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Vergés C, Giménez-Capitán A, Ribas V, Salgado-Borges J, March de Ribot F, Mayo-de-Las-Casas C, Armiger-Borras N, Pedraz C, Molina-Vila MÁ. Gene expression signatures in conjunctival fornix aspirates of patients with dry eye disease associated with Meibomian gland dysfunction. A proof-of-concept study. Ocul Surf 2023; 30:42-50. [PMID: 37524297 DOI: 10.1016/j.jtos.2023.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Meibomian gland dysfunction (MGD) is one of the most common conditions in ophthalmic practice and the most frequent cause of evaporative dry eye disease (DED). However, the immune mechanisms leading to this pathology are not fully understood and the diagnostic tests available are limited. Here, we used the nCounter technology to analyze immune gene expression in DED-MGD that can be used for developing diagnostic signatures for DED. METHODS Conjunctival cell samples were obtained by aspiration from patients with DED-MGD (n = 27) and asymptomatic controls (n = 22). RNA was purified, converted to cDNA, preamplified and analyzed using the Gene Expression Human Immune V2 panel (NanoString), which includes 579 target and 15 housekeeping genes. A machine learning (ML) algorithm was applied to design a signature associated with DED-MGD. RESULTS Forty-five immune genes were found upregulated in DED-MGD vs. controls, involved in eight signaling pathways, IFN I/II, MHC class I/II, immunometabolism, B cell receptor, T Cell receptor, and T helper-17 (Th-17) differentiation. Additionally, statistically significant correlations were found between 31 genes and clinical characteristics of the disease such as lid margin or tear osmolarity (Pearson's r < 0.05). ML analysis using a recursive feature elimination (RFE) algorithm selected a 4-gene mRNA signature that discriminated DED-MGD from control samples with an area under the ROC curve (AUC ROC) of 0.86 and an accuracy of 77.5%. CONCLUSIONS Multiplexed mRNA analysis of conjunctival cells can be used to analyze immune gene expression patterns in patients with DED-MGD and to generate diagnostic signatures.
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Affiliation(s)
- Carlos Vergés
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain.
| | - Ana Giménez-Capitán
- Pangaea Oncology, Laboratory of Oncology, Dexeus University Hospital, Barcelona, Spain
| | - Verónica Ribas
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain
| | - José Salgado-Borges
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain
| | - Francesc March de Ribot
- Department of Ophthalmology, Hospital Universitari Dexeus, Area Oftalmológica Avanzada, Universitat Politécnica de Catalunya, Barcelona, Spain
| | | | - Noelia Armiger-Borras
- Pangaea Oncology, Laboratory of Oncology, Dexeus University Hospital, Barcelona, Spain
| | - Carlos Pedraz
- Pangaea Oncology, Laboratory of Oncology, Dexeus University Hospital, Barcelona, Spain
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Malapelle U, Pepe F, Pisapia P, Altimari A, Bellevicine C, Brunnström H, Bruno R, Büttner R, Cirnes L, De Andrea CE, de Biase D, Dumur CI, Ericson Lindquist K, Fontanini G, Gautiero E, Gentien D, Hofman P, Hofman V, Iaccarino A, Lozano MD, Mayo-de-Las-Casas C, Merkelbach-Bruse S, Pagni F, Roman R, Schmitt FC, Siemanowski J, Roy-Chowdhuri S, Tallini G, Tresserra F, Vander Borght S, Vielh P, Vigliar E, Vita GAC, Weynand B, Rosell R, Molina Vila MA, Troncone G. Reference standards for gene fusion molecular assays on cytological samples: an international validation study. J Clin Pathol 2023; 76:47-52. [PMID: 34429353 DOI: 10.1136/jclinpath-2021-207825] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/06/2021] [Indexed: 02/05/2023]
Abstract
AIMS Gene fusions assays are key for personalised treatments of advanced human cancers. Their implementation on cytological material requires a preliminary validation that may make use of cell line slides mimicking cytological samples. In this international multi-institutional study, gene fusion reference standards were developed and validated. METHODS Cell lines harbouring EML4(13)-ALK(20) and SLC34A2(4)-ROS1(32) gene fusions were adopted to prepare reference standards. Eight laboratories (five adopting amplicon-based and three hybridisation-based platforms) received, at different dilution points two sets of slides (slide A 50.0%, slide B 25.0%, slide C 12.5% and slide D wild type) stained by Papanicolaou (Pap) and May Grunwald Giemsa (MGG). Analysis was carried out on a total of 64 slides. RESULTS Four (50.0%) out of eight laboratories reported results on all slides and dilution points. While 12 (37.5%) out of 32 MGG slides were inadequate, 27 (84.4%) out of 32 Pap slides produced libraries adequate for variant calling. The laboratories using hybridisation-based platforms showed the highest rate of inadequate results (13/24 slides, 54.2%). Conversely, only 10.0% (4/40 slides) of inadequate results were reported by laboratories adopting amplicon-based platforms. CONCLUSIONS Reference standards in cytological format yield better results when Pap staining and processed by amplicon-based assays. Further investigation is required to optimise these standards for MGG stained cells and for hybridisation-based approaches.
