CNAs) in 19 genes and gene fusions involving 23 genes in cancer samples. For this study we retrospectively selected 106 patients that were submitted to surgical resection for lung, gastric, colon or rectal cancer. We found that 56 patients out of 106 showed at least one alteration (53%), with 47 patients carrying at least one relevant nucleotide variant, 10 patients carrying at least one CNA and 3 patients carrying one gene fusion. On the basis of the mutational profiles obtained, we have identified 22 patients (20.7%) that were potentially eligible for targeted therapy. The most frequently mutated genes across all tumor types included KRAS (30 patients), PIK3CA (16 patients), BRAF (6 patients), EGFR (5 patients), NRAS (4 patients) and ERBB2 (3 patients) whereas CCND1, ERBB2, EGFR and MYC were the genes most frequently subjected to copy number gain. Finally, gene fusions were identified only in lung cancer patients and involved MET [MET(13)–MET(15) fusion] and FGFR3 [FGFR3(chr 17)–TACC3(chr 11)]. In conclusion, we demonstrate that the analysis with a multi-biomarker panel of cancer patients after surgery, may present several potential advantages in clinical daily practice, including the simultaneous detection of different potentially druggable alterations, reasonable costs, short time of testing and automated interpretation of results.
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20
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High-throughput detection of clinically targetable alterations using next-generation sequencing. Oncotarget 2018; 8:40345-40358. [PMID: 28404952 PMCID: PMC5522202 DOI: 10.18632/oncotarget.15875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/23/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) has revolutionized the therapeutic care of patients by allowing high-throughput and parallel sequencing of large numbers of genes in a single run. However, most of available commercialized cancer panels target a large number of mutations that do not have direct therapeutic implications and that are not fully adapted to low quality formalin-fixed, paraffin-embedded (FFPE) samples. Here, we designed an amplicon-based NGS panel assay of 16 currently actionable genes according to the most recent recommendations of the French National Cancer Institute (NCI). We developed a panel of short amplicons (<150 bp) using dual-strand library preparation. The clinical validation of this panel was performed on well-characterized controls and 140 routine diagnostic samples, including highly degraded and cross-linked genomic DNA extracted from FFPE tumor samples. All mutations were detected with elevated inter-laboratory and inter-run reproducibility. Importantly, we could detect clinically actionable alterations in FFPE samples with variant allele frequencies as low as 1%. In addition, the overall molecular diagnosis rate was increased from 40.7% with conventional techniques to 59.2% with our NGS panel, including 41 novel actionable alterations normally not explored by conventional techniques. Taken together, we believe that this new actionable target panel represents a relevant, highly scalable and robust tool that is easy to implement and is fully adapted to daily clinical practice in hospital and academic laboratories.
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21
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Strell C, Hilscher MM, Laxman N, Svedlund J, Wu C, Yokota C, Nilsson M. Placing RNA in context and space - methods for spatially resolved transcriptomics. FEBS J 2018. [PMID: 29542254 DOI: 10.1111/febs.14435] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Single-cell transcriptomics provides us with completely new insights into the molecular diversity of different cell types and the different states they can adopt. The technique generates inventories of cells that constitute the building blocks of multicellular organisms. However, since the method requires isolation of discrete cells, information about the original location within tissue is lost. Therefore, it is not possible to draw detailed cellular maps of tissue architecture and their positioning in relation to other cells. In order to better understand the cellular and tissue function of multicellular organisms, we need to map the cells within their physiological, morphological, and anatomical context and space. In this review, we will summarize and compare the different methods of in situ RNA analysis and the most recent developments leading to more comprehensive and highly multiplexed spatially resolved transcriptomic approaches. We will discuss their highlights and advantages as well as their limitations and challenges and give an outlook on promising future applications and directions both within basic research as well as clinical integration.
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Affiliation(s)
- Carina Strell
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Markus M Hilscher
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Navya Laxman
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Jessica Svedlund
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Chenglin Wu
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Chika Yokota
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biophysics and biochemistry, Stockholm University, Solna, Sweden
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22
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Yamasaki M, Funaishi K, Saito N, Sakano A, Fujihara M, Daido W, Ishiyama S, Deguchi N, Taniwaki M, Ohashi N, Hattori N. Putative lung adenocarcinoma with epidermal growth factor receptor mutation presenting as carcinoma of unknown primary site: A case report. Medicine (Baltimore) 2018; 97:e9942. [PMID: 29443782 PMCID: PMC5839817 DOI: 10.1097/md.0000000000009942] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
RATIONALE Only a few cases of putative lung adenocarcinoma presenting as carcinoma of unknown primary site (CUP) with epidermal growth factor receptor (EGFR) mutation have been reported, and the efficacy of EGFR-tyrosine kinase inhibitors (TKIs) for these cases is unclear. PATIENT CONCERNS AND DIAGNOSES A 67-year-old man complained of paresis of the right lower extremity, dysarthria, and memory disturbance. Computed tomography and magnetic resonance imaging showed multiple brain tumors with brain edema and swelling of the left supraclavicular, mediastinal, and upper abdominal lymph nodes. Moreover, a metastatic duodenal tumor was detected via upper gastrointestinal endoscopy examination. The biopsy specimen of the lesion was examined and was diagnosed as adenocarcinoma with CK7 and TTF-1 positivity. Finally, the case was diagnosed as EGFR mutation-positive putative lung adenocarcinoma presenting as CUP. INTERVENTIONS AND OUTCOMES Oral erlotinib, an EGFR-TKI, was administered at 150 mg daily. Five weeks later, the brain lesions and several swollen lymph nodes showed marked improvement, and the symptoms of the patient also improved. Three months later, the duodenal lesion was undetected on upper gastrointestinal endoscopy. After an 8-month follow-up, the patient was well with no disease progression. LESSONS Putative lung adenocarcinoma presenting as CUP may have EGFR mutation, and EGFR-TKI therapy may be effective for such malignancy.
