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Zhou D, Zhang Y, Chen W, Jiang J, Chen Y, Zhou X, Tang Q. Enhanced ultrasound-guided versus non-enhanced ultrasound-guided percutaneous needle biopsy in tissue cellularity of lung malignancies: a propensity score matched study. Quant Imaging Med Surg 2022; 12:5056-5067. [PMID: 36330190 PMCID: PMC9622440 DOI: 10.21037/qims-22-119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2023]
Abstract
BACKGROUND Though ultrasound-guided percutaneous lung needle biopsy (US-PLNB) is a first-line small biopsy method for peripheral lung lesions, quality of cellularity in specimens obtained via US-PLNB is uncertain. This study investigated the accuracy, sensitivity, and cellularity of US-PLNB. It examined the ability of contrast-enhanced ultrasound (CEUS) to improve the effectiveness of US-PLNB. METHODS We retrospectively analyzed all data of patients with subpleural lung lesions who underwent US-PLNB. The cellularity of US-PLNB from malignant lesions included the tumor cell number and proportion. The definition of high-quality cellularity (HQC) was concurrently achieving a tumor cell number ≥400 and a proportion ≥20%. The sensitivity, the actual numbers of tumor cell number/proportion, and the rate of HQC were calculated and compared between the CEUS and non-enhanced US groups after propensity score matching (PSM) with subgroup analyses by lesion size (small lesion ≤30 mm and large lesion >30 mm). RESULTS A total of 345 patients undergoing 345 US-PLNBs were evaluated, with 3.7±1.1 of punctures on average. There were 201 malignant and 144 benign lesions with a mean size of 43.8±24.1 mm. Among the 201 malignant lesions, 124 cases underwent CEUS and 77 underwent non-enhanced US. The quantity of tumor cells, the proportion of tumor cells, and the rate of HQC in 201 cases of US-PLNB from malignant lesions were 2,862.1±2,288.0, 44.6%±24.5%, and 82.1% [95% confidence interval (CI): 76.6% to 87.1%], respectively. The quantity of tumor cells, the proportion of tumor cells, and rate of HQC were significantly higher in the CEUS group than that in the non-enhanced US group, both in the analysis of overall malignant lesions and in large malignant lesions (all P<0.05). CONCLUSIONS The US-PLNB has high sensitivity and thereby obtains HQC samples for subpleural lung malignant lesions. The CEUS helps improve the rate of HQC and tissue cellularity of lung malignancies.
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Affiliation(s)
- Dazhi Zhou
- Department of Ultrasound, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuxin Zhang
- Department of Ultrasound, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wuxi Chen
- Department of Ultrasound, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Juhong Jiang
- The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yanbin Chen
- Department of Ultrasound, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinghua Zhou
- Department of Ultrasound, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qing Tang
- Department of Ultrasound, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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2
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Penault-Llorca F, Kerr KM, Garrido P, Thunnissen E, Dequeker E, Normanno N, Patton SJ, Fairley J, Kapp J, de Ridder D, Ryška A, Moch H. Expert opinion on NSCLC small specimen biomarker testing - Part 1: Tissue collection and management. Virchows Arch 2022; 481:335-350. [PMID: 35857102 PMCID: PMC9485167 DOI: 10.1007/s00428-022-03343-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 12/11/2022]
Abstract
Biomarker testing is crucial for treatment selection in advanced non-small cell lung cancer (NSCLC). However, the quantity of available tissue often presents a key constraint for patients with advanced disease, where minimally invasive tissue biopsy typically returns small samples. In Part 1 of this two-part series, we summarise evidence-based recommendations relating to small sample processing for patients with NSCLC. Generally, tissue biopsy techniques that deliver the greatest quantity and quality of tissue with the least risk to the patient should be selected. Rapid on-site evaluation can help to ensure sufficient sample quality and quantity. Sample processing should be managed according to biomarker testing requirements, because tissue fixation methodology influences downstream nucleic acid, protein and morphological analyses. Accordingly, 10% neutral buffered formalin is recommended as an appropriate fixative, and the duration of fixation is recommended not to exceed 24–48 h. Tissue sparing techniques, including the ‘one biopsy per block’ approach and small sample cutting protocols, can help preserve tissue. Cytological material (formalin-fixed paraffin-embedded [FFPE] cytology blocks and non-FFPE samples such as smears and touch preparations) can be an excellent source of nucleic acid, providing either primary or supplementary patient material to complete morphological and molecular diagnoses. Considerations on biomarker testing, reporting and quality assessment are discussed in Part 2.
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Affiliation(s)
| | - Keith M Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen, UK
| | - Pilar Garrido
- Medical Oncology Department, Hospital Universitario Ramón Y Cajal, University of Alcalá, Madrid, Spain
| | - Erik Thunnissen
- Amsterdam University Medical Center, VU Medical Center, Amsterdam, the Netherlands
| | - Elisabeth Dequeker
- Department of Public Health, Biomedical Quality Assurance Research Unit, Campus Gasthuisberg, University Leuven, Leuven, Belgium
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale" IRCCS, Naples, Italy
| | | | | | | | | | - Aleš Ryška
- Department of Pathology, Charles University Medical Faculty Hospital, Hradec Králové, Czech Republic
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
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Huang LT, Zhang SL, Han CB, Ma JT. Impact of EGFR Exon 19 Deletion Subtypes on Clinical Outcomes in EGFR-TKI-Treated Advanced Non-Small-Cell Lung Cancer. Lung Cancer 2022; 166:9-16. [DOI: 10.1016/j.lungcan.2022.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 12/24/2022]
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Russo A, Incorvaia L, Capoluongo E, Tagliaferri P, Galvano A, Del Re M, Malapelle U, Chiari R, Conte P, Danesi R, Fassan M, Ferrara R, Genuardi M, Ghiorzo P, Gori S, Guadagni F, Marchetti A, Marchetti P, Midiri M, Normanno N, Passiglia F, Pinto C, Silvestris N, Tallini G, Vatrano S, Vincenzi B, Cinieri S, Beretta G. The challenge of the Molecular Tumor Board empowerment in clinical oncology practice: A Position Paper on behalf of the AIOM- SIAPEC/IAP-SIBioC-SIC-SIF-SIGU-SIRM Italian Scientific Societies. Crit Rev Oncol Hematol 2021; 169:103567. [PMID: 34896250 DOI: 10.1016/j.critrevonc.2021.103567] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 10/19/2022] Open
Abstract
The development of innovative technologies and the advances in the genetics and genomics, have offered new opportunities for personalized treatment in oncology. Although the selection of the patient based on the molecular characteristics of the neoplasm has the potential to revolutionize the therapeutic scenario of oncology, this approach is extremely challenging. The access, homogeneity, and economic sustainability of the required genomic tests should be warranted in the clinical practice, as well as the specific scientific and clinical expertise for the choice of medical therapies. All these elements make essential the collaboration of different specialists within the Molecular Tumor Boards (MTBs). In this position paper, based on experts' opinion, the AIOM-SIAPEC/IAP-SIBioC-SIC-SIF-SIGU-SIRM Italian Scientific Societies critically discuss the available molecular profiling technologies, the proposed criteria for the selection of patients candidate for evaluation by the MTB, the criteria for the selection and analysis of biological samples, and the regulatory and pharmaco-economic issues.
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Affiliation(s)
- Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy.
| | - Lorena Incorvaia
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Ettore Capoluongo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Pansini 5, 80131, Naples, Italy; CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80131, Naples, Italy
| | - Pierosandro Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, 88100, Catanzaro, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80138, Naples, Italy
| | - Rita Chiari
- Medical Oncology, AULSS 6 Euganea, South Padova Hospital, Monselice, PD, Italy
| | - Pierfranco Conte
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Medical Oncology 2, Istituto Oncologico Veneto - IRCCS, Via Gattamelata 64, 35128, Padua, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy; Veneto Institute of Oncology, IOV - IRCCS, Padua, Italy
| | - Roberto Ferrara
- Department of Medical Oncology, Thoracic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133, Milan, Italy
| | - Maurizio Genuardi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo F. Vito 1, 00168, Roma, Italy; UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy; Department of Internal Medicine and Medical Specialties, University of Genoa, 16132, Genoa, Italy
| | - Stefania Gori
- Department of Oncology, IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - Fiorella Guadagni
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, 00166, Rome, Italy
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Italy
| | - Paolo Marchetti
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Massimo Midiri
- Section of Radiology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), University of Palermo, Via del Vespro 129, 90127, Palermo, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Naples, Italy
| | - Francesco Passiglia
- Department of Oncology, University of Turin, San Luigi Hospital, Turin, Italy
| | - Carmine Pinto
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS-AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology, Department of Internal Medicine and Oncology (DIMO), University of Bari, Bari, Italy
| | - Giovanni Tallini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Simona Vatrano
- Department of Pathology, Cannizzaro Hospital, Catania, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, Campus Bio-Medico University, 00128, Rome, Italy
| | - Saverio Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
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Torres GF, Bonilla CE, Buitrago G, Arrieta O, Malapelle U, Rolfo C, Cardona AF. How clinically useful is comprehensive genomic profiling for patients with non-small cell lung cancer? A systematic review. Crit Rev Oncol Hematol 2021; 166:103459. [PMID: 34461270 DOI: 10.1016/j.critrevonc.2021.103459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 08/22/2021] [Indexed: 12/18/2022] Open
Abstract
Given the lack of a gold standard, the clinical usefulness of Comprehensive Genomic Profiling (CGP) has not been established. This systematic review aimed to evaluate evidence about the clinical benefit of CGP for patients with Non-small cell lung carcinoma (NSCLC). All controlled studies that evaluated the ability of CGP to detect actionable targets (ATs) reported increases in the number of samples with ATs. The frequency of ATs detected in uncontrolled case series ranged from 0.7 % for RET mutations to 45 % for EGFR mutations. The studies that evaluated therapies targeted to EGFR, ALK, ROS-1, MET, and RET mutations documented significant improvement in clinical outcomes. This review suggests that CGP tests may be clinically helpful for treating patients with NSCLC. Although current evidence is associated with a high risk of bias, the significant impact of NSCLC on individuals and society may justify the routine use of CGP testing for this disease.