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Affiliation(s)
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Annalisa Altimari
- Molecular Pathology, University of Bologna Hospital of Bologna Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
| | | | - Hans Brunnström
- Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden
| | - Rossella Bruno
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | | | | | | | - Dario de Biase
- Pharmacy and Biotechnology (FaBiT), Molecular Pathology Laboratory, University of Bologna, Bologna, Italy
| | | | | | - Gabriella Fontanini
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | | | - David Gentien
- Translational Research Department, Genomics Platform, Curie Institute Hospital Group, Paris, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Centre Nice Pasteur Hospital, Nice, France
| | - Veronique Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Centre Nice Pasteur Hospital, Nice, France
| | | | | | | | | | - Fabio Pagni
- Medicine and Surgery, San Gerardo Hospital, Monza, Italy
| | - Ruth Roman
- Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | | | - Sinchita Roy-Chowdhuri
- Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Giovanni Tallini
- Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Sara Vander Borght
- Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Philippe Vielh
- Pathology, Medipath and American Hospital of Paris, Paris, France
| | - Elena Vigliar
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Birgit Weynand
- Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Rafael Rosell
- Oncology, Hospital Municipal de Badalona, Barcelona, Spain
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Sánchez-Herrero E, Giménez-Capitán A, Robado de Lope L, Serna-Blasco R, Viteri S, Sanz-Moreno S, Mayo-de-Las-Casas C, Calvo V, Rosell R, González-Rumayor V, Provencio M, Romero A, Molina M. EP16.02-007 Detection of Clinically Relevant Fusions and Exon Skipping Alterations in Non Small Cell Lung Cancer Patients Liquid Biopsies. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.1038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Giménez-Capitán A, Bracht J, García JJ, Jordana-Ariza N, García B, Garzón M, Mayo-de-Las-Casas C, Viteri-Ramirez S, Martinez-Bueno A, Aguilar A, Sullivan IG, Johnson E, Huang CY, Gerlach JL, Warren S, Beechem JM, Teixidó C, Rosell R, Reguart N, Molina-Vila MA. Multiplex Detection of Clinically Relevant Mutations in Liquid Biopsies of Cancer Patients Using a Hybridization-Based Platform. Clin Chem 2021; 67:554-563. [PMID: 33439966 DOI: 10.1093/clinchem/hvaa248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/30/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND With the advent of precision oncology, liquid biopsies are quickly gaining acceptance in the clinical setting. However, in some cases, the amount of DNA isolated is insufficient for Next-Generation Sequencing (NGS) analysis. The nCounter platform could be an alternative, but it has never been explored for detection of clinically relevant alterations in fluids. METHODS Circulating-free DNA (cfDNA) was purified from blood, cerebrospinal fluid, and ascites of patients with cancer and analyzed with the nCounter 3 D Single Nucleotide Variant (SNV) Solid Tumor Panel, which allows for detection of 97 driver mutations in 24 genes. RESULTS Validation experiments revealed that the nCounter SNV panel could detect mutations at allelic fractions of 0.02-2% in samples with ≥5 pg mutant DNA/µL. In a retrospective analysis of 70 cfDNAs from patients with cancer, the panel successfully detected EGFR, KRAS, BRAF, PIK3CA, and NRAS mutations when compared with previous genotyping in the same liquid biopsies and paired tumor tissues [Cohen kappa of 0.96 (CI = 0.92-1.00) and 0.90 (CI = 0.74-1.00), respectively]. In a prospective study including 91 liquid biopsies from patients with different malignancies, 90 yielded valid results with the SNV panel and mutations in EGFR, KRAS, BRAF, PIK3CA, TP53, NFE2L2, CTNNB1, ALK, FBXW7, and PTEN were found. Finally, serial liquid biopsies from a patient with NSCLC revealed that the semiquantitative results of the mutation analysis by the SNV panel correlated with the evolution of the disease. CONCLUSIONS The nCounter platform requires less DNA than NGS and can be employed for routine mutation testing in liquid biopsies of patients with cancer.