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Affiliation(s)
- Masahiro Yamasaki
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Kunihiko Funaishi
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Naomi Saito
- Department of Respiratory Medicine, Mazda Hospital, Aki-gun
| | | | - Megumu Fujihara
- Department of Pathology, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital
| | - Wakako Daido
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Sayaka Ishiyama
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Naoko Deguchi
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Masaya Taniwaki
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
| | - Nobuyuki Ohashi
- Department of Respiratory Disease, Hiroshima Red Cross Hospital & Atomic Bomb Survivors Hospital, Naka-ku
- Ohashi Clinic, Naka-ku
| | - Noboru Hattori
- Department of Molecular and Internal Medicine, Institute of Biomedical & Health Sciences, Hiroshima University, Minami-ku, Hiroshima, Japan
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23
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Hirsch B, Endris V, Lassmann S, Weichert W, Pfarr N, Schirmacher P, Kovaleva V, Werner M, Bonzheim I, Fend F, Sperveslage J, Kaulich K, Zacher A, Reifenberger G, Köhrer K, Stepanow S, Lerke S, Mayr T, Aust DE, Baretton G, Weidner S, Jung A, Kirchner T, Hansmann ML, Burbat L, von der Wall E, Dietel M, Hummel M. Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics. Virchows Arch 2018; 472:557-565. [PMID: 29374318 PMCID: PMC5924673 DOI: 10.1007/s00428-017-2288-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/05/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022]
Abstract
The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series. Detailed information regarding pre-characterized mutations was not disclosed to the partners. Commercially available and custom-designed cancer gene panels were used for library preparation and subsequent sequencing on several devices of two NGS different platforms. For every case, centrally extracted DNA and FFPE tissue sections for local processing were delivered to each partner site to be sequenced with the commercial gene panel and local bioinformatics. For cancer-specific panel-based sequencing, only centrally extracted DNA was analyzed at seven sequencing sites. Subsequently, local data were compiled and bioinformatics was performed centrally. We were able to demonstrate that all pre-characterized mutations were re-identified correctly, irrespective of NGS platform or gene panel used. However, locally processed FFPE tissue sections disclosed that the DNA extraction method can affect the detection of mutations with a trend in favor of magnetic bead-based DNA extraction methods. In conclusion, targeted NGS is a very robust method for simultaneous detection of various mutations in FFPE tissue specimens if certain pre-analytical conditions are carefully considered.
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Affiliation(s)
- B Hirsch
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
| | - V Endris
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - S Lassmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - W Weichert
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - N Pfarr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - P Schirmacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - V Kovaleva
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - M Werner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - I Bonzheim
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - F Fend
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - J Sperveslage
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - K Kaulich
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - A Zacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - G Reifenberger
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - K Köhrer
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Stepanow
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Lerke
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - T Mayr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - D E Aust
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - G Baretton
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - S Weidner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - A Jung
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - T Kirchner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - M L Hansmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Dr. Senckenberg Institute of Pathology, University Hospital, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - L Burbat
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - E von der Wall
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Dietel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Hummel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
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24
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Tsoulos N, Papadopoulou E, Metaxa-Mariatou V, Tsaousis G, Efstathiadou C, Tounta G, Scapeti A, Bourkoula E, Zarogoulidis P, Pentheroudakis G, Kakolyris S, Boukovinas I, Papakotoulas P, Athanasiadis E, Floros T, Koumarianou A, Barbounis V, Dinischiotu A, Nasioulas G. Tumor molecular profiling of NSCLC patients using next generation sequencing. Oncol Rep 2017; 38:3419-3429. [PMID: 29130105 PMCID: PMC5783588 DOI: 10.3892/or.2017.6051] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/05/2017] [Indexed: 01/10/2023] Open
Abstract
Non‑small cell lung cancer (NSCLC) is the most common type of lung cancer and a tumor with a broad spectrum of targeted therapies already available or in clinical trials. Thus, molecular characterization of the tumor using next generation sequencing (NGS) technology, has become a key tool for facilitating treatment decisions and the clinical management of NSCLC patients. The performance of a custom 23 gene multiplex amplification hot spot panel, based on Ion AmpliSeq™ technology, was evaluated for the analysis of tumor DNA extracted from formalin-fixed and paraffin-embedded (FFPE) tissues. Furthermore, the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel was used for fusion RNA transcript analysis. The mutation spectrum of the tumors was determined in a cohort of 502 patients with NSCLC using the aforementioned targeted gene panels. The panel used for tumor DNA analysis in this study exhibited high rates (100%) of sensitivity, specificity and reproducibility at a mutation allelic frequency of 3%. At least one DNA mutation was detected in 374 patients (74.5%) and an RNA fusion was identified in 16 patients, (3.2%). In total, alterations in a cancer-driver gene were identified (including point mutations, gene rearrangements and MET amplifications) in 77.6% of the tumors tested. Among the NSCLC patients, 23% presented a mutation in a gene associated with approved or emerging targeted therapy. More specifically, 13.5% (68/502) presented a mutation in a gene with approved targeted therapy (EGFR, ALK, ROS1) and 9.4% (47/502) had an alteration in a gene related to emerging targeted therapies (ERBB2, BRAF, MET and RET). Furthermore, 51.6% of the patients had a mutation in a gene that could be related to an off label therapy or indicative for access to a clinical trial. Thus, the targeted NGS panel used in this study is a reliable approach for tumor molecular profiling and can be applied in personalized treatment decision making for NSCLC patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pavlos Zarogoulidis
- Pulmonary Department, Oncology Unit, ‘G. Papanikolaou’ General Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - George Pentheroudakis
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Stylianos Kakolyris
- Department of Medical Oncology, University General Hospital of Alexandroupoli, Alexandroupoli 68100, Greece
| | - Ioannis Boukovinas
- Medical Oncology, ‘Bioclinic’ of Thessaloniki, Thessaloniki 54622, Greece
| | - Pavlos Papakotoulas