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Affiliation(s)
| | - Carlos Eduardo Bonilla
- Clinical Oncology Department, Instituto Nacional de Cancerología - INC, Bogotá, Colombia
| | - Giancarlo Buitrago
- Instituto de Investigaciones Clínicas, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Oscar Arrieta
- Thoracic Oncology Unit, National Cancer Institute (INCan), México City, Mexico
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Center, Mount Sinai Hospital System & Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia; Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad el Bosque, Bogotá, Colombia; Clinical and Traslational Oncology Group, Clínica del Country, Bogotá, Colombia
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Impact of Endoscopic Ultrasound-Guided Tissue Acquisition on Decision-Making in Precision Medicine for Pancreatic Cancer: Beyond Diagnosis. Diagnostics (Basel) 2021; 11:diagnostics11071195. [PMID: 34209310 PMCID: PMC8307595 DOI: 10.3390/diagnostics11071195] [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: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Precision medicine in cancer treatment refers to targeted therapy based on the evaluation of biomarkers. Although precision medicine for pancreatic cancer (PC) remains challenging, novel biomarker-based therapies, such as pembrolizumab, olaparib, and entrectinib, have been emerging. Most commonly, endoscopic ultrasound-guided tissue acquisition (EUS-TA) had been used for the diagnosis of PC until now. However, advances in EUS-TA devices and biomarker testing, especially next-generation sequencing, have opened up the possibility of sequencing of various genes even in limited amounts of tissue samples obtained by EUS-TA, and identifying potential genetic alterations as therapeutic targets. Precision medicine benefits only a small population of patients with PC, but biomarker-based therapy has shown promising results in patients who once had no treatment options. Now, the role of EUS-TA has extended beyond diagnosis into decision-making regarding the treatment of PC. In this review, we mainly discuss tissue sampling by EUS-TA for biomarker testing and the current status of precision medicine for PC.
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Franceschi E, De Biase D, Di Nunno V, Pession A, Tosoni A, Gatto L, Tallini G, Visani M, Lodi R, Bartolini S, Brandes AA. IDH1 Non-Canonical Mutations and Survival in Patients with Glioma. Diagnostics (Basel) 2021; 11:diagnostics11020342. [PMID: 33669525 PMCID: PMC7922632 DOI: 10.3390/diagnostics11020342] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Non-canonical mutations of the isocitrate dehydrogenase (IDH) genes have been described in about 20-25% and 5-12% of patients with WHO grade II and III gliomas, respectively. To date, the prognostic value of these rare mutations is still a topic of debate. METHODS We selected patients with WHO grade II and III gliomas and IDH1 mutations with available tissue samples for next-generation sequencing. The clinical outcomes and baseline behaviors of patients with canonical IDH1 R132H and non-canonical IDH1 mutations were compared. RESULTS We evaluated 433 patients harboring IDH1 mutations. Three hundred and ninety patients (90.1%) had a canonical IDH1 R132H mutation while 43 patients (9.9%) had a non-canonical IDH1 mutation. Compared to those with the IDH1 canonical mutation, patients with non-canonical mutations were younger (p < 0.001) and less frequently presented the 1p19q codeletion (p = 0.017). Multivariate analysis confirmed that the extension of surgery (p = 0.003), the presence of the 1p19q codeletion (p = 0.001), and the presence of a non-canonical mutation (p = 0.041) were variables correlated with improved overall survival. CONCLUSION the presence of non-canonical IDH1 mutations could be associated with improved survival among patients with IDH1 mutated grade II-III glioma.
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Affiliation(s)
- Enrico Franceschi
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
- Correspondence: ; Tel.: +39-05-1622-5697
| | - Dario De Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, 40126 Bologna, Italy; (D.D.B.); (A.P.)
| | - Vincenzo Di Nunno
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, 40126 Bologna, Italy; (D.D.B.); (A.P.)
| | - Alicia Tosoni
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Lidia Gatto
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, 40126 Bologna, Italy; (G.T.); (M.V.)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale)-Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, 40126 Bologna, Italy; (G.T.); (M.V.)
| | - Raffaele Lodi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy;
| | - Stefania Bartolini
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
| | - Alba Ariela Brandes
- Department of Oncology, AUSL Bologna, 40139 Bologna, Italy; (V.D.N.); (A.T.); (L.G.); (S.B.); (A.A.B.)
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Schluckebier L, Caetano R, Garay OU, Montenegro GT, Custodio M, Aran V, Gil Ferreira C. Cost-effectiveness analysis comparing companion diagnostic tests for EGFR, ALK, and ROS1 versus next-generation sequencing (NGS) in advanced adenocarcinoma lung cancer patients. BMC Cancer 2020; 20:875. [PMID: 32928143 PMCID: PMC7489015 DOI: 10.1186/s12885-020-07240-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/30/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The treatment of choice for advanced non-small cell lung cancer is selected according to the presence of specific alterations. Patients should undergo molecular testing for relevant modifications and the mutational status of EGFR and translocation of ALK and ROS1 are commonly tested to offer the best intervention. In addition, the tests costs should also be taken in consideration. Therefore, this work was performed in order to evaluate the cost-effectiveness of a unique exam using NGS (next generation sequencing) versus other routinely used tests which involve RT-PCR and FISH. METHODS The target population was NSCLC, adenocarcinoma, and candidates to first-line therapy. Two strategies were undertaken, strategy 1 corresponded to sequential tests with EGFR RT-PCR, then FISH for ALK and ROS1. Strategy 2 differed from 1 in that ALK and ROS1 translocation testing were performed simultaneously by FISH. Strategy 3 considered single test next-generation sequencing, a platform that includes EGFR, ALK and ROS1 genes. A decision tree analysis was used to model genetic testing options. From the test results, a microsimulation model was nested to estimate survival outcomes and costs of therapeutic options. RESULTS The use of NGS added 24% extra true cases as well as extra costs attributed to the molecular testing. The ICER comparing NGS with sequential tests was US$ 3479.11/correct case detected. The NGS improved a slight gain in life years and QALYs. CONCLUSION Our results indicated that, although precise, the molecular diagnosis by NGS of patients with advanced stage NSCLC adenocarcinoma histology was not cost-effective in terms of quality-adjusted life years from the perspective of the Brazilian supplementary health system.
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Affiliation(s)
| | - Rosangela Caetano
- Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Osvaldo Ulises Garay
- Instituto de Efectividad Clinica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina
- Roche Diagnóstica, Buenos Aires, Argentina
| | | | | | - Veronica Aran
- Fundação do Câncer, 212 - Centro, Rio de janeiro, 20231-048, Brazil.
- Instituto Estadual do Cérebro Paulo Niemeyer, R. do Rezende, 156 - Centro, Rio de Janeiro, 20231-092, Brazil.
| | - Carlos Gil Ferreira
- Fundação do Câncer, 212 - Centro, Rio de janeiro, 20231-048, Brazil
- Oncoclínicas, Rio de Janeiro, Brazil
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Stewart DJ, Bosse D, Robinson A, Ong M, Fung-Kee-Fung M, Brule S, Hilton JF, Ocana A. Potential insights from population kinetic assessment of progression-free survival curves. Crit Rev Oncol Hematol 2020; 153:103039. [PMID: 32622319 DOI: 10.1016/j.critrevonc.2020.103039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022] Open
Abstract
Progression-free survival (PFS) curves follow first order kinetics on exponential decay nonlinear regression analysis (EDNLRA). Some exhibit 1-phase-decay, some have 2-phase-decay, some are convex. We digitized, performed EDNLRA and generated log-linear plots for 887 published PFS curves for incurable solid tumors treated with various systemic therapies. Proportion of curves fitting 2-phase-decay varied by therapy (p < 0.0001). For 13 therapies, >64 % of PFS curves had 2-phase-decay. This included epidermal growth factor receptor inhibitors in unselected lung cancer patients (some with, some without mutations), immune checkpoint inhibitors, interferon, breast cancer hormonal therapies, and selected others, suggesting 2 distinct, potentially identifiable subpopulations with differing progression rates. For 22 other therapies, <25 % of PFS curves had 2-phase-decay. Only 1 therapy was in the mid-range. Small cell lung and colon carcinomas were particularly likely to yield highly convex curves (p < 0.006), probably from discontinuation of effective therapies. PFS curve shape may yield biological and clinical insights.