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Affiliation(s)
- Ana Giménez-Capitán
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Jillian Bracht
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.,Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Juan José García
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Núria Jordana-Ariza
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Beatriz García
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Mónica Garzón
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Clara Mayo-de-Las-Casas
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | | | - Andrés Aguilar
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | | | | | | | | | | | - Cristina Teixidó
- Department of Pathology, Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Rafael Rosell
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.,Cancer Biology and Precision Medicine Program, Catalán Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Barcelona, Spain
| | - Noemí Reguart
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,Medical Oncology, Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
| | - Miguel A Molina-Vila
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
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5
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Bracht JWP, Mayo-de-Las-Casas C, Berenguer J, Karachaliou N, Rosell R. Correction to: The Present and Future of Liquid Biopsies in Non-Small Cell Lung Cancer: Combining Four Biosources for Diagnosis, Prognosis, Prediction, and Disease Monitoring. Curr Oncol Rep 2020; 22:52. [PMID: 32363551 DOI: 10.1007/s11912-020-00914-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The original version of this review article unfortunately contained a mistake in the Funding section.
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Affiliation(s)
- Jillian Wilhelmina Paulina Bracht
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain.,Universitat Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Clara Mayo-de-Las-Casas
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain
| | - Jordi Berenguer
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain
| | - Niki Karachaliou
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain. .,Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, QuironSalud Group, Viladomat 288, 08029, Barcelona, Spain.
| | - Rafael Rosell
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain. .,Institut Català d'Oncologia, Hospital Germans Trias i Pujol, Carretera de Canyet, s/n, 08916 Badalona, Barcelona, Spain. .,Institut d'Investigació en Ciències Germans Trias i Pujol, Camí de les Escoles, s/n, 08916 Badalona, Barcelona, Spain. .,Instituto Oncológico Dr Rosell (IOR), Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain.
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Mayo-de-Las-Casas C, Velasco A, Sanchez D, Martínez-Bueno A, Garzón-Ibáñez M, Gatius S, Ruiz-Miró M, Gonzalez-Tallada X, Llordella I, Tresserra F, Rodríguez S, Aldeguer E, Roman-Canal B, Bertran-Alamillo J, García-Peláez B, Rosell R, Molina-Vila MA, Matias-Guiu X. Detection of somatic mutations in peritoneal lavages and plasma of endometrial cancer patients: A proof-of-concept study. Int J Cancer 2020; 147:277-284. [PMID: 31953839 DOI: 10.1002/ijc.32872] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/10/2019] [Accepted: 01/03/2020] [Indexed: 12/18/2022]
Abstract
Endometrial cancer (EC) is the most common gynecologic malignancy in developed countries. Although most patients are diagnosed at early stages, 15-20% will relapse despite local treatment. Presently, there are no reliable markers to identify patients with worse outcomes who may benefit from adjuvant treatments, such as chemotherapy, and liquid biopsies may be of use in this setting. Peritoneal lavages are systematically performed during endometrial surgery but little data are available about their potential as liquid biopsies. We analyzed KRAS and PIK3CA mutations in paired surgical biopsies, blood and cytology-negative peritoneal lavages in a cohort of 50 EC patients. Surgical biopsies were submitted to next-generation sequencing (NGS) while circulating-free DNA (cfDNA) purified from plasma and peritoneal lavages was analyzed for KRAS and PIK3CA hotspot mutations using a sensitive quantitative polymerase chain reaction (PCR) assay. NGS of biopsies revealed KRAS, PIK3CA or concomitant KRAS + PIK3CA mutations in 33/50 (66%) EC patients. Of those, 19 cases carried hotspot mutations. Quantitative PCR revealed KRAS and/or PIK3CA mutations in the lavages of 9/19 (47.4%) hotspot EC patients. In contrast, only 2/19 (10.5%) blood samples from hotspot EC patients were positive. Mutations found in cfDNA consistently matched those in paired biopsies. One of the two patients positive in plasma and lavage died in less than 6 months. In conclusion, mutational analysis in peritoneal lavages and blood from early stage EC is feasible. Further studies are warranted to determine if it might help to identify patients with worse prognosis. Human genes discussed: KRAS, KRAS proto-oncogene, GTPase; PIK3CA, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha.