- Second Department of Medical Oncology, Theagenion Anticancer Hospital of Thessaloniki, Thessaloniki 54639, Greece
| | | | | | - Anna Koumarianou
- Hematology-Oncology Unit, Fourth Department of Internal Medicine, Attikon Hospital, National and Kapodistrian University of Athens, Athens 12462, Greece
| | - Vasileios Barbounis
- Third Medical Oncology Department, ‘Metropolitan’ Hospital, Pireas 18547, Greece
| | - Anca Dinischiotu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 0050095, Romania
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25
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Luchini C, Cheng L. Predicting the biological behavior of non-muscle-invasive bladder cancer: from histology to molecular taxonomy. Transl Androl Urol 2017; 6:987-990. [PMID: 29184801 PMCID: PMC5673828 DOI: 10.21037/tau.2017.08.04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023] Open
Affiliation(s)
- Claudio Luchini
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, Verona, Italy
- Surgical Pathology Unit, Santa Chiara Hospital, Trento, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
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26
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Roma C, Rachiglio AM, Pasquale R, Fenizia F, Iannaccone A, Tatangelo F, Antinolfi G, Parrella P, Graziano P, Sabatino L, Colantuoni V, Botti G, Maiello E, Normanno N. BRAF V600E mutation in metastatic colorectal cancer: Methods of detection and correlation with clinical and pathologic features. Cancer Biol Ther 2017; 17:840-8. [PMID: 27261210 DOI: 10.1080/15384047.2016.1195048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The screening for BRAF V600E mutation is employed in clinical practice for its prognostic and potentially predictive role in patients with metastatic colorectal carcinoma (mCRC). Little information is available on the sensitivity and specificity of the testing methods to detect this mutation in CRC. By using serial dilution of BRAF mutant DNA with wild type DNA, we found that the sensitivity of allelic discrimination-Real Time PCR was higher than PCR-Sequencing (10% vs 20%). In agreement, the Real Time PCR assay displayed increased analytical sensitivity in detecting the BRAF V600E mutation as compared with PCR-Sequencing in a cohort of 510 consecutive CRCs (21 vs 16 cases). Targeted resequencing demonstrated that all cases negative by PCR-Sequencing had an allelic frequency of the BRAF mutation <20%, thus suggesting tumor heterogeneity. The association of BRAF mutations with clinical and pathological features was assessed next in a cohort of 840 KRAS exon 2 wild type CRC patients screened with the Real Time PCR assay. The BRAF V600E mutation frequency in this cohort was 7.8% that increased to 33.4% in females over 70 y of age with right-sided tumor location. BRAF mutations were also detected in 4.4% of male patients with left-sided tumors and aged <70 y. Fourteen of 61 (22.9%) BRAF V600E mutation bearing patients exhibited microsatellite instability (MSI) as assessed by T17 mononucleotide sequence within intron 8 of HSP110. Our study indicates that Real Time PCR-based assays are more sensitive than PCR-Sequencing to detect the BRAF V600E mutation in CRC and that BRAF mutations screening should not be restricted to selected patients on the basis of the clinical-pathological characteristics.
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Affiliation(s)
- Cristin Roma
- a Laboratory of Pharmacogenomics , Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
| | - Anna Maria Rachiglio
- a Laboratory of Pharmacogenomics , Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
| | - Raffaella Pasquale
- a Laboratory of Pharmacogenomics , Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
| | - Francesca Fenizia
- a Laboratory of Pharmacogenomics , Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
| | - Alessia Iannaccone
- a Laboratory of Pharmacogenomics , Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
| | - Fabiana Tatangelo
- b Pathology Unit , Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
| | - Giuseppe Antinolfi
- c Surgical Pathology Unit , Azienda Ospedaliera dei Colli , Naples , Italy
| | - Paola Parrella
- d Laboratory of Oncology , Hospital "Casa Sollievo Della Sofferenza," San Giovanni Rotondo , FG , Italy
| | - Paolo Graziano
- e Surgical Pathology Unit , Hospital "Casa Sollievo Della Sofferenza," San Giovanni Rotondo , FG , Italy
| | - Lina Sabatino
- f Department of Science and Technology , University of Sannio , Benevento , Italy
| | - Vittorio Colantuoni
- f Department of Science and Technology , University of Sannio , Benevento , Italy
| | - Gerardo Botti
- b Pathology Unit , Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
| | - Evaristo Maiello
- g Department of Oncology , Hospital "Casa Sollievo Della Sofferenza," San Giovanni Rotondo , FG , Italy
| | - Nicola Normanno
- h Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS , Naples , Italy
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27
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Reiman A, Kikuchi H, Scocchia D, Smith P, Tsang YW, Snead D, Cree IA. Validation of an NGS mutation detection panel for melanoma. BMC Cancer 2017; 17:150. [PMID: 28228113 PMCID: PMC5322598 DOI: 10.1186/s12885-017-3149-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 02/18/2017] [Indexed: 11/10/2022] Open
Abstract
Background Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. Methods While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time. We describe here an Ampliseq hotspot panel for melanoma for use with the IonTorrent Personal Genome Machine (PGM) which covers the mutations currently of most clinical interest. Results We have validated this in 151 cases of skin and uveal melanoma from our files, and correlated the data with PCR based assessment of BRAF status. There was excellent agreement, with few discrepancies, though NGS does have greater coverage and picks up some mutations that would be missed by PCR. However, these are often rare and of unknown significance for treatment. Conclusions PCR methods are rapid, less time-consuming and less expensive than NGS, and could be used as triage for patients requiring more extensive diagnostic workup. The NGS panel described here is suitable for clinical use with formalin-fixed paraffin-embedded (FFPE) samples. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3149-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Reiman
- Department of Pathology - Coventry and Warwickshire Pathology Services (CWPS), University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK.,Centre for Research in Applied Biological and Exercise Sciences, Coventry University, Coventry, CV1 5FB, UK
| | - Hugh Kikuchi
- Department of Pathology - Coventry and Warwickshire Pathology Services (CWPS), University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK.,Centre for Research in Applied Biological and Exercise Sciences, Coventry University, Coventry, CV1 5FB, UK
| | - Daniela Scocchia
- Department of Pathology - Coventry and Warwickshire Pathology Services (CWPS), University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK
| | - Peter Smith
- Department of Pathology - Coventry and Warwickshire Pathology Services (CWPS), University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK
| | - Yee Wah Tsang
- Department of Pathology - Coventry and Warwickshire Pathology Services (CWPS), University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK
| | - David Snead
- Department of Pathology - Coventry and Warwickshire Pathology Services (CWPS), University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK
| | - Ian A Cree
- Department of Pathology - Coventry and Warwickshire Pathology Services (CWPS), University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK. .,Institute of Ophthalmology, University College London, Bath Street, London, EC1V 9EL, UK. .,Centre for Technology Enabled Health Research (CTEHR), Faculty of Health & Life Sciences, Coventry University, Coventry, CV1 5FB, UK.