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Affiliation(s)
| | | | | | - Michael Ong
- University of Ottawa, Ottawa, ON, United States
| | | | | | | | - Alberto Ocana
- Experimental Therapeutics Unit, Hospital Clínico San Carlos, and CIBERONC, Madrid, Spain
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Analysis of Single Nucleotide-Mutated Single-Cancer Cells Using the Combined Technologies of Single-Cell Microarray Chips and Peptide Nucleic Acid-DNA Probes. MICROMACHINES 2020; 11:mi11070628. [PMID: 32605095 PMCID: PMC7407912 DOI: 10.3390/mi11070628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022]
Abstract
Research into cancer cells that harbor gene mutations relating to anticancer drug-resistance at the single-cell level has focused on the diagnosis of, or treatment for, cancer. Several methods have been reported for detecting gene-mutated cells within a large number of non-mutated cells; however, target single nucleotide-mutated cells within a large number of cell samples, such as cancer tissue, are still difficult to analyze. In this study, a new system is developed to detect and isolate single-cancer cells expressing the T790M-mutated epidermal growth factor receptor (EGFR) mRNA from multiple non-mutated cancer cells by combining single-cell microarray chips and peptide nucleic acid (PNA)-DNA probes. The single-cell microarray chip is made of polystyrene with 62,410 microchambers (31-40 µm diameter). The T790M-mutated lung cancer cell line, NCI-H1975, and non-mutated lung cancer cell line, A549, were successfully separated into single cells in each microchambers on the chip. Only NCI-H1975 cell was stained on the chip with a fluorescein isothiocyanate (FITC)-conjugated PNA probe for specifically detecting T790M mutation. Of the NCI-H1975 cells that spiked into A549 cells, 0–20% were quantitatively analyzed within 1 h, depending on the spike concentration. Therefore, our system could be useful in analyzing cancer tissue that contains a few anticancer drug-resistant cells.
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de Biase D, Acquaviva G, Visani M, Sanza V, Argento CM, De Leo A, Maloberti T, Pession A, Tallini G. Molecular Diagnostic of Solid Tumor Using a Next Generation Sequencing Custom-Designed Multi-Gene Panel. Diagnostics (Basel) 2020; 10:diagnostics10040250. [PMID: 32340363 PMCID: PMC7236002 DOI: 10.3390/diagnostics10040250] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 02/05/2023] Open
Abstract
Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid lesions. We report a custom-designed 128 multi-gene panel engineered to cover the relevant targets in 22 oncogene/oncosuppressor genes for the analysis of the solid tumors most frequently subjected to routine genotyping. A total of 1695 solid tumors were analyzed for panel validation. The analytical sensitivity is 5%. Analytical validation: (i) Accuracy: sequencing results obtained using the multi-gene panel are concordant using two different NGS platforms and single-gene approach sequencing (100% of 83 cases); (ii) Precision: consistent results are obtained in the samples analyzed twice with the same platform (100% of 20 cases). Clinical validation: the frequency of mutations identified in different tumor types is consistent with the published literature. This custom-designed multi-gene panel allows to analyze with high sensitivity and throughput 22 oncogenes/oncosuppressor genes involved in diagnostic/prognostic/predictive characterization of central nervous system tumors, non-small-cell lung carcinomas, colorectal carcinomas, thyroid nodules, pancreatic lesions, melanoma, oral squamous carcinomas and gastrointestinal stromal tumors.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
- Correspondence: ; Tel.: +39-051-2144717; Fax: +39-051-6363689
| | - Viviana Sanza
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Chiara M. Argento
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Antonio De Leo
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Thais Maloberti
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
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12
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Gray JE, Okamoto I, Sriuranpong V, Vansteenkiste J, Imamura F, Lee JS, Pang YK, Cobo M, Kasahara K, Cheng Y, Nogami N, Cho EK, Su WC, Zhang G, Huang X, Li-Sucholeiki X, Lentrichia B, Dearden S, Jenkins S, Saggese M, Rukazenkov Y, Ramalingam SS. Tissue and Plasma EGFR Mutation Analysis in the FLAURA Trial: Osimertinib versus Comparator EGFR Tyrosine Kinase Inhibitor as First-Line Treatment in Patients with EGFR-Mutated Advanced Non-Small Cell Lung Cancer. Clin Cancer Res 2019; 25:6644-6652. [PMID: 31439584 PMCID: PMC7209579 DOI: 10.1158/1078-0432.ccr-19-1126] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/04/2019] [Accepted: 08/13/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE To assess the utility of the cobas EGFR Mutation Test, with tissue and plasma, for first-line osimertinib therapy for patients with EGFR-mutated (EGFRm; Ex19del and/or L858R) advanced or metastatic non-small cell lung cancer (NSCLC) from the FLAURA study (NCT02296125). EXPERIMENTAL DESIGN Tumor tissue EGFRm status was determined at screening using the central cobas tissue test or a local tissue test. Baseline circulating tumor (ct)DNA EGFRm status was retrospectively determined with the central cobas plasma test. RESULTS Of 994 patients screened, 556 were randomized (289 and 267 with central and local EGFR test results, respectively) and 438 failed screening. Of those randomized from local EGFR test results, 217 patients had available central test results; 211/217 (97%) were retrospectively confirmed EGFRm positive by central cobas tissue test. Using reference central cobas tissue test results, positive percent agreements with cobas plasma test results for Ex19del and L858R detection were 79% [95% confidence interval (CI), 74-84] and 68% (95% CI, 61-75), respectively. Progression-free survival (PFS) superiority with osimertinib over comparator EGFR-TKI remained consistent irrespective of randomization route (central/local EGFRm-positive tissue test). In both treatment arms, PFS was prolonged in plasma ctDNA EGFRm-negative (23.5 and 15.0 months) versus -positive patients (15.2 and 9.7 months). CONCLUSIONS Our results support utility of cobas tissue and plasma testing to aid selection of patients with EGFRm advanced NSCLC for first-line osimertinib treatment. Lack of EGFRm detection in plasma was associated with prolonged PFS versus patients plasma EGFRm positive, potentially due to patients having lower tumor burden.
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Affiliation(s)
- Jhanelle E Gray
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Isamu Okamoto
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University Hospital, Fukuoka, Japan
| | - Virote Sriuranpong
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and the King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | | | - Fumio Imamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Jong Seok Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; and National University Bundang Hospital, Seongnam, Republic of Korea
| | - Yong-Kek Pang
- Division of Respiratory Medicine, Department of Medicine, Faculty of Medicine, University of Malaya Medical Centre, Lembah Pantai, Kuala Lumpur, Malaysia
| | - Manuel Cobo
- Medical Oncology Section, Hospital Universitario Málaga Regional, Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain
| | - Kazuo Kasahara
- Department of Respiratory Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - Ying Cheng
- Department of Oncology, Jilin Provincial Cancer Hospital, Changchun, China
| | - Naoyuki Nogami
- Department of Thoracic Oncology and Medicine, National Hospital Organization, Shikoku Cancer Centre, Ehime, Japan
| | - Eun Kyung Cho
- Division of Oncology, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon, South Korea
| | - Wu Chou Su
- National Cheng Kung University Hospital, Tainan, Taiwan
| | - Guili Zhang
- Roche Molecular Systems, Pleasanton, California
| | - Xiangning Huang
- Global Medicines Development, AstraZeneca, Cambridge, United Kingdom
| | - Xiaocheng Li-Sucholeiki
- Precision Medicine and Genomics, Innovative Medicines and Early Development, AstraZeneca, Boston, Massachusetts
| | - Brian Lentrichia
- Precision Medicine and Genomics, Innovative Medicines and Early Development, AstraZeneca, Boston, Massachusetts
| | - Simon Dearden
- Precision Medicine and Genomics, Innovative Medicines and Early Development, AstraZeneca, Cambridge, United Kingdom
| | - Suzanne Jenkins
- Precision Medicine and Genomics, Innovative Medicines and Early Development, AstraZeneca, Cambridge, United Kingdom
| | - Matilde Saggese
- Global Medicines Development, AstraZeneca, Cambridge, United Kingdom
| | - Yuri Rukazenkov
- Global Medicines Development, AstraZeneca, Cambridge, United Kingdom
| | - Suresh S Ramalingam
- Emory University School of Medicine, Winship Cancer Institute, Atlanta, Georgia
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13
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Huang JK, Fan L, Wang TY, Wu PS. A new primer construction technique that effectively increases amplification of rare mutant templates in samples. BMC Biotechnol 2019; 19:62. [PMID: 31443709 PMCID: PMC6708177 DOI: 10.1186/s12896-019-0555-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023] Open
Abstract
Background In personalized medicine, companion diagnostic tests provide additional information to help select a treatment option likely to be optimal for a patient. Although such tests include several techniques for detecting low levels of mutant genes in wild-type backgrounds with fairly high sensitivity, most tests are not specific, and may exhibit high false positive rates. In this study, we describe a new primer structure, named ‘stuntmer’, to selectively suppress amplification of wild-type templates, and promote amplification of mutant templates. Results A single stuntmer for a defined region of DNA can detect several kinds of mutations, including point mutations, deletions, and insertions. Stuntmer PCRs are also highly sensitive, being able to amplify mutant sequences that may make up as little as 0.1% of the DNA sample. Conclusion In conclusion, our technique, stuntmer PCR, can provide a simple, low-cost, highly sensitive, highly accurate, and highly specific platform for developing companion diagnostic tests. Electronic supplementary material The online version of this article (10.1186/s12896-019-0555-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jr-Kai Huang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Ling Fan
- Department of Nuclear Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tao-Yeuan Wang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Pao-Shu Wu
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan. .,Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan.