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Affiliation(s)
- Clara Mayo-de-Las-Casas
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Ana Velasco
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | - Douglas Sanchez
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | | | - Mónica Garzón-Ibáñez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Sònia Gatius
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | | | | | - Ivana Llordella
- Department of Gynecology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | - Francesc Tresserra
- Department of Pathology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Sonia Rodríguez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Erika Aldeguer
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | - Jordi Bertran-Alamillo
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Beatriz García-Peláez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Rafael Rosell
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
- Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Spain
| | - Miguel A Molina-Vila
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
- Hospital Universitari de Bellvitge, IDIBELL, Barcelona, Spain
- University of Lleida, CIBERONC, Lleida, Spain
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7
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Villatoro S, Mayo-de-Las-Casas C, Jordana-Ariza N, Viteri-Ramírez S, Garzón-Ibañez M, Moya-Horno I, García-Peláez B, González-Cao M, Malapelle U, Balada-Bel A, Martínez-Bueno A, Campos R, Reguart N, Majem M, Blanco R, Blasco A, Catalán MJ, González X, Troncone G, Karachaliou N, Rosell R, Molina-Vila MA. Prospective detection of mutations in cerebrospinal fluid, pleural effusion, and ascites of advanced cancer patients to guide treatment decisions. Mol Oncol 2019; 13:2633-2645. [PMID: 31529604 PMCID: PMC6887582 DOI: 10.1002/1878-0261.12574] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/06/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022] Open
Abstract
Many advanced cases of cancer show central nervous system, pleural, or peritoneal involvement. In this study, we prospectively analyzed if cerebrospinal fluid (CSF), pleural effusion (PE), and/or ascites (ASC) can be used to detect driver mutations and guide treatment decisions. We collected 42 CSF, PE, and ASC samples from advanced non‐small‐cell lung cancer and melanoma patients. Cell‐free DNA (cfDNA) was purified and driver mutations analyzed and quantified by PNA‐Q‐PCR or next‐generation sequencing. All 42 fluid samples were evaluable; clinically relevant mutations were detected in 41 (97.6%). Twenty‐three fluids had paired blood samples, 22 were mutation positive in fluid but only 14 in blood, and the abundance of the mutant alleles was significantly higher in fluids. Of the 34 fluids obtained at progression to different therapies, EGFR resistance mutations were detected in nine and ALK acquired mutations in two. The results of testing of CSF, PE, and ASC were used to guide treatment decisions, such as initiation of osimertinib treatment or selection of specific ALK tyrosine–kinase inhibitors. In conclusion, fluids close to metastatic sites are superior to blood for the detection of relevant mutations and can offer valuable clinical information, particularly in patients progressing to targeted therapies.
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Affiliation(s)
- Sergio Villatoro
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Clara Mayo-de-Las-Casas
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Núria Jordana-Ariza
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | - Mónica Garzón-Ibañez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Irene Moya-Horno
- Dr Rosell Oncology Institute, General Hospital of Catalonia, Sant Cugat del Vallés, Spain
| | - Beatriz García-Peláez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - María González-Cao
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Italy
| | - Ariadna Balada-Bel
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | - Raquel Campos
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Noemí Reguart
- Department of Medical Oncology, Hospital Clínic, Barcelona, Spain
| | - Margarita Majem
- Medical Oncology Service, Hospital de Sant Pau, Barcelona, Spain
| | - Remei Blanco
- Medical Oncology Service, Hospital de Terrassa, Spain
| | - Ana Blasco
- Medical Oncology Department, Hospital General Universitario de Valencia, Spain
| | - María J Catalán
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Xavier González
- Dr Rosell Oncology Institute, General Hospital of Catalonia, Sant Cugat del Vallés, Spain
| | | | - Niki Karachaliou
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.,Dr Rosell Oncology Institute, University Hospital Sagrat Cor, Barcelona, Spain
| | - Rafael Rosell
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.,Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.,Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Spain
| | - Miguel A Molina-Vila
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
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8
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Pisapia P, Malapelle U, Roma G, Saddar S, Zheng Q, Pepe F, Bruzzese D, Vigliar E, Bellevicine C, Luthra R, Nikiforov YE, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R, Bihl M, Savic S, Bubendorf L, de Biase D, Tallini G, Hwang DH, Sholl LM, Vander Borght S, Weynand B, Stieber D, Vielh P, Rappa A, Barberis M, Fassan M, Rugge M, De Andrea CE, Lozano MD, Lupi C, Fontanini G, Schmitt F, Dumur CI, Bisig B, Bongiovanni M, Merkelbach-Bruse S, Büttner R, Nikiforova MN, Roy-Chowdhuri S, Troncone G. Consistency and reproducibility of next-generation sequencing in cytopathology: A second worldwide ring trial study on improved cytological molecular reference specimens. Cancer Cytopathol 2019; 127:285-296. [PMID: 31021538 DOI: 10.1002/cncy.22134] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/05/2019] [Accepted: 04/02/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Artificial genomic reference standards in a