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Ham JC, Tops BBJ, Driessen CML, van Raaij AWM, Slootweg PJ, Melchers WJG, Ligtenberg MJL, van Herpen CML. Using a semi-conductor sequencing-based panel for genotyping of HPV-positive and HPV-negative oropharyngeal cancer: a retrospective pilot study. Clin Otolaryngol 2017; 42:681-686. [PMID: 27882657 DOI: 10.1111/coa.12800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The aim of this study was to assess the feasibility of testing actionable mutations in small amounts of formalin-fixed paraffin-embedded material in multiple genes of the receptor tyrosine kinase pathway and to determine the frequency of these mutations in human papillomavirus (HPV)-positive and HPV-negative oropharyngeal cancer (OPC). DESIGN A retrospective pilot study was performed. SETTING In OPC, no predictive markers for response to epidermal growth factor receptor inhibition are known. Therefore, identifying predictive biomarkers is of utmost importance, but is often hampered by the small amount of tumour material available. PARTICIPANTS We included the archival material of 45 OPC, all treated with concomitant chemoradiotherapy between 2003 and 2010. MAIN OUTCOME MEASURES Besides the HPV status, we assessed mutations using a gene panel that targets 16 genes in the receptor tyrosine kinase pathway and six other genes. The polymerase chain reaction required only 10 ng DNA. RESULTS In total, 42 of the 45 biopsies have been successfully analysed. In total 20 of 42 samples were HPV-positive and 22 of 42 were HPV-negative. In the receptor tyrosine kinase pathway, mutations in PIK3CA were most frequently identified. A TP53 mutation was identified in one HPV-positive sample and in 13 HPV-negative samples. Additionally, three mutations in three different genes were found. CONCLUSIONS We evaluated an assay to identify mutations in the receptor tyrosine kinase pathway. As only small amounts of formalin-fixed paraffin-embedded material are sufficient for reliable analysis, this test opens up new possibilities for personalised medicine.
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Affiliation(s)
- J C Ham
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - B B J Tops
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C M L Driessen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A W M van Raaij
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - P J Slootweg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - W J G Melchers
- Department of Medical Microbiology and Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C M L van Herpen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
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29
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Cree IA, Charlton P. Molecular chess? Hallmarks of anti-cancer drug resistance. BMC Cancer 2017; 17:10. [PMID: 28056859 PMCID: PMC5214767 DOI: 10.1186/s12885-016-2999-1] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/13/2016] [Indexed: 12/14/2022] Open
Abstract
Background The development of resistance is a problem shared by both classical chemotherapy and targeted therapy. Patients may respond well at first, but relapse is inevitable for many cancer patients, despite many improvements in drugs and their use over the last 40 years. Review Resistance to anti-cancer drugs can be acquired by several mechanisms within neoplastic cells, defined as (1) alteration of drug targets, (2) expression of drug pumps, (3) expression of detoxification mechanisms, (4) reduced susceptibility to apoptosis, (5) increased ability to repair DNA damage, and (6) altered proliferation. It is clear, however, that changes in stroma and tumour microenvironment, and local immunity can also contribute to the development of resistance. Cancer cells can and do use several of these mechanisms at one time, and there is considerable heterogeneity between tumours, necessitating an individualised approach to cancer treatment. As tumours are heterogeneous, positive selection of a drug-resistant population could help drive resistance, although acquired resistance cannot simply be viewed as overgrowth of a resistant cancer cell population. The development of such resistance mechanisms can be predicted from pre-existing genomic and proteomic profiles, and there are increasingly sophisticated methods to measure and then tackle these mechanisms in patients. Conclusion The oncologist is now required to be at least one step ahead of the cancer, a process that can be likened to ‘molecular chess’. Thus, as well as an increasing role for predictive biomarkers to clinically stratify patients, it is becoming clear that personalised strategies are required to obtain best results.
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Affiliation(s)
- Ian A Cree
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX, UK. .,Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB, UK.
| | - Peter Charlton
- Imperial Innovations, 52 Princes Gate, Exhibition Road, London, SW7 2PG, UK
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30
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Deans ZC, Costa JL, Cree I, Dequeker E, Edsjö A, Henderson S, Hummel M, Ligtenberg MJ, Loddo M, Machado JC, Marchetti A, Marquis K, Mason J, Normanno N, Rouleau E, Schuuring E, Snelson KM, Thunnissen E, Tops B, Williams G, van Krieken H, Hall JA. Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL. Virchows Arch 2017; 470:5-20. [PMID: 27678269 PMCID: PMC5243883 DOI: 10.1007/s00428-016-2025-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/27/2016] [Accepted: 09/16/2016] [Indexed: 10/31/2022]
Abstract
The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guidelines establish consensus standards for somatic diagnostic testing, specifically for identifying and reporting mutations in solid tumours. These guidelines cover the testing strategy, implementation of testing within clinical service, sample requirements, data analysis and reporting of results. In conjunction with appropriate staff training and international standards for laboratory testing, these consensus standards for the use of NGS in molecular pathology of solid tumours will assist laboratories in implementing NGS in clinical services.