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14
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New Era of Endoscopic Ultrasound-Guided Tissue Acquisition: Next-Generation Sequencing by Endoscopic Ultrasound-Guided Sampling for Pancreatic Cancer. J Clin Med 2019; 8:jcm8081173. [PMID: 31387310 PMCID: PMC6723875 DOI: 10.3390/jcm8081173] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/20/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022] Open
Abstract
Pancreatic cancer is a lethal cancer with an increasing incidence. Despite improvements in chemotherapy, patients with pancreatic cancer continue to face poor prognoses. Endoscopic ultrasound-guided tissue acquisition (EUS-TA) is the primary method for obtaining tissue samples of pancreatic cancer. Due to advancements in next-generation sequencing (NGS) technologies, multiple parallel sequencing can be applied to EUS-TA samples. Genomic biomarkers for therapeutic stratification in pancreatic cancer are still lacking, however, NGS can unveil potential predictive genomic biomarkers of treatment response. Thus, the importance of NGS using EUS-TA samples is becoming recognized. In this review, we discuss the recent advances in EUS-TA application for NGS of pancreatic cancer.
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15
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Sarcar B, Gimbrone NT, Wright G, Remsing Rix LL, Gordian ER, Rix U, Chiappori AA, Reuther GW, Santiago-Cardona PG, Muñoz-Antonia T, Cress WD. Characterization of epidermal growth factor receptor (EGFR) P848L, an unusual EGFR variant present in lung cancer patients, in a murine Ba/F3 model. FEBS Open Bio 2019; 9:1689-1704. [PMID: 31314158 PMCID: PMC6768113 DOI: 10.1002/2211-5463.12702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/22/2019] [Accepted: 07/16/2019] [Indexed: 11/06/2022] Open
Abstract
Lung cancer patients with mutations in epidermal growth factor receptor (EGFR) benefit from treatments targeting tyrosine kinase inhibitors (TKIs). However, both intrinsic and acquired resistance of tumors to TKIs are common, and EGFR variants have been identified that are resistant to multiple TKIs. In the present study, we characterized selected EGFR variants previously observed in lung cancer patients and expressed in a murine bone marrow pro-B Ba/F3 cell model. Among these EGFR variants, we report that an exon 20 deletion/insertion mutation S768insVGH is resistant to erlotinib (a first-generation TKI), but sensitive to osimertinib (a third-generation TKI). We also characterized a rare exon 21 germline variant, EGFR P848L, which transformed Ba/F3 cells and conferred resistance to multiple EGFR-targeting TKIs. Our analysis revealed that P848L (a) does not bind erlotinib; (b) is turned over less rapidly than L858R (a common tumor-derived EGFR mutation); (c) is not autophosphorylated at Tyr 1045 [the major docking site for Cbl proto-oncogene (c-Cbl) binding]; and (d) does not bind c-Cbl. Using viability assays including 300 clinically relevant targeted compounds, we observed that Ba/F3 cells transduced with EGFR P848L, S768insVGH, or L858R have very different drug-sensitivity profiles. In particular, EGFR P848L, but not L858R or S768insVGH, was sensitive to multiple Janus kinase 1/2 inhibitors. In contrast, cells driven by L858R, but not by P848L, were sensitive to multikinase MAPK/extracellular-signal-regulated kinase (ERK) kinase and ERK inhibitors including EGFR-specific TKIs. These observations suggest that continued investigation of rare TKI-resistant EGFR variants is warranted to identify optimal treatments for cancer.
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Affiliation(s)
- Bhaswati Sarcar
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Nicholas T Gimbrone
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gabriela Wright
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Edna R Gordian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alberto A Chiappori
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gary W Reuther
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Teresita Muñoz-Antonia
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - William Douglas Cress
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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16
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Shigeto H, Ohtsuki T, Iizuka A, Akiyama Y, Yamamura S. Imaging analysis of EGFR mutated cancer cells using peptide nucleic acid (PNA)-DNA probes. Analyst 2019; 144:4613-4621. [PMID: 31241068 DOI: 10.1039/c9an00725c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung cancer cells harbor various gene mutations in the mRNA sequence of the Epidermal Growth Factor Receptor (EGFR), especially the mutations of exon19del E746-A750, T790M, and L858R. This results in cancer progression and resistance to anticancer drugs (tyrosine kinase inhibitor; TKI). Therefore, the imaging analysis of EGFR mutations is required for the treatment planning for non-small cell lung cancers. This study focused on the imaging analysis of a single nucleotide substitute in EGFR mutated cancer cells. We developed three novel peptide nucleic acid (PNA)-DNA probes for recognizing and detecting the following three gene mutations in EGFR gene mutations. The PNA-DNA probes consist of fluorescein isothiocyanate (FITC) conjugated PNA as a detection probe and Dabcyl conjugated DNA as a quencher probe. The PNA-DNA probes were used to validate the feasibility for detecting three EGFR mutated sequences: exon19del E746-A750, T790M, and L858R. The three probes emitted fluorescent dose-dependent signals against three target DNA and RNA. Using the three PNA-DNA probes, we succeeded in distinguishing three kinds of lung-cancer cell lines (H1975, PC-9, and A549) which have different EGFR mutations by the fluorescence in situ hybridization (FISH) method.
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Affiliation(s)
- Hajime Shigeto
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan.
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Shohei Yamamura
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan.
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17
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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] [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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18
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Huang M, Wei S. Overview of Molecular Testing of Cytology Specimens. Acta Cytol 2019; 64:136-146. [PMID: 30917368 DOI: 10.1159/000497187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Utilizing cytology specimens for molecular testing has attracted increasing attention in the era of personalized medicine. Cytology specimens are clinically easier to access. The samples can be quickly and completely fixed in a very short time of fixation before tissue degradation occurs, compared to hours or days of fixation in surgical pathology specimens. In addition, cytology specimens can be fixed without formalin, which can significantly damage DNA and RNA. All these factors contribute to the superb quality of DNA and RNA in cytology specimens for molecular tests. STUDY DESIGN We summarize the most pertinent information in the literature regarding molecular testing in the field of cytopathology. RESULTS The first part focuses on the types of cytological specimens that can be used for molecular testing, including the advantages and limitations. The second section describes the common molecular tests and their clinical application. CONCLUSION Various types of cytology specimens are suitable for many molecular tests, which may require additional clinical laboratory validation.
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Affiliation(s)
- Min Huang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA,
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19
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Lin O, Rudomina D, Feratovic R, Sirintrapun SJ. Rapid on-site evaluation using telecytology: A major cancer center experience. Diagn Cytopathol 2019; 47:15-19. [PMID: 29575752 PMCID: PMC8059101 DOI: 10.1002/dc.23925] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Rapid on-site evaluation (ROSE) with cytology preparations plays a critical role in minimally invasive procedures. The time spent by a pathologist performing ROSE is unpredictable and could be used for more cost-effective activities. The solution encountered by several institutions to address this issue is the use of telecytology (TC). This study analyzes the experience of using telecytology for ROSE in a major cancer center over a period of over 2 years. METHODS A retrospective analysis of all remote TC evaluations for adequacy on fine needle aspiration (FNA) and touch preparations (TP) of core biopsies (CB) performed at a major cancer center was performed. The preliminary adequacy assessment was then compared to the adequacy assessment at final diagnosis. RESULTS A total of 12 949 adequacy assessments were analyzed. The most common sites biopsied in our institution were lymph node, lung, and liver. There were 7725 adequacy assessments for CB (59.7%), while adequacy assessment for FNA specimens represented 40.3% (n = 5224) of the total number of specimens evaluated by ROSE. Perfect concordance between initial adequacy assessment and the adequacy assessment at final cytologic diagnosis was 93% (12 049/12 949). The final diagnosis adequacy upgrade rate was 6.7% (n = 863), and the adequacy downgrade (a specimen considered adequate on-site that was determined to be nondiagnostic on final examination) was 0.3% (n = 37). CONCLUSIONS TC can be easily implemented with the current technologies available. It is cost-effective and allows for better patient care with a more efficient use of the pathologist's time and laboratory resources.
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Affiliation(s)
- Oscar Lin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Dorota Rudomina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Rusmir Feratovic
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - S Joseph Sirintrapun
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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20
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Demaree B, Weisgerber D, Dolatmoradi A, Hatori M, Abate AR. Direct quantification of EGFR variant allele frequency in cell-free DNA using a microfluidic-free digital droplet PCR assay. Methods Cell Biol 2018; 148:119-131. [PMID: 30473066 DOI: 10.1016/bs.mcb.2018.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Analysis of liquid biopsy samples is a promising diagnostic intervention for noninvasive detection and monitoring of cancer genotypes. However, current methods used to assess mutation status are either costly, in the case of next-generation sequencing-based assays, or lacking in sensitivity, in the case of bulk quantitative PCR measurements. Digital droplet PCR (ddPCR) is at once a sensitive and low-cost method for detecting rare cancer mutations and measuring their variant allele frequency. In this chapter, we describe a method for conducting ddPCR assays without microfluidics in a process called "particle-templated emulsification" (PTE). Using hydrogel particles and a standard benchtop vortexer to rapidly emulsify large volumes, the method forgoes the specialized instrumentation required for conventional ddPCR assays and is capable of high experimental throughput. To assess the quantitative performance of the method, we apply PTE ddPCR to analysis of variant allele frequency in EGFR, a commonly mutated gene in lung adenocarcinomas.
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Affiliation(s)
- Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, United States; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, United States
| | - Daniel Weisgerber
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, United States
| | - Ata Dolatmoradi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, United States
| | - Makiko Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, United States; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, United States; Chan Zuckerberg Biohub, San Francisco, CA, United States.