cytocentrifuge/cytospin format with well-annotated genomic data are useful for validating next-generation sequencing (NGS) on routine cytopreparations. Here, reference standards were optimized to be stained by different laboratories before DNA extraction and to contain a lower number of cells (2 × 105 ). This was done to better reflect the clinical challenge of working with insufficient cytological material. METHODS A total of 17 worldwide laboratories analyzed customized reference standard slides (slides A-D). Each laboratory applied its standard workflow. The sample slides were engineered to harbor epidermal growth factor receptor (EGFR) c.2235_2249del15 p.E746_A750delELREA, EGFR c.2369C>T p.T790M, Kirsten rat sarcoma viral oncogene homolog (KRAS) c.38G>A p.G13D, and B-Raf proto-oncogene, serine/threonine kinase (BRAF) c.1798_1799GT>AA p.V600K mutations at various allele frequencies (AFs). RESULTS EGFR and KRAS mutation detection showed excellent interlaboratory reproducibility, especially on slides A and B (10% and 5% AFs). On slide C (1% AF), either the EGFR mutation or the KRAS mutation was undetected by 10 of the 17 laboratories (58.82%). A reassessment of the raw data in a second-look analysis highlighted the mutations (n = 10) that had been missed in the first-look analysis. BRAF c.1798_1799GT>AA p.V600K showed a lower concordance rate for mutation detection and AF quantification. CONCLUSIONS The data show that the detection of low-abundance mutations is still clinically challenging and may require a visual inspection of sequencing reads to detect. Genomic reference standards in a cytocentrifuge/cytospin format are a valid tool for regular quality assessment of laboratories performing molecular studies on cytology with low-AF mutations.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Roma
- AccuRef Diagnostics, Applied Stem Cell, Inc, Milpitas, California
| | - Sonika Saddar
- AccuRef Diagnostics, Applied Stem Cell, Inc, Milpitas, California
| | - Qi Zheng
- AccuRef Diagnostics, Applied Stem Cell, Inc, Milpitas, California
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Rajyalakshmi Luthra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuri E Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | - Rafael Rosell
- Catalan Institute of Oncology, Badalona, Spain
- Rosell Cancer Institute, Quiròn-Dexeus University Institute, Barcelona, Spain
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Anatomic Pathology, University of Bologna Medical Center, Bologna, Italy
| | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Birgit Weynand
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Alessandra Rappa
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine, University of Padua, Padua, Italy
| | - Massimo Rugge
- Surgical Pathology Unit, Department of Medicine, University of Padua, Padua, Italy
| | | | - Maria D Lozano
- Department of Pathology, University Clinic of Navarra, Pamplona, Spain
| | - Cristiana Lupi
- Department of Surgical, Medical, and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Fernando Schmitt
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Pathology, Medical Faculty, Porto University, Porto, Portugal
| | - Catherine I Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Bettina Bisig
- Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Sabine Merkelbach-Bruse
- Institute of Pathology and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Marina N Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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9
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Bracht JWP, Mayo-de-Las-Casas C, Berenguer J, Karachaliou N, Rosell R. The Present and Future of Liquid Biopsies in Non-Small Cell Lung Cancer: Combining Four Biosources for Diagnosis, Prognosis, Prediction, and Disease Monitoring. Curr Oncol Rep 2018; 20:70. [PMID: 30030656 DOI: 10.1007/s11912-018-0720-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsies have potential as tools for diagnosis, prognosis, and prediction of response to therapy. Herein, we will extensively review four liquid biosources, tumor-educated platelets (TEPs), cell-free DNA (cfDNA), circulating tumor cells (CTCs), and extracellular vesicles (EVs) and we will clarify their optimal application in non-small cell lung cancer (NSCLC) diagnosis and therapy. RECENT FINDINGS Liquid biopsies are a minimally invasive alternative to tissue biopsies-especially important in NSCLC patients-since tumor tissue is often unavailable or insufficient for complete genetic analysis. The main advantages of liquid biopsies include the possibility for repeated sampling, the lower cost, and the fact that they can reflect the complete molecular status of the patient better than a single-site biopsy. This is specifically important for lung adenocarcinoma patients since the detection of specific genetic alterations can predict response to targeted therapies. Molecular analysis is currently cardinal for therapy decision-making and disease monitoring in lung cancer patients. Liquid biopsies can make easier our daily clinical practice and if prospectively tested and validated may serve as a means for lung cancer early detection.
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Affiliation(s)
| | - Clara Mayo-de-Las-Casas
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain
| | - Jordi Berenguer
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain
| | - Niki Karachaliou
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain. .,Instituto Oncológico Dr Rosell (IOR), University Hospital Sagrat Cor, QuironSalud Group, Viladomat 288, 08029, Barcelona, Spain.
| | - Rafael Rosell
- Pangaea Oncology, Laboratory of Molecular Biology, Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain. .,Institut Català d'Oncologia, Hospital Germans Trias i Pujol, Carretera de Canyet, s/n, 08916, Badalona, Barcelona, Spain. .,Institut d'Investigació en Ciències Germans Trias i Pujol, Camí de les Escoles, s/n, 08916, Badalona, Barcelona, Spain. .,Instituto Oncológico Dr Rosell (IOR), Quirón-Dexeus University Institute, Sabino Arana 5-19, 08028, Barcelona, Spain.