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Affiliation(s)
- Zandra C Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK.
| | - Jose Luis Costa
- i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ian Cree
- Department of Pathology, University Hospital Coventry and Warwickshire, Coventry, CV2 2DX, UK
| | - Els Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven-University of Leuven, Leuven, Belgium
| | - Anders Edsjö
- Clinical Pathology, Laboratory Medicine, Medical Services, Region Skåne, Lund, Sweden
| | - Shirley Henderson
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
| | - Michael Hummel
- Institute of Pathology, Berlin, Germany and the DGP, German Society of Pathology, Charite, University Medicine Berlin, Berlin, Germany
| | - Marjolijn Jl Ligtenberg
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marco Loddo
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Jose Carlos Machado
- i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, CeSI-MeT, University of Chieti, Chieti, Italy
| | - Katherine Marquis
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Joanne Mason
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumouri "Fondazione Giovanni Pascale" IRCCS, Naples, Italy
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Genetic and Pathology Molecular Service, Gustave Roussy, 114 Rue Edouard Vaillant, 94800, Villejuif, France
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center of Groningen, Groningen, The Netherlands
| | - Keeda-Marie Snelson
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Erik Thunnissen
- Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Bastiaan Tops
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gareth Williams
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Han van Krieken
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacqueline A Hall
- International Quality Network for Pathology (IQN Path) Association Sans But Lucratif (A.S.B.L), 17 Boulevard Royal, L2449, Luxembourg City, Luxembourg
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
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31
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Pietrasz D, Pécuchet N, Garlan F, Didelot A, Dubreuil O, Doat S, Imbert-Bismut F, Karoui M, Vaillant JC, Taly V, Laurent-Puig P, Bachet JB. Plasma Circulating Tumor DNA in Pancreatic Cancer Patients Is a Prognostic Marker. Clin Cancer Res 2016; 23:116-123. [PMID: 27993964 DOI: 10.1158/1078-0432.ccr-16-0806] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 10/05/2016] [Accepted: 10/08/2016] [Indexed: 12/12/2022]
Abstract
PURPOSE Despite recent therapeutic advances, prognosis of patients with pancreatic adenocarcinoma remains poor. Analyses from tumor tissues present limitations; identification of informative marker from blood might be a promising alternative. The aim of this study was to assess the feasibility and the prognostic value of circulating tumor DNA (ctDNA) in pancreatic adenocarcinoma. EXPERIMENTAL DESIGN From 2011 to 2015, blood samples were prospectively collected from all consecutive patients with pancreatic adenocarcinoma treated in our center. Identification of ctDNA was done with next-generation sequencing targeted on referenced mutations in pancreatic adenocarcinoma and with picoliter droplet digital PCR. RESULTS A total of 135 patients with resectable (n = 31; 23%), locally advanced (n = 36; 27%), or metastatic (n = 68; 50%) pancreatic adenocarcinoma were included. In patients with advanced pancreatic adenocarcinoma (n = 104), 48% (n = 50) had ctDNA detectable with a median mutation allelic frequency (MAF) of 6.1%. The presence of ctDNA was strongly correlated with poor overall survival (OS; 6.5 vs. 19.0 months; P < 0.001) in univariate and multivariate analyses (HR = 1.96; P = 0.007). To evaluate the impact of ctDNA level, patients were grouped according to MAF tertiles: OS were 18.9, 7.8, and 4.9 months (P < 0.001). Among patients who had curative intent resection (n = 31), 6 had ctDNA detectable after surgery, with an MAF of 4.4%. The presence of ctDNA was associated with a shorter disease-free survival (4.6 vs.17.6 months; P = 0.03) and shorter OS (19.3 vs. 32.2 months; P = 0.027). CONCLUSIONS ctDNA is an independent prognostic marker in advanced pancreatic adenocarcinoma. Furthermore, it arises as an indicator of shorter disease-free survival in resected patients when detected after surgery. Clin Cancer Res; 23(1); 116-23. ©2016 AACR.
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Affiliation(s)
- Daniel Pietrasz
- Department of Digestive and Hepatobiliary Surgery, Pitié-Salpêtrière Hospital, Paris, France.,Université Paris Sorbonne Cité, INSERM UMR-S1147 MEPPOT, CNRS SNC5014, Centre Universitaire des Saints-Péres, Paris, France. Equipe labélisée Ligue contre le Cancer.,Sorbonne University, UPMC University, Paris 06, France
| | - Nicolas Pécuchet
- Université Paris Sorbonne Cité, INSERM UMR-S1147 MEPPOT, CNRS SNC5014, Centre Universitaire des Saints-Péres, Paris, France. Equipe labélisée Ligue contre le Cancer
| | - Fanny Garlan
- Université Paris Sorbonne Cité, INSERM UMR-S1147 MEPPOT, CNRS SNC5014, Centre Universitaire des Saints-Péres, Paris, France. Equipe labélisée Ligue contre le Cancer
| | - Audrey Didelot
- Université Paris Sorbonne Cité, INSERM UMR-S1147 MEPPOT, CNRS SNC5014, Centre Universitaire des Saints-Péres, Paris, France. Equipe labélisée Ligue contre le Cancer
| | - Olivier Dubreuil
- Gastroenterology and Digestive Oncology Department, Pitié-Salpêtrière Hospital, Paris, France
| | - Solène Doat
- Gastroenterology and Digestive Oncology Department, Pitié-Salpêtrière Hospital, Paris, France
| | | | - Mehdi Karoui
- Department of Digestive and Hepatobiliary Surgery, Pitié-Salpêtrière Hospital, Paris, France.,Sorbonne University, UPMC University, Paris 06, France
| | - Jean-Christophe Vaillant
- Department of Digestive and Hepatobiliary Surgery, Pitié-Salpêtrière Hospital, Paris, France.,Sorbonne University, UPMC University, Paris 06, France
| | - Valérie Taly
- Université Paris Sorbonne Cité, INSERM UMR-S1147 MEPPOT, CNRS SNC5014, Centre Universitaire des Saints-Péres, Paris, France. Equipe labélisée Ligue contre le Cancer
| | - Pierre Laurent-Puig
- Université Paris Sorbonne Cité, INSERM UMR-S1147 MEPPOT, CNRS SNC5014, Centre Universitaire des Saints-Péres, Paris, France. Equipe labélisée Ligue contre le Cancer
| | - Jean-Baptiste Bachet
- Université Paris Sorbonne Cité, INSERM UMR-S1147 MEPPOT, CNRS SNC5014, Centre Universitaire des Saints-Péres, Paris, France. Equipe labélisée Ligue contre le Cancer. .,Sorbonne University, UPMC University, Paris 06, France.,Gastroenterology and Digestive Oncology Department, Pitié-Salpêtrière Hospital, Paris, France
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32
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Fontanges Q, De Mendonca R, Salmon I, Le Mercier M, D'Haene N. Clinical Application of Targeted Next Generation Sequencing for Colorectal Cancers. Int J Mol Sci 2016; 17:ijms17122117. [PMID: 27999270 PMCID: PMC5187917 DOI: 10.3390/ijms17122117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 01/01/2023] Open
Abstract
Promising targeted therapy and personalized medicine are making molecular profiling of tumours a priority. For colorectal cancer (CRC) patients, international guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-epidermal growth factor receptor agents (anti-EGFR). Daily, new data emerge on the theranostic and prognostic role of molecular biomarkers, which is a strong incentive for a validated, sensitive and broadly available molecular screening test in order to implement and improve multi-modal therapy strategy and clinical trials. Next generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. Targeted NGS is a method that allows parallel sequencing of thousands of short DNA sequences in a single test offering a cost-effective approach for detecting multiple genetic alterations with a minimum amount of DNA. In the present review, we collected data concerning the clinical application of NGS technology in the setting of colorectal cancer.