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21
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Zhang Y, Li J, Hua P, Liu N, Li Q, Zhu X, Jiang L, Zheng K, Su X. Targeted next-generation sequencing in cytology specimens for molecular profiling of lung adenocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3647-3655. [PMID: 31949745 PMCID: PMC6962840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/27/2018] [Indexed: 06/10/2023]
Abstract
AIMS Molecular profiling is important for cancer diagnosis and treatment. For many advanced stage lung cancer patients, cytology specimens may be the only materials available for molecular testing. The aim of this study is to evaluate the utility of Next-Generation Sequencing (NGS) of cytology specimens for the molecular profiling of lung adenocarcinoma. METHODS NGS was performed on cell blocks of pleural effusions and fine-needle aspiration (FNA) samples of lung adenocarcinoma to determine the mutation status of EGFR, KRAS, PIK3CA, BRAF, ALK, PDGFRA, and DDR2. Then, quantitative Real-Time PCR (qPCR) was performed and the results were compared to those of NGS. Next, NGS was performed on available histological specimens from the same patients. Last, DNA Quality Index analysis was performed to further explore the applicability of using cytology samples as the source for NGS. RESULTS NGS detected mutations in EGFR, PIK3CA, and KRAS. NGS and qPCR results showed high concordance. NGS exhibited advantages over qPCR in detecting non-hotspot mutations and providing accurate information for allele sequence and mutation frequency. NGS of cytological and histological samples from the same patients showed high concordance. DNA Quality Index analysis showed that DNA extracted from cell blocks of pleural fluid was of similar quality compared to FFPE tissue blocks. CONCLUSIONS NGS can be successfully performed on both FNA and pleural fluid samples from lung adenocarcinomas. The high quality DNA of FFPE cell block of pleural effusion makes it the first choice for molecular profiling, especially when cytology specimens are the only available samples for molecular profiling.
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Affiliation(s)
- Yuan Zhang
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
- Chengdu Women and Children’s Central HospitalChengdu, China
| | - Jinnan Li
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Ping Hua
- Chengdu Women and Children’s Central HospitalChengdu, China
| | - Nian Liu
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Qiyuan Li
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Xianglan Zhu
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Lili Jiang
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Ke Zheng
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Xueying Su
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
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22
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Kim E, Feldman R, Wistuba II. Update on EGFR Mutational Testing and the Potential of Noninvasive Liquid Biopsy in Non–Small-cell Lung Cancer. Clin Lung Cancer 2018; 19:105-114. [DOI: 10.1016/j.cllc.2017.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022]
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23
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Bonaparte E, Pesenti C, Fontana L, Falcone R, Paganini L, Marzorati A, Ferrero S, Nosotti M, Mendogni P, Bareggi C, Sirchia SM, Tabano S, Bosari S, Miozzo M. Molecular profiling of lung cancer specimens and liquid biopsies using MALDI-TOF mass spectrometry. Diagn Pathol 2018; 13:4. [PMID: 29368620 PMCID: PMC6389067 DOI: 10.1186/s13000-017-0683-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of predictive molecular alterations in lung adenocarcinoma is essential for accurate therapeutic decisions. Although several molecular approaches are available, a number of issues, including tumor heterogeneity, frequent material scarcity, and the large number of loci to be investigated, must be taken into account in selecting the most appropriate technique. MALDI-TOF mass spectrometry (MS), which allows multiplexed genotyping, has been adopted in routine diagnostics as a sensitive, reliable, fast, and cost-effective method. Our aim was to test the reliability of this approach in detecting targetable mutations in non-small cell lung cancer (NSCLC). In addition, we also analyzed low-quality samples, such as cytologic specimens, that often, are the unique source of starting material in lung cancer cases, to test the sensitivity of the system. METHODS We designed a MS-based assay for testing 158 mutations in the EGFR, KRAS, BRAF, ALK, PIK3CA, ERBB2, DDR2, AKT, and MEK1 genes and applied it to 92 NSCLC specimens and 13 liquid biopsies from another subset of NSCLC patients. We also tested the sensitivity of the method to distinguish low represented mutations using serial dilutions of mutated DNA. RESULTS Our panel is able to detect the most common NSCLC mutations and the frequency of the mutations observed in our cohort was comparable to literature data. The assay identifies mutated alleles at frequencies of 2.5-10%. In addition, we found that the amount of DNA template was irrelevant to efficiently uncover mutated alleles present at high frequency. However, when using less than 10 ng of DNA, the assay can detect mutations present in at least 10% of the alleles. Finally, using MS and a commercial kit for RT-PCR we tested liquid biopsy from 13 patients with identified mutations in cancers and detected the mutations in 4 (MS) and in 5 samples (RT-PCR). CONCLUSIONS MS is a powerful method for the routine predictive tests of lung cancer also using low quality and scant tissues. Finally, after appropriate validation and improvement, MS could represent a promising and cost-effective strategy for monitoring the presence and percentage of the mutations also in non-invasive sampling.
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Affiliation(s)
- Eleonora Bonaparte
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 –20122 Milan, Italy
| | - Chiara Pesenti
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 –20122 Milan, Italy
| | - Laura Fontana
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
| | - Rossella Falcone
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
| | - Leda Paganini
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 –20122 Milan, Italy
| | - Anna Marzorati
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
| | - Stefano Ferrero
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 –20122 Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Medical School, Via Francesco Sforza, 35 -20122 Milan, Italy
| | - Mario Nosotti
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
- Thoracic Surgery and Lung Transplantation Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 -20122 Milan, Italy
| | - Paolo Mendogni
- Thoracic Surgery and Lung Transplantation Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 -20122 Milan, Italy
| | - Claudia Bareggi
- Oncology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 -20122 Milan, Italy
| | - Silvia Maria Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, via Antonio di Rudini, 8 –20142 Milan, Italy
| | - Silvia Tabano
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 –20122 Milan, Italy
| | - Silvano Bosari
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 –20122 Milan, Italy
| | - Monica Miozzo
- Department of Pathophysiology & Transplantation, Università degli Studi di Milano, Via Francesco Sforza, 35 -20122 Milan, Italy
- Division of Pathology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza, 35 –20122 Milan, Italy
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24
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Su J, Zhong W, Zhang X, Huang Y, Yan H, Yang J, Dong Z, Xie Z, Zhou Q, Huang X, Lu D, Yan W, Wu YL. Molecular characteristics and clinical outcomes of EGFR exon 19 indel subtypes to EGFR TKIs in NSCLC patients. Oncotarget 2017; 8:111246-111257. [PMID: 29340050 PMCID: PMC5762318 DOI: 10.18632/oncotarget.22768] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 09/03/2017] [Indexed: 12/21/2022] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) with activating epidermal growth factor receptor (EGFR) mutations (exon 19 deletions and L858R) benefit from EGFR tyrosine kinase inhibitors (TKIs). However, some researchers have reported that responses to TKIs differ by subtypes of EGFR exon 19 mutations. We retrospectively analyzed EGFR exon 19 deletion subtypes and their correlation with clinical outcomes of treatment with TKIs. A cohort of 2664 consecutive patients with NSCLC was enrolled. A total of 440 EGFR exon 19 deletions were defined as 39 subtypes. Among them, 158 patients with advanced lung adenocarcinoma with EGFR exon 19 deletion mutations received EGFR-TKIs. There were no significant differences in progression-free survival or overall survival among patients with non-LRE deletions, delE746, or delL747 (P = 0.463 and P = 0.464, respectively). Furthermore, two patients with EGFR exon19 insertion had durable response to EGFR-TKIs. In conclusion, EGFR exon 19 is highly fragile, resulting in many different deletion and insertion subtypes. There were no significant differences in clinical outcomes after TKI treatment across the different subtypes. It is necessary to attempt to identify all patients with exon 19 deletions so that they can be offered TKI treatment.
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Affiliation(s)
- Jian Su
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenzhao Zhong
- Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xuchao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Ying Huang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Honghong Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jinji Yang
- Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Zhongyi Dong
- Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Zhi Xie
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xiaosui Huang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Danxia Lu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenqing Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Medical Research Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou 510080, China
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25
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Illei PB, Belchis D, Tseng LH, Nguyen D, De Marchi F, Haley L, Riel S, Beierl K, Zheng G, Brahmer JR, Askin FB, Gocke CD, Eshleman JR, Forde PM, Lin MT. Clinical mutational profiling of 1006 lung cancers by next generation sequencing. Oncotarget 2017; 8:96684-96696. [PMID: 29228562 PMCID: PMC5722514 DOI: 10.18632/oncotarget.18042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/10/2017] [Indexed: 12/15/2022] Open
Abstract
Analysis of lung adenocarcinomas for actionable mutations has become standard of care. Here, we report our experience using next generation sequencing (NGS) to examine AKT1, BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA genes in 1006 non-small cell lung cancers in a clinical diagnostic setting. NGS demonstrated high sensitivity. Among 760 mutations detected, the variant allele frequency (VAF) was 2-5% in 33 (4.3%) mutations and 2-10% in 101 (13%) mutations. A single bioinformatics pipeline using Torrent Variant Caller, however, missed a variety of EGFR mutations. Mutations were detected in KRAS (36% of tumors), EGFR (19%) including 8 (0.8%) within the extracellular domain (4 at codons 108 and 4 at codon 289), BRAF (6.3%), and PIK3CA (3.7%). With a broader reportable range, exon 19 deletion and p.L858R accounted for only 36% and 26% of EGFR mutations and p.V600E accounted for only 24% of BRAF mutations. NGS provided accurate sequencing of complex mutations seen in 19% of EGFR exon 19 deletion mutations. Doublet (compound) EGFR mutations were observed in 29 (16%) of 187 EGFR-mutated tumors, including 69% with two non-p.L858R missense mutations and 24% with p.L858 and non-p.L858R missense mutations. Concordant VAFs suggests doublet EGFR mutations were present in a dominant clone and cooperated in oncogenesis. Mutants with predicted impaired kinase, observed in 25% of BRAF-mutated tumors, were associated with a higher incidence of concomitant activating KRAS mutations. NGS demonstrates high analytic sensitivity, broad reportable range, quantitative VAF measurement, single molecule sequencing to resolve complex deletion mutations, and simultaneous detection of concomitant mutations.