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10
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Mayo-de-Las-Casas C, Jordana-Ariza N, Garzón-Ibañez M, Balada-Bel A, Bertrán-Alamillo J, Viteri-Ramírez S, Reguart N, Muñoz-Quintana MA, Lianes-Barragan P, Camps C, Jantús E, Remon-Massip J, Calabuig S, Aguiar D, Gil ML, Viñolas N, Santos-Rodríguez AK, Majem M, García-Peláez B, Villatoro S, Pérez-Rosado A, Monasterio JC, Ovalle E, Catalán MJ, Campos R, Morales-Espinosa D, Martínez-Bueno A, González-Cao M, González X, Moya-Horno I, Sosa AE, Karachaliou N, Rosell R, Molina-Vila MA. Large scale, prospective screening of EGFR mutations in the blood of advanced NSCLC patients to guide treatment decisions. Ann Oncol 2018; 28:2248-2255. [PMID: 28911086 DOI: 10.1093/annonc/mdx288] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background In a significant percentage of advanced non-small-cell lung cancer (NSCLC) patients, tumor tissue is unavailable or insufficient for genetic analyses. We prospectively analyzed if circulating-free DNA (cfDNA) purified from blood can be used as a surrogate in this setting to select patients for treatment with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). Patients and methods Blood samples were collected in 119 hospitals from 1138 advanced NSCLC patients at presentation (n = 1033) or at progression to EGFR-TKIs (n = 105) with no biopsy or insufficient tumor tissue. Serum and plasma were sent to a central laboratory, cfDNA purified and EGFR mutations analyzed and quantified using a real-time PCR assay. Response data from a subset of patients (n = 18) were retrospectively collected. Results Of 1033 NSCLC patients at presentation, 1026 were assessable; with a prevalence of males and former or current smokers. Sensitizing mutations were found in the cfDNA of 113 patients (11%); with a majority of females, never smokers and exon 19 deletions. Thirty-one patients were positive only in plasma and 11 in serum alone and mutation load was higher in plasma and in cases with exon 19 deletions. More than 50% of samples had <10 pg mutated genomes/µl with allelic fractions below 0.25%. Patients treated first line with TKIs based exclusively on EGFR positivity in blood had an ORR of 72% and a median PFS of 11 months. Of 105 patients screened after progression to EGFR-TKIs, sensitizing mutations were found in 56.2% and the p.T790M resistance mutation in 35.2%. Conclusions Large-scale EGFR testing in the blood of unselected advanced NSCLC patients is feasible and can be used to select patients for targeted therapy when testing cannot be done in tissue. The characteristics and clinical outcomes to TKI treatment of the EGFR-mutated patients identified are undistinguishable from those positive in tumor.
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Affiliation(s)
- C Mayo-de-Las-Casas
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - N Jordana-Ariza
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - M Garzón-Ibañez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - A Balada-Bel
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - J Bertrán-Alamillo
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - S Viteri-Ramírez
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona
| | - N Reguart
- Department of Medical Oncology, Hospital Clínic, Barcelona
| | - M A Muñoz-Quintana
- Department of Medical Oncology, Valencia Institute of Oncology, Valencia
| | | | - C Camps
- Molecular Oncology Laboratory, Fundación Investigación, Valencia General University Hospital, Valencia.,CIBERONC, Valencia.,Medical Oncology Department, Valencia General University Hospital, Valencia.,Department of Medicine, Universitat de València
| | - E Jantús
- Molecular Oncology Laboratory, Fundación Investigación, Valencia General University Hospital, Valencia.,CIBERONC, Valencia.,Department of Biotechnology, Universitat Politècnica de València
| | | | - S Calabuig
- Molecular Oncology Laboratory, Fundación Investigación, Valencia General University Hospital, Valencia.,CIBERONC, Valencia.,Department of Biotechnology, Universitat Politècnica de València
| | - D Aguiar
- Department of Medical Oncology, Hospital Dr Negrín of Gran Canaria, Las Palmas
| | - M L Gil
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - N Viñolas
- Department of Medical Oncology, Hospital Clínic, Barcelona
| | | | - M Majem
- Medical Oncology Service, Hospital de Sant Pau, Barcelona
| | - B García-Peláez
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - S Villatoro
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - A Pérez-Rosado
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - J C Monasterio
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - E Ovalle
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - M J Catalán
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - R Campos
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
| | - D Morales-Espinosa
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona
| | - A Martínez-Bueno
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona
| | - M González-Cao
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona
| | - X González
- Dr Rosell Oncology Institute, General Hospital of Catalonia, Sant Cugat del Vallés
| | - I Moya-Horno
- Dr Rosell Oncology Institute, General Hospital of Catalonia, Sant Cugat del Vallés
| | - A E Sosa
- Dr Rosell Oncology Institute, University Hospital Sagrat Cor, Barcelona
| | - N Karachaliou
- Dr Rosell Oncology Institute, University Hospital Sagrat Cor, Barcelona
| | - R Rosell
- Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Spain
| | - M A Molina-Vila
- Laboratory of Oncology, Pangaea Oncology, Quirón Dexeus University Hospital, Barcelona
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11
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Mayo-de-Las-Casas C, Garzón Ibáñez M, Jordana-Ariza N, García-Peláez B, Balada-Bel A, Villatoro S, Malapelle U, Karachaliou N, Troncone G, Rosell R, Molina-Vila MA. An update on liquid biopsy analysis for diagnostic and monitoring applications in non-small cell lung cancer. Expert Rev Mol Diagn 2017; 18:35-45. [PMID: 29172773 DOI: 10.1080/14737159.2018.1407243] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients. Expert commentary: Detection of somatic alterations in cfDNA is already in use in clinical practice and provides valuable information for patient management. Monitoring baseline alterations and emergence of resistance mutations is one of the most important clinical applications and can be used to non-invasively track disease evolution. Today, different technologies are available for cfDNA analysis, including whole-genome or exome sequencing and targeted methods that focus on a selection of genes of interest in a specific disease. In the case of Next Generation Sequencing (NGS) approaches, in depth coverage of candidate mutation loci can be achieved by selecting a limited number of targeted genes.