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Affiliation(s)
- Quitterie Fontanges
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Ricardo De Mendonca
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
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Serratì S, De Summa S, Pilato B, Petriella D, Lacalamita R, Tommasi S, Pinto R. Next-generation sequencing: advances and applications in cancer diagnosis. Onco Targets Ther 2016; 9:7355-7365. [PMID: 27980425 PMCID: PMC5144906 DOI: 10.2147/ott.s99807] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Technological advances have led to the introduction of next-generation sequencing (NGS) platforms in cancer investigation. NGS allows massive parallel sequencing that affords maximal tumor genomic assessment. NGS approaches are different, and concern DNA and RNA analysis. DNA sequencing includes whole-genome, whole-exome, and targeted sequencing, which focuses on a selection of genes of interest for a specific disease. RNA sequencing facilitates the detection of alternative gene-spliced transcripts, posttranscriptional modifications, gene fusion, mutations/single-nucleotide polymorphisms, small and long noncoding RNAs, and changes in gene expression. Most applications are in the cancer research field, but lately NGS technology has been revolutionizing cancer molecular diagnostics, due to the many advantages it offers compared to traditional methods. There is greater knowledge on solid cancer diagnostics, and recent interest has been shown also in the field of hematologic cancer. In this review, we report the latest data on NGS diagnostic/predictive clinical applications in solid and hematologic cancers. Moreover, since the amount of NGS data produced is very large and their interpretation is very complex, we briefly discuss two bioinformatic aspects, variant-calling accuracy and copy-number variation detection, which are gaining a lot of importance in cancer-diagnostic assessment.
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Affiliation(s)
- Simona Serratì
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Simona De Summa
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Brunella Pilato
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Daniela Petriella
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
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Eijkelenboom A, Kamping EJ, Kastner-van Raaij AW, Hendriks-Cornelissen SJ, Neveling K, Kuiper RP, Hoischen A, Nelen MR, Ligtenberg MJ, Tops BB. Reliable Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue Using Single Molecule Tags. J Mol Diagn 2016; 18:851-863. [DOI: 10.1016/j.jmoldx.2016.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/04/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022] Open
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35
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Pécuchet N, Rozenholc Y, Zonta E, Pietrasz D, Didelot A, Combe P, Gibault L, Bachet JB, Taly V, Fabre E, Blons H, Laurent-Puig P. Analysis of Base-Position Error Rate of Next-Generation Sequencing to Detect Tumor Mutations in Circulating DNA. Clin Chem 2016; 62:1492-1503. [DOI: 10.1373/clinchem.2016.258236] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/15/2016] [Indexed: 12/18/2022]
Abstract
AbstractBACKGROUNDDetecting single-nucleotide variations and insertions/deletions in circulating tumor DNA is challenging because of their low allele frequency. The clinical use of circulating tumor DNA to characterize tumor genetic alterations requires new methods based on next-generation sequencing.METHODSWe developed a method based on quantification of error rate of each base position [position error rate (PER)]. To identify mutations, a binomial test was used to compare the minor-allele frequency to the measured PER at each base position. This process was validated in control samples and in 373 plasma samples from patients with lung or pancreatic cancer.RESULTSMinimal mutated allele frequencies were 0.003 for single-nucleotide variations and 0.001 for insertions/deletions. Independent testing performed by droplet digital PCR (n = 231 plasma samples) showed strong agreement with the base-PER method (κ = 0.90).CONCLUSIONSTargeted next-generation sequencing analyzed with the base-PER method represents a robust and low cost method to detect circulating tumor DNA in patients with cancer.
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Affiliation(s)
- Nicolas Pécuchet
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Yves Rozenholc
- MERIT–UMR IRD 216, Paris Sorbonne Cité Université, Paris, France
| | - Eleonora Zonta
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Daniel Pietrasz
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Audrey Didelot
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Pierre Combe
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Laure Gibault
- Department of Pathology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Jean-Baptiste Bachet
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Gastro-enterology, Hôpital Pitié-Salpêtrière, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Elizabeth Fabre
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Hélène Blons
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Biochemistry, Pharmacogenetic and Molecular Oncology Unit, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Pierre Laurent-Puig
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Biochemistry, Pharmacogenetic and Molecular Oncology Unit, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
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Cree IA. Progress and potential of RAS mutation detection for diagnostics and companion diagnostics. Expert Rev Mol Diagn 2016; 16:1067-1072. [PMID: 27494709 DOI: 10.1080/14737159.2016.1221345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The importance of RAS mutation in carcinogenesis is established, and knowledge of an individual cancer's mutation status is important for optimal treatment. Areas covered: This paper is restricted to RAS testing in cancer, and highlights papers relevant to current practice. Expert commentary: Multiple laboratory methods are available for RAS gene analysis. PCR is commonly used to determine RAS status, providing a robust and inexpensive technology for clinical use. Next generation sequencing (NGS) platforms are changing the way in which mutation status is determined, though they require considerable expertise. Pre-analytical issues affect both methods and should be considered. The interpretation and reporting of results is not simple, particularly for NGS. External quality assurance is a pre-requisite for success, and is mandated by most laboratory accreditation schemes. The use of RAS testing is now extending beyond biopsy material to include the detection of mutations in circulating cell-free DNA and tumour cells.