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Affiliation(s)
- Peter B. Illei
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Deborah Belchis
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Li-Hui Tseng
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Doreen Nguyen
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Federico De Marchi
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
- Division of Hematology and Bone Marrow Transplantation, University of Udine Hospital, Udine, Italy
| | - Lisa Haley
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Stacy Riel
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Katie Beierl
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Gang Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Julie R. Brahmer
- Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Frederic B. Askin
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Christopher D. Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - James R. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Patrick M. Forde
- Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
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26
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Visani M, Acquaviva G, Marucci G, Paccapelo A, Mura A, Franceschi E, Grifoni D, Pession A, Tallini G, Brandes AA, de Biase D. Non-canonical IDH1 and IDH2 mutations: a clonal and relevant event in an Italian cohort of gliomas classified according to the 2016 World Health Organization (WHO) criteria. J Neurooncol 2017; 135:245-254. [PMID: 28748342 DOI: 10.1007/s11060-017-2571-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/13/2017] [Indexed: 02/05/2023]
Abstract
According to the 2016 World Health Organization (WHO) classification of tumors of the central nervous system, assessment of exon 4 mutations in isocitrate dehydrogenase 1 or 2 genes (IDH1 or IDH2) is an essential step in the characterization of gliomas. The p.R132H mutation is the most frequent alteration in IDH genes, however other non-canonical IDH mutations can be identified. The aim of this study is to investigate in depth the prevalence of non-R132H IDH ("non-canonical") mutations in brain tumors classified according to the 2016 WHO scheme and their clonal distribution in neoplastic cells. A total of 288 consecutive cases of brain gliomas (grade II-IV) were analyzed for exon 4 IDH1 and IDH2 mutations. IDH1 and IDH2 analysis was performed using next generation sequencing. Non-canonical IDH mutations were identified in 13/52 (25.0%) grade II gliomas (astrocytomas: 8/31, 25.8%; oligodendrogliomas: 5/21, 23.8%) and in 5/40 (12.5%) grade III gliomas (astrocytomas: 3/25, 12.0%; oligodendrogliomas: 2/15, 13.3%). They were not identified in 196 grade IV gliomas (192 glioblastomas, 4 gliosarcomas). In the large majority (>80%) of tumors IDH mutations, both IDH1-R132H and the non-canonical ones, were present in the large majority (>80%) of neoplastic cells. Our data highlight the importance of investigating not only the IDH1-R132H mutation but also the non-canonical ones. These mutations are clonally distributed, with proportions of mutated neoplastic cells overlapping with those of p.R132H, a finding consistent with their driver role in gliomagenesis.
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Affiliation(s)
- Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Gianluca Marucci
- Anatomic Pathology Unit, AUSL of Bologna, Via Altura 3, 40139, Bologna, Italy
- Department of Neuropathology, IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Alexandro Paccapelo
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Antonella Mura
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Enrico Franceschi
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Daniela Grifoni
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy.
- Anatomia Patologica, ASL Bologna, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Scuola di Medicina e Chirurgia, Università di Bologna, Via Altura 3, 40139, Bologna, Italy.
| | - Alba A Brandes
- Department of Oncology, AUSL Bologna - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
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27
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Vornetti G, Marucci G, Zenesini C, de Biase D, Michelucci R, Tinuper P, Tallini G, Giulioni M. Relationship among clinical, pathological and bio-molecular features in low-grade epilepsy-associated neuroepithelial tumors. J Clin Neurosci 2017; 44:158-163. [PMID: 28673671 DOI: 10.1016/j.jocn.2017.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/12/2017] [Indexed: 02/08/2023]
Abstract
The aim of this study was to evaluate the relationship between molecular markers and clinicopathological features in patients operated on for low-grade epilepsy-associated neuroepithelial tumors. Molecular-genetic signatures are becoming increasingly important in characterizing these lesions, which represent the second most common cause of focal epilepsy in patients undergoing epilepsy surgery. Data from 22 patients operated on for histopathologically confirmed low-grade epilepsy-associated neuroepithelial tumors were retrospectively collected. All specimens were examined for BRAF and IDH mutational status, 1p/19q codeletion and CD34 expression. The relationship between bio-molecular markers and several demographic, clinical and pathological features were analyzed. BRAF mutation was found in 11 (50.0%) patients and CD34 expression in 13 (59.1%). No patients presented IDH mutation or 1p/19q codeletion. Multiple seizure types were present in 5 (45.5%) patients with BRAF mutation and in none of those with BRAF wild type (p=0.035). Moreover, BRAF mutation was predominant in right-sided lesions (p=0.004) and CD34 expression was significantly associated with a longer duration of epilepsy (p=0.027). Several other clinicopathological features, such as association with focal cortical dysplasia and postoperative seizure outcome, showed no significant correlation with molecular markers. Further studies are necessary both to confirm these data in larger cohort of patients and to investigate possible relationships between molecular markers and other clinicopathological features.
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Affiliation(s)
- Gianfranco Vornetti
- IRCCS Institute of Neurological Sciences of Bologna, Division of Neurosurgery, Bellaria Hospital, Bologna, Italy.
| | - Gianluca Marucci
- Department of Neuropathology, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Corrado Zenesini
- Unit of Epidemiology and Biostatistics, IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Roberto Michelucci
- IRCCS Institute of Neurological Sciences of Bologna, Unit of Neurology, Bellaria Hospital, Bologna, Italy
| | - Paolo Tinuper
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Marco Giulioni
- IRCCS Institute of Neurological Sciences of Bologna, Division of Neurosurgery, Bellaria Hospital, Bologna, Italy
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Forti Parri SN, Bonfanti B, Cancellieri A, De Biase D, Trisolini R, Zoboli S, Bertolaccini L, Solli P, Tallini G. Molecular analysis driven video-assisted thoracic surgery resections in bilateral synchronous lung cancers: from the test tube to the operatory room. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:397. [PMID: 29152497 PMCID: PMC5673775 DOI: 10.21037/atm.2017.07.41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Synchronous cancers are not such rare clinical conditions. Nevertheless, even after the 8th edition of the TNM classification of the lung cancer, the surgical approach for patients presenting with synchronous bilateral lung cancer is still under debate. The resection of both lesions in the case of synchronous bilateral lung cancer is reasonable, but, on the other hand, is the lobectomy the correct choice in the event of the single primary with a contralateral metastatic lesion? In this case report, we describe how the molecular analysis and the detection of the EGFR, KRAS and TP53 mutations in both tumours have determined in a patient the two tumours as primary and both the right surgical approach. We also discuss how molecular analysis found differences in all the three genes examined in the two lesions and allowed to exclude the clonal nature of the two tumours. In conclusion, genetic studies help to offer a more radical surgical treatment to this patient.
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Affiliation(s)
| | - Barbara Bonfanti
- Thoracic Surgery Unit, AUSL Bologna, Maggiore-Bellaria Hospital, Bologna, Italy
| | | | - Dario De Biase
- Department of Pharmacy and Biotechnology (FaBiT), Molecular Diagnostic Unit, AUSL Bologna, University of Bologna, Bologna, Italy
| | - Rocco Trisolini
- Interventional Pulmonology Unit, Policlinico Sant’Orsola-Malpighi, Bologna, Italy
| | - Stefania Zoboli
- Nuclear Medicine Unit, AUSL Bologna, Maggiore Hospital, Bologna, Italy
| | - Luca Bertolaccini
- Department of Thoracic Surgery, AUSL Romagna Teaching Hospitals, Ravenna, Italy
| | - Piergiorgio Solli
- Thoracic Surgery Unit, AUSL Bologna, Maggiore-Bellaria Hospital, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine, Molecular Diagnostic Unit, AUSL Bologna, University of Bologna, School of Medicine, Bologna, Italy
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Memon AA, Zhang H, Gu Y, Luo Q, Shi J, Deng Z, Ma J, Ma W. EGFR with TKI-sensitive mutations in exon 19 is highly expressed and frequently detected in Chinese patients with lung squamous carcinoma. Onco Targets Ther 2017; 10:4607-4613. [PMID: 29075127 PMCID: PMC5609803 DOI: 10.2147/ott.s130051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recently, tyrosine kinase inhibitors (TKIs) have been recommended as a first-line treatment for advanced non-small cell lung cancer (NSCLC), significantly improving the treatment outcomes of lung adenocarcinoma patients with the EGFR mutation. However, the application of TKIs for lung squamous cell carcinoma (SCC), the second largest pathological subtype of NSCLC, remains controversial because available data for the EGFR mutation profile and frequency in SCC patients are limited. In this study, 89 bronchoscopic-biopsy specimens from Chinese SCC male patients were assayed for EGFR exon 19 mutation, using improved polymerase chain reaction-denature gel gradient electrophoresis. EGFR exon 19 mutations were detected in 77 of 89 (86.5%) patients, and included six kinds of point mutations (11.6%) and two deletions (Del_747-751 [64.9%] and Del_746-751 [23.3%]). We found that the proportion of mutated EGFR varied from 0.98% to 100% in positive specimens and increased with the development of the disease. The difference of proportion between Stage IV patients and Stage II patients or Stage III patients was significant (P<0.001). These results provided valuable clues to explain the reason why patients harboring the same mutation responded distinctly to TKI treatment. Del_747-751 and Del_746-751 were the dominant mutations in the assayed SCC patients (76.4%), and both belong to the EGFR-TKI-sensitive mutation. Recently research demonstrated that Del_746-751 patients have better response to EGFR-TKI than Del_L747-751 patients. However, our study indicated that majority of SCC patients (55.5%) carried Del_ L747-751. We suggest that the unique clinic features of SCC should be further studied to reveal the mechanism of poorer treatment outcome of EGFR-TKI therapy, and that a better treatment plan and more specific, potent targeted drugs for lung SCC need to be developed.