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Affiliation(s)
| | | | | | | | - Ariadna Balada-Bel
- a Pangaea Oncology , Quirón Dexeus University Hospital , Barcelona , Spain
| | - Sergio Villatoro
- a Pangaea Oncology , Quirón Dexeus University Hospital , Barcelona , Spain
| | - Umberto Malapelle
- b Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Niki Karachaliou
- c Dr Rosell Oncology Institute , University Hospital Sagrat Cor , Barcelona , Spain
| | - Giancarlo Troncone
- b Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Rafael Rosell
- d Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology , Germans Trias i Pujol Health Sciences Institute and Hospital , Badalona , Spain
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12
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Malapelle U, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R, Savic S, Bihl M, Bubendorf L, Salto-Tellez M, de Biase D, Tallini G, Hwang DH, Sholl LM, Luthra R, Weynand B, Vander Borght S, Missiaglia E, Bongiovanni M, Stieber D, Vielh P, Schmitt F, Rappa A, Barberis M, Pepe F, Pisapia P, Serra N, Vigliar E, Bellevicine C, Fassan M, Rugge M, de Andrea CE, Lozano MD, Basolo F, Fontanini G, Nikiforov YE, Kamel-Reid S, da Cunha Santos G, Nikiforova MN, Roy-Chowdhuri S, Troncone G. Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens. Cancer Cytopathol 2017; 125:615-626. [PMID: 28475299 DOI: 10.1002/cncy.21868] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/23/2017] [Accepted: 03/10/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears. However, the current literature reflects single-institution studies rather than multicenter experiences. METHODS Quantitative cytological molecular reference slides were produced with cell lines designed to harbor concurrent mutations in the EGFR, KRAS, NRAS, BRAF, and PIK3CA genes at various allelic ratios, including low allele frequencies (AFs; 1%). This interlaboratory ring trial study included 14 institutions across the world that performed multigene mutational assays, from tissue extraction to data analysis, on these reference slides, with each laboratory using its own mutation analysis platform and methodology. RESULTS All laboratories using NGS (n = 11) successfully detected the study's set of mutations with minimal variations in the means and standard errors of variant fractions at dilution points of 10% (P = .171) and 5% (P = .063) despite the use of different sequencing platforms (Illumina, Ion Torrent/Proton, and Roche). However, when mutations at a low AF of 1% were analyzed, the concordance of the NGS results was low, and this reflected the use of different thresholds for variant calling among the institutions. In contrast, laboratories using matrix-assisted laser desorption/ionization-time of flight (n = 2) showed lower concordance in terms of mutation detection and mutant AF quantification. CONCLUSIONS Quantitative molecular reference slides are a useful tool for monitoring the performance of different multigene mutational assays, and this could lead to better standardization of molecular cytopathology procedures. Cancer Cytopathol 2017;125:615-26. © 2017 American Cancer Society.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | | | - Rafael Rosell
- Catalan Institute of Oncology, Badalona, Spain
- Instituto Oncológico Dr Rosell (IOR), Quirón-Dexeus University Institute, Barcelona, Spain
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Manuel Salto-Tellez
- Molecular Pathology Programme, Centre for Cancer Research and Cell Biology Queen's University Belfast, Belfast, United Kingdom
| | - Dario de Biase
- Department of Pharmacy and Biotechnology - University of Bologna, Bologna, Italy
| | | | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Rajyalakshmi Luthra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Birgit Weynand
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Sara Vander Borght
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Edoardo Missiaglia
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Massimo Bongiovanni
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | | | | | - Alessandra Rappa
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Nicola Serra
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | - Massimo Rugge
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | | | - Maria D Lozano
- Department of Pathology, University Clinic of Navarra, Pamplona, Spain
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Yuri E Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Suzanne Kamel-Reid
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Gilda da Cunha Santos
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Marina N Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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13