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Affiliation(s)
- Ian A Cree
- a Department of Pathology , University Hospitals Coventry and Warwickshire , Coventry , United Kingdom
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Diagnostic RAS mutation analysis by polymerase chain reaction (PCR). BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 8:29-32. [PMID: 27335808 PMCID: PMC4906127 DOI: 10.1016/j.bdq.2016.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/26/2016] [Accepted: 05/17/2016] [Indexed: 02/07/2023]
Abstract
RAS mutation analysis is an important companion diagnostic test. Treatment of colorectal cancer with anti-Epidermal Growth Factor Receptor (EGFR) therapy requires demonstration of RAS mutation status (both KRAS and NRAS), and it is good practice to include BRAF. In Non-Small Cell Lung Cancer (NSCLC) and melanoma, assessment of RAS mutation status can be helpful in triaging patient samples for more extensive testing. This mini-review will discuss the role of PCR methods in providing rapid diagnostic information for cancer patients.
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Armengol G, Sarhadi VK, Ghanbari R, Doghaei-Moghaddam M, Ansari R, Sotoudeh M, Puolakkainen P, Kokkola A, Malekzadeh R, Knuutila S. Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing. J Mol Diagn 2016; 18:471-9. [PMID: 27155048 DOI: 10.1016/j.jmoldx.2016.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 11/25/2015] [Accepted: 01/20/2016] [Indexed: 12/13/2022] Open
Abstract
Detection of driver gene mutations in stool DNA represents a promising noninvasive approach for screening colorectal cancer (CRC). Amplicon-based next-generation sequencing (NGS) is a good option to study mutations in many cancer genes simultaneously and from a low amount of DNA. Our aim was to assess the feasibility of identifying mutations in 22 cancer driver genes with Ion Torrent technology in stool DNA from a series of 65 CRC patients. The assay was successful in 80% of stool DNA samples. NGS results showed 83 mutations in cancer driver genes, 29 hotspot and 54 novel mutations. One to five genes were mutated in 75% of cases. TP53, KRAS, FBXW7, and SMAD4 were the top mutated genes, consistent with previous studies. Of samples with mutations, 54% presented concomitant mutations in different genes. Phosphatidylinositol 3-kinase/mitogen-activated protein kinase pathway genes were mutated in 70% of samples, with 58% having alterations in KRAS, NRAS, or BRAF. Because mutations in these genes can compromise the efficacy of epidermal growth factor receptor blockade in CRC patients, identifying mutations that confer resistance to some targeted treatments may be useful to guide therapeutic decisions. In conclusion, the data presented herein show that NGS procedures on stool DNA represent a promising tool to detect genetic mutations that could be used in the future for diagnosis, monitoring, or treating CRC.
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Affiliation(s)
- Gemma Armengol
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Autonomous University of Barcelona, Barcelona, Spain
| | - Virinder K Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Reza Ansari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Pauli Puolakkainen
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Arto Kokkola
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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Van Krieken JHJM, Rouleau E, Ligtenberg MJL, Normanno N, Patterson SD, Jung A. RAS testing in metastatic colorectal cancer: advances in Europe. Virchows Arch 2016; 468:383-96. [PMID: 26573425 PMCID: PMC4830882 DOI: 10.1007/s00428-015-1876-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Personalized medicine shows promise for maximizing efficacy and minimizing toxicity of anti-cancer treatment. KRAS exon 2 mutations are predictive of resistance to epidermal growth factor receptor-directed monoclonal antibodies in patients with metastatic colorectal cancer. Recent studies have shown that broader RAS testing (KRAS and NRAS) is needed to select patients for treatment. While Sanger sequencing is still used, approaches based on various methodologies are available. Few CE-approved kits, however, detect the full spectrum of RAS mutations. More recently, "next-generation" sequencing has been developed for research use, including parallel semiconductor sequencing and reversible termination. These techniques have high technical sensitivities for detecting mutations, although the ideal threshold is currently unknown. Finally, liquid biopsy has the potential to become an additional tool to assess tumor-derived DNA. For accurate and timely RAS testing, appropriate sampling and prompt delivery of material is critical. Processes to ensure efficient turnaround from sample request to RAS evaluation must be implemented so that patients receive the most appropriate treatment. Given the variety of methodologies, external quality assurance programs are important to ensure a high standard of RAS testing. Here, we review technical and practical aspects of RAS testing for pathologists working with metastatic colorectal cancer tumor samples. The extension of markers from KRAS to RAS testing is the new paradigm for biomarker testing in colorectal cancer.
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Affiliation(s)
- J Han J M Van Krieken
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands.
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Naples, Italy
| | - Scott D Patterson
- Amgen Inc., Thousand Oaks, CA, USA
- Gilead Sciences, Inc., Foster City, CA, USA
| | - Andreas Jung
- Institute of Pathology, University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Malapelle U, Pisapia P, Sgariglia R, Vigliar E, Biglietto M, Carlomagno C, Giuffrè G, Bellevicine C, Troncone G. Less frequently mutated genes in colorectal cancer: evidences from next-generation sequencing of 653 routine cases. J Clin Pathol 2016; 69:767-71. [PMID: 26797410 PMCID: PMC5036215 DOI: 10.1136/jclinpath-2015-203403] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/29/2015] [Indexed: 12/20/2022]
Abstract
AIMS The incidence of RAS/RAF/PI3KA and TP53 gene mutations in colorectal cancer (CRC) is well established. Less information, however, is available on other components of the CRC genomic landscape, which are potential CRC prognostic/predictive markers. METHODS Following a previous validation study, ion-semiconductor next-generation sequencing (NGS) was employed to process 653 routine CRC samples by a multiplex PCR targeting 91 hotspot regions in 22 CRC significant genes. RESULTS A total of 796 somatic mutations in 499 (76.4%) tumours were detected. Besides RAS/RAF/PI3KA and TP53, other 12 genes showed at least one mutation including FBXW7 (6%), PTEN (2.8%), SMAD4 (2.1%), EGFR (1.2%), CTNNB1 (1.1%), AKT1 (0.9%), STK11 (0.8%), ERBB2 (0.6%), ERBB4 (0.6%), ALK (0.2%), MAP2K1 (0.2%) and NOTCH1 (0.2%). CONCLUSIONS In a routine diagnostic setting, NGS had the potential to generate robust and comprehensive genetic information also including less frequently mutated genes potentially relevant for prognostic assessments or for actionable treatments.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Chiara Carlomagno
- Department of Surgical and Clinical Medicine, University of Naples Federico II, Naples, Italy
| | - Giuseppe Giuffrè
- Department of "Patologia Umana dell'Adulto e dell'età evolutiva, G.Barresi", University of Messina, Messina, 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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D’Haene N, Le Mercier M, De Nève N, Blanchard O, Delaunoy M, El Housni H, Dessars B, Heimann P, Remmelink M, Demetter P, Tejpar S, Salmon I. Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers. PLoS One 2015; 10:e0138245. [PMID: 26366557 PMCID: PMC4569137 DOI: 10.1371/journal.pone.0138245] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 08/27/2015] [Indexed: 11/18/2022] Open
Abstract
Objective Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation. Methods We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed. Results Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%. Conclusions Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.