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Affiliation(s)
- Aadil Ahmed Memon
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
| | | | - Ye Gu
- Endoscope Department, Shanghai Pulmonary Hospital, Tongji University School of Medicine
| | - Qian Luo
- Core Facility and Technical Service Center, School of Life Science and Biotechnology, Shanghai Jiao Tong University
| | - Jiajun Shi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
| | - Jian Ma
- Pneumology Department, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University
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Goh F, Duhig EE, Clarke BE, McCaul E, Passmore L, Courtney D, Windsor M, Naidoo R, Franz L, Parsonson K, Yang IA, Bowman RV, Fong KM. Low tumour cell content in a lung tumour bank: implications for molecular characterisation. Pathology 2017; 49:611-617. [PMID: 28811084 DOI: 10.1016/j.pathol.2017.07.001] [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] [Received: 04/24/2017] [Accepted: 07/08/2017] [Indexed: 12/23/2022]
Abstract
Lung cancer encompasses multiple malignant epithelial tumour types, each with specific targetable, potentially actionable mutations, such that precision management mandates accurate tumour typing. Molecular characterisation studies require high tumour cell content and low necrosis content, yet lung cancers are frequently a heterogeneous mixture of tumour and stromal cells. We hypothesised that there may be systematic differences in tumour cell content according to histological subtype, and that this may have implications for tumour banks as a resource for comprehensive molecular characterisation studies in lung cancer. To investigate this, we estimated tumour cell and necrosis content of 4267 samples resected from 752 primary lung tumour specimens contributed to a lung tissue bank. We found that banked lung cancer samples had low tumour cell content (33%) generally, although it was higher in carcinoids (77.5%) than other lung cancer subtypes. Tumour cells comprise a variable and often small component of banked resected tumour samples, and are accompanied by stromal reaction, inflammation, fibrosis, and normal structures. This has implications for the adequacy of unselected tumour bank samples for diagnostic and molecular investigations, and further research is needed to determine whether tumour cell content has a significant impact on analytical results in studies using tissue from tumour bank resources.
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Affiliation(s)
- Felicia Goh
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia.
| | - Edwina E Duhig
- Sullivan Nicolaides Pathology, The John Flynn Hospital, Tugun, Qld, Australia
| | - Belinda E Clarke
- Pathology Queensland, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Elizabeth McCaul
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Linda Passmore
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Deborah Courtney
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Morgan Windsor
- Cardiothoracic Surgery, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Rishendren Naidoo
- Cardiothoracic Surgery, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Louise Franz
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Kylie Parsonson
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Ian A Yang
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Rayleen V Bowman
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Kwun M Fong
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
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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] [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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Abstract
PURPOSE OF REVIEW The concept of mutually exclusive oncogenic driver alterations has prevailed over the past decade, but recent reports have stressed the possible occurrence of dual-positive non-small-cell lung cancer (NSCLC) and even triple-positive disease for these oncogenes. This entity presents novel prognostic and therapeutic challenges. The present review highlights the available data in an effort to clarify the clinical and pathological significance of coexisting mutations as well as the subsequent therapeutic consequences. RECENT FINDINGS Patients with a known driver oncogene can be successfully treated with the appropriate tyrosine kinase inhibitor, which will provide them with significant responses and lesser toxicities compared with cytotoxic therapy. Unfortunately, most patients will eventually progress. Although some resistance mechanisms have been identified, others remain to be determined but the emergence of secondary oncogenes could be part of the answer. SUMMARY Approximately 20-25% of NSCLC harbor treatable driver mutations/rearrangements; epidermal growth factor receptor mutation, anaplastic lymphoma kinase and ROS-1 gene rearrangements are the main alterations for which a Food and Drug Administration-approved tyrosine kinase inhibitor can be used.Because of recent technological advances, high sensitivity assays with a broad range of genomic targets have become more easily accessible in clinical practice, which has led to an increased detection of coexisting driver alterations in patients with advanced NSCLC. The prognostic/predictive and therapeutic implications of this novel entity are still unsettled for the time being. Randomized trials specifically designed to address this subset of patients will soon be necessary to help determine the optimal therapeutic agent to administer.
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Koinis F, Voutsina A, Kalikaki A, Koutsopoulos A, Lagoudaki E, Tsakalaki E, Dermitzaki EK, Kontopodis E, Pallis AG, Georgoulias V, Kotsakis A. Long-term clinical benefit from salvage EGFR tyrosine kinase inhibitors in advanced non-small-cell lung cancer patients with EGFR wild-type tumors. Clin Transl Oncol 2017. [DOI: 10.1007/s12094-017-1702-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Genestreti G, de Biase D, Di Battista M, Cavallo G, Degli Esposti R, Visani M, Acquaviva G, Brand T, Pession A, Tallini G, Brandes AA. Epidermal Growth Factor Receptor (EGFR) Mutation in Exon 19 (p.E749Q) Confers Resistance to Gefitinib in One Patient With Lung Adenocarcinoma. Clin Lung Cancer 2017; 18:e215-e217. [PMID: 28162944 DOI: 10.1016/j.cllc.2017.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 12/22/2016] [Accepted: 01/03/2017] [Indexed: 02/08/2023]
Affiliation(s)
- Giovenzio Genestreti
- Department of Medical Oncology, Bellaria Hospital, AUSL Bologna-IRCCS Institute of Neurological Sciences, Bologna, Italy.
| | - Dario de Biase
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Monica Di Battista
- Department of Medical Oncology, Bellaria Hospital, AUSL Bologna-IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Giovanna Cavallo
- Department of Medical Oncology, Bellaria Hospital, AUSL Bologna-IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Roberta Degli Esposti
- Department of Medical Oncology, Bellaria Hospital, AUSL Bologna-IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Michela Visani
- Department of Medicine (DIMES)-Molecular Diagnostic Unit, AUSL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (DIMES)-Molecular Diagnostic Unit, AUSL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Thomas Brand
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES)-Molecular Diagnostic Unit, AUSL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Alba A Brandes
- Department of Medical Oncology, Bellaria Hospital, AUSL Bologna-IRCCS Institute of Neurological Sciences, Bologna, Italy
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Performance Assessment of Epidermal Growth Factor Receptor Gene Sequencing According to Sample Size in Daily Practice Conditions. Appl Immunohistochem Mol Morphol 2017; 26:495-500. [PMID: 28248723 DOI: 10.1097/pai.0000000000000455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Lung carcinoma is the main cause of cancer death worldwide. Adenocarcinoma molecular biomarkers have been discovered, and targeted therapies have been developed with encouraging results. The epidermal growth factor receptor gene is one of these biomarkers. Exons 18 to 21 should be studied in patients with advanced adenocarcinoma, who are candidates for treatment with tyrosine kinase inhibitors. The objective was to compare the performance of the determination in large and small samples in daily practice conditions, trying to adjust to published consensus guidelines. A retrospective observational study of 141 cases was carried out, with exons 19 and 21 sequencing. Sample size (small vs. large), including number of satisfactory polymerase chain reaction (PCR), sequencing, deletions, and mutations, were evaluated. In small biopsies, sample type, fragment number, and percentage of tumor per sample were analyzed. The results shown 114/141 (80.8) cases that met selection criteria; 60/114 (53%) were large (surgical) and 54/114 (47%) were small samples (19/54 endoscopic, 17/54 fine needle aspiration clots, 4/54 lymph nodes, 14/54 core and other). All large samples were satisfactory PCR, 56/60 (93%) satisfactory sequencing, and 12/56 (21%) had deletions in exon 19. Small samples were satisfactory PCRs in 50/54 (93%) cases, and satisfactory sequencing in 35/50 (65%), 8/35 (23%) showed alterations in exon 19, and 1/35 (3%) in exon 21. In conclusion, the proportion of samples unfit for the study of the epidermal growth factor receptor gene mutational status increased from 7% in large samples to 35% in small ones. Nineteen small samples were inconclusive, with cell blocks predominating, 10/19 (53%).