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Molina-Vila MA, Mayo-de-Las-Casas C, Giménez-Capitán A, Jordana-Ariza N, Garzón M, Balada A, Villatoro S, Teixidó C, García-Peláez B, Aguado C, Catalán MJ, Campos R, Pérez-Rosado A, Bertran-Alamillo J, Martínez-Bueno A, Gil MDLL, González-Cao M, González X, Morales-Espinosa D, Viteri S, Karachaliou N, Rosell R. Liquid Biopsy in Non-Small Cell Lung Cancer. Front Med (Lausanne) 2016; 3:69. [PMID: 28066769 PMCID: PMC5179978 DOI: 10.3389/fmed.2016.00069] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022] Open
Abstract
Liquid biopsy analyses are already incorporated in the routine clinical practice in many hospitals and oncology departments worldwide, improving the selection of treatments and monitoring of lung cancer patients. Although they have not yet reached its full potential, liquid biopsy-based tests will soon be as widespread as “standard” biopsies and imaging techniques, offering invaluable diagnostic, prognostic, and predictive information. This review summarizes the techniques available for the isolation and analysis of circulating free DNA and RNA, exosomes, tumor-educated platelets, and circulating tumor cells from the blood of cancer patients, presents the methodological challenges associated with each of these materials, and discusses the clinical applications of liquid biopsy testing in lung cancer.
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Affiliation(s)
- Miguel A Molina-Vila
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Clara Mayo-de-Las-Casas
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Ana Giménez-Capitán
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Núria Jordana-Ariza
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Mónica Garzón
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Ariadna Balada
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Sergi Villatoro
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Cristina Teixidó
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Beatriz García-Peláez
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Cristina Aguado
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - María José Catalán
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Raquel Campos
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Ana Pérez-Rosado
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Jordi Bertran-Alamillo
- Laboratory of Oncology, Pangaea Biotech, Quirón Dexeus University Hospital , Barcelona , Spain
| | | | | | - María González-Cao
- Instituto Oncológico Dr Rosell, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Xavier González
- Instituto Oncológico Dr Rosell, Quirón Dexeus University Hospital , Barcelona , Spain
| | | | - Santiago Viteri
- Instituto Oncológico Dr Rosell, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Niki Karachaliou
- Instituto Oncológico Dr Rosell, Quirón Dexeus University Hospital , Barcelona , Spain
| | - Rafael Rosell
- Instituto Oncológico Dr Rosell, Quirón Dexeus University Hospital, Barcelona, Spain; Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Spain
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14
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Karachaliou N, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R. Real-time liquid biopsies become a reality in cancer treatment. Ann Transl Med 2015; 3:36. [PMID: 25815297 DOI: 10.3978/j.issn.2305-5839.2015.01.16] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/05/2015] [Indexed: 11/14/2022]
Affiliation(s)
- Niki Karachaliou
- 1 Instituto Oncológico Dr Rosell (IOR), Quirón Dexeus University Hospital, Barcelona, Spain ; 2 Pangaea Biotech, Barcelona, Spain ; 3 Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain ; 4 MORE Foundation, Barcelona, Spain ; 5 Cancer Therapeutic Innovation Group, New York, NY, USA
| | - Clara Mayo-de-Las-Casas
- 1 Instituto Oncológico Dr Rosell (IOR), Quirón Dexeus University Hospital, Barcelona, Spain ; 2 Pangaea Biotech, Barcelona, Spain ; 3 Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain ; 4 MORE Foundation, Barcelona, Spain ; 5 Cancer Therapeutic Innovation Group, New York, NY, USA
| | - Miguel Angel Molina-Vila
- 1 Instituto Oncológico Dr Rosell (IOR), Quirón Dexeus University Hospital, Barcelona, Spain ; 2 Pangaea Biotech, Barcelona, Spain ; 3 Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain ; 4 MORE Foundation, Barcelona, Spain ; 5 Cancer Therapeutic Innovation Group, New York, NY, USA
| | - Rafael Rosell
- 1 Instituto Oncológico Dr Rosell (IOR), Quirón Dexeus University Hospital, Barcelona, Spain ; 2 Pangaea Biotech, Barcelona, Spain ; 3 Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Spain ; 4 MORE Foundation, Barcelona, Spain ; 5 Cancer Therapeutic Innovation Group, New York, NY, USA
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