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Affiliation(s)
- Nicky D’Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Nancy De Nève
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Oriane Blanchard
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Mélanie Delaunoy
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Hakim El Housni
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Barbara Dessars
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Pierre Heimann
- Department of Genetics, Erasme Hospital,Université Libre de Bruxelles, Brussels, Belgium
| | - Myriam Remmelink
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Pieter Demetter
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Sabine Tejpar
- Department of Oncology, University Hospital Leuven, Leuven, Belgium
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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Fassunke J, Haller F, Hebele S, Moskalev EA, Penzel R, Pfarr N, Merkelbach-Bruse S, Endris V. Utility of different massive parallel sequencing platforms for mutation profiling in clinical samples and identification of pitfalls using FFPE tissue. Int J Mol Med 2015; 36:1233-43. [PMID: 26352389 PMCID: PMC4601747 DOI: 10.3892/ijmm.2015.2339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/05/2015] [Indexed: 12/19/2022] Open
Abstract
In the growing field of personalised medicine, the analysis of numerous potential targets is becoming a challenge in terms of work load, tissue availability, as well as costs. The molecular analysis of non-small cell lung cancer (NSCLC) has shifted from the analysis of the epidermal growth factor receptor (EGFR) mutation status to the analysis of different gene regions, including resistance mutations or translocations. Massive parallel sequencing (MPS) allows rapid comprehensive mutation testing in routine molecular pathological diagnostics even on small formalin-fixed, paraffin-embedded (FFPE) biopsies. In this study, we compared and evaluated currently used MPS platforms for their application in routine pathological diagnostics. We initiated a first round-robin testing of 30 cases diagnosed with NSCLC and a known EGFR gene mutation status. In this study, three pathology institutes from Germany received FFPE tumour sections that had been individually processed. Fragment libraries were prepared by targeted multiplex PCR using institution-specific gene panels. Sequencing was carried out using three MPS systems: MiSeq™, GS Junior and PGM Ion Torrent™. In two institutes, data analysis was performed with the platform-specific software and the Integrative Genomics Viewer. In one institute, data analysis was carried out using an in-house software system. Of 30 samples, 26 were analysed by all institutes. Concerning the EGFR mutation status, concordance was found in 26 out of 26 samples. The analysis of a few samples failed due to poor DNA quality in alternating institutes. We found 100% concordance when comparing the results of the EGFR mutation status. A total of 38 additional mutations were identified in the 26 samples. In two samples, minor variants were found which could not be confirmed by qPCR. Other characteristic variants were identified as fixation artefacts by reanalyzing the respective sample by Sanger sequencing. Overall, the results of this study demonstrated good concordance in the detection of mutations using different MPS platforms. The failure with samples can be traced back to different DNA extraction systems and DNA quality. Unknown or ambiguous variations (transitions) need verification with another method, such as qPCR or Sanger sequencing.
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Affiliation(s)
- Jana Fassunke
- Institute of Pathology, University of Cologne, Medical Centre, D-50924 Cologne, Germany
| | - Florian Haller
- Institute of Pathology, University of Erlangen, Medical Centre, D-91054 Erlangen, Germany
| | - Simone Hebele
- Institute of Pathology, University of Erlangen, Medical Centre, D-91054 Erlangen, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, University of Erlangen, Medical Centre, D-91054 Erlangen, Germany
| | - Roland Penzel
- Institute of Pathology, University of Heidelberg, Medical Centre, D-69120 Heidelberg, Germany
| | - Nicole Pfarr
- Institute of Pathology, University of Heidelberg, Medical Centre, D-69120 Heidelberg, Germany
| | | | - Volker Endris
- Institute of Pathology, University of Heidelberg, Medical Centre, D-69120 Heidelberg, Germany
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The homogeneous mutation status of a 22 gene panel justifies the use of serial sections of colorectal cancer tissue for external quality assessment. Virchows Arch 2015; 467:273-8. [PMID: 26047774 PMCID: PMC4552773 DOI: 10.1007/s00428-015-1789-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 05/13/2015] [Indexed: 10/27/2022]
Abstract
Testing for treatment related biomarkers in clinical care, like Ras mutation status in colorectal cancer (CRC), has increased drastically over recent years. Reliable testing of these markers is pivotal for optimal treatment of patients. Participation in external quality assessment (EQA) programs is an important element in quality management and often obligatory to comply with regulations or for accreditation. Formalin-fixed paraffin-embedded (FFPE) clinical specimens would ideally form the basis for these assessments, as they represent the most common starting material for molecular testing. However, molecular heterogeneity of a lesion in a FFPE tissue block could potentially affect test results of participating laboratories, which might compromise reliability of the quality assessment results. To assess the actual impact of this potential problem, we determined the mutation status of 22 genes commonly mutated in colon cancer in four levels covering 360 μm of 30 FFPE tissue blocks, by Next Generation Sequencing. In each block, the genotype of these genes was identical at all four levels, with only little variation in mutation load. This result shows that the mutation status of the selected 22 genes in CRC specimens is homogeneous within a 360 μm segment of the tumor. These data justify the use of serial sections, within a defined segment of a CRC tissue block, for external quality assessment of mutation analysis.
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