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Malapelle U, Sirera R, Jantus-Lewintre E, Reclusa P, Calabuig-Fariñas S, Blasco A, Pisapia P, Rolfo C, Camps C. Profile of the Roche cobas® EGFR mutation test v2 for non-small cell lung cancer. Expert Rev Mol Diagn 2017; 17:209-215. [PMID: 28129709 DOI: 10.1080/14737159.2017.1288568] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION The discovery of driver mutations in non-small cell lung cancer (NSCLC) has led to the development of genome-based personalized medicine. Fifteen to 20% of adenocarcinomas harbor an epidermal growth factor receptor (EGFR) activating mutation associated with responses to EGFR tyrosine kinase inhibitors (TKIs). Individual laboratories' expertise and the availability of appropriate equipment are valuable assets in predictive molecular pathology, although the choice of methods should be determined by the nature of the samples to be tested and whether the detection of only well-characterized EGFR mutations or rather, of all detectable mutations, is required. Areas covered: The EGFR mutation testing landscape is manifold and includes both screening and targeted methods, each with their own pros and cons. Here we review one of these companion tests, the Roche cobas® EGFR mutation test v2, from a methodological point of view, also exploring its liquid-biopsy applications. Expert commentary: The Roche cobas® EGFR mutation test v2, based on real time RT-PCR, is a reliable option for testing EGFR mutations in clinical practice, either using tissue-derived DNA or plasma-derived cfDNA. This application will be valuable for laboratories with whose purpose is purely diagnostic and lacking high-throughput technologies.
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Affiliation(s)
- Umberto Malapelle
- a Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Rafael Sirera
- b Department of Biotechnology , Universitat Politècnica de València , Valencia , Spain.,c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain
| | - Eloísa Jantus-Lewintre
- b Department of Biotechnology , Universitat Politècnica de València , Valencia , Spain.,c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain
| | - Pablo Reclusa
- e Phase I-Early Clinical Trials Unit, Oncology Department , Antwerp University Hospital , Antwerp , Belgium.,f Center for Oncological Research (CORE) , Antwerp University , Antwerp , Belgium
| | - Silvia Calabuig-Fariñas
- c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain.,g Department of Pathology , Universitat de València , Valencia , Spain
| | - Ana Blasco
- c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain
| | - Pasquale Pisapia
- a Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Christian Rolfo
- e Phase I-Early Clinical Trials Unit, Oncology Department , Antwerp University Hospital , Antwerp , Belgium.,f Center for Oncological Research (CORE) , Antwerp University , Antwerp , Belgium
| | - Carlos Camps
- c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain.,h Department of Medicine , Universitat de València , Valencia , Spain.,i CIBERONC , Valencia , Spain
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de Biase D, Genestreti G, Visani M, Acquaviva G, Di Battista M, Cavallo G, Paccapelo A, Cancellieri A, Trisolini R, Degli Esposti R, Bartolini S, Pession A, Tallini G, Brandes AA. The percentage of Epidermal Growth Factor Receptor (EGFR)-mutated neoplastic cells correlates to response to tyrosine kinase inhibitors in lung adenocarcinoma. PLoS One 2017; 12:e0177822. [PMID: 28520821 PMCID: PMC5433779 DOI: 10.1371/journal.pone.0177822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/03/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Epidermal Growth Factor Receptor (EGFR) molecular analysis is performed to assess the responsiveness to Tyrosine Kinase Inhibitors (TKIs) in patients with Non-Small Cell Lung Cancer (NSCLC). The existence of molecular intra-tumoral heterogeneity has been observed in lung cancers. The aim of the present study is to investigate if the percentage of mutated neoplastic cells within the tumor sample might influence the responsiveness to TKIs treatment. MATERIAL AND METHODS A total of 931 cases of NSCLC were analyzed for EGFR mutational status (exon 18, 19, 20, 21) using Next Generation Sequencer. The percentage of mutated neoplastic cells was calculated after normalizing the percentage of mutated alleles obtained after next generation sequencer analysis with the percentage of neoplastic cells in each tumor. RESULTS Next generation sequencing revealed an EGFR mutation in 167 samples (17.9%), mainly deletions in exon 19. In 18 patients treated with TKIs and with available follow-up, there was a significant correlation between the percentage of mutated neoplastic cells and the clinical response (P = 0.017). Patients with a percentage of mutated neoplastic cells greater than 56%, have a statistical trend (P = 0.081) for higher Overall Survival (26.3 months) when compared to those with a rate of mutated neoplastic cells lower than 56% (8.2 months). CONCLUSIONS The percentage of EGFR-mutated neoplastic cells in the tumor is associated with response to TKIs. A "quantitative result" of EGFR mutational status might provide useful information in order to recognize those patients which might have the greatest benefit from TKIs.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
- * E-mail: (DdB); (GG)
| | - Giovenzio Genestreti
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
- * E-mail: (DdB); (GG)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Monica Di Battista
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Giovanna Cavallo
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Alexandro Paccapelo
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | | | - Rocco Trisolini
- Interventional Pulmology, Sant'Orsola, Malpighi Hospital, Bologna, Italy
| | - Roberta Degli Esposti
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Stefania Bartolini
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Alba A. Brandes
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
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Leichsenring J, Volckmar AL, Magios N, Morais de Oliveira CM, Penzel R, Brandt R, Kirchner M, Bozorgmehr F, Thomas M, Schirmacher P, Warth A, Endris V, Stenzinger A. Synonymous EGFR variant p.Q787Q is neither prognostic nor predictive in patients with lung adenocarcinoma. Genes Chromosomes Cancer 2016; 56:214-220. [PMID: 27750395 DOI: 10.1002/gcc.22427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 01/05/2023] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) harboring activating mutations in the Epidermal Growth Factor Receptor (EGFR) benefit from targeted therapies. A synonymous polymorphism (rs1050171, p.Q787Q) was shown to be associated with improved overall survival (OS) in colorectal cancer patients. As data in NSCLC are limited, we retrospectively analyzed associations of p.Q787Q with clinicopathological parameters including clinical response and outcome in patients with lung adenocarcinoma (ADC) who received tyrosine kinase inhibitor (TKI) therapy. Of 642 ADC patients whose tumors were profiled by next generation sequencing, 102 (15.9%) carried EGFR mutations targetable by TKIs (30.4% male patients, median age 65.1 y, 19.6% smokers with 12.8 median pack years). Seventy-nine patients (77.5%) received TKI therapy either as a first- or second-line therapy. Of the 102 EGFR-mutant tumors, 72 (70.6%) exhibited the p.Q787Q polymorphism and another 12 (11.8%) cases with p.Q787Q harbored an additional TKI insensitive mutation (p.T790M). The polymorphism was neither associated with classic clinicopathological parameters nor with overall survival (21.1 months vs. 20.1 months; P-value = 0.91) or clinical response (P-value = 0.122). The patients with p.T790M had worse survival compared to EGFR activating mutation carriers with and without p.Q787Q when analyzed as a separate group (27.5 months, P-value = 0.02). In conclusion, p.Q787Q is neither a suitable prognostic nor predictive biomarker for ADC patients receiving anti-EGFR therapy in first- or second-line of therapy. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jonas Leichsenring
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nikolaus Magios
- Thoracic Oncology, Thoraxklinik, University of Heidelberg, Translational Lung Research Center, Heidelberg, Germany
| | | | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Regine Brandt
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Farastuk Bozorgmehr
- Thoracic Oncology, Thoraxklinik, University of Heidelberg, Translational Lung Research Center, Heidelberg, Germany
| | - Michael Thomas
- Thoracic Oncology, Thoraxklinik, University of Heidelberg, Translational Lung Research Center, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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Padmanabhan V, Steinmetz HB, Rizzo EJ, Erskine AJ, Fairbank TL, de Abreu FB, Tsongalis GJ, Tafe LJ. Improving Adequacy of Small Biopsy and Fine-Needle Aspiration Specimens for Molecular Testing by Next-Generation Sequencing in Patients With Lung Cancer: A Quality Improvement Study at Dartmouth-Hitchcock Medical Center. Arch Pathol Lab Med 2016; 141:402-409. [DOI: 10.5858/arpa.2016-0096-oa] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
At our medical center, cytopathologists perform rapid on-site evaluation for specimen adequacy of fine-needle aspiration and touch imprint of needle core biopsy lung cancer samples. Two years ago the molecular diagnostics laboratory at our institution changed to next-generation sequencing using the Ion Torrent PGM and the 50-gene AmpliSeq Cancer Hotspot Panel v2 for analyzing mutations in a 50-gene cancer hot spot panel. This was associated with a dramatic fall in adequacy rate (68%).
Objective.—
To improve the adequacy rate to at least 90% for molecular testing using next-generation sequencing for all specimens collected by rapid on-site evaluation by the cytology laboratory.
Design.—
After baseline data on adequacy rate of cytology specimens with rapid on-site evaluation for molecular testing had been collected, 2 changes were implemented. Change 1 concentrated all the material in one block but did not produce desired results; change 2, in addition, faced the block only once with unstained slides cut up front for molecular testing. Data were collected in an Excel spreadsheet and adequacy rate was assessed.
Results.—
Following process changes 1 and 2 we reached our goal of at least 90% adequacy rate for molecular testing by next-generation sequencing on samples collected by rapid on-site evaluation including computed tomography–guided needle core biopsies (94%; 17 of 18) and fine-needle aspiration samples (94%; 30 of 32).
Conclusion.—
This study focused on factors that are controllable in a pathology department and on maximizing use of scant tissue. Optimizing the adequacy of the specimen available for molecular tests avoids the need for a second procedure to obtain additional tissue.
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Affiliation(s)
| | | | | | | | | | | | | | - Laura J. Tafe
- From the Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire. Dr Padmanabhan is now with the Department of Pathology, Baylor College of Medicine, Ben Taub General Hospital, Houston, Texas
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40
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Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, Wallis J, Wendl MC, Chen F, Ding L. Protein-structure-guided discovery of functional mutations across 19 cancer types. Nat Genet 2016; 48:827-37. [PMID: 27294619 PMCID: PMC5315576 DOI: 10.1038/ng.3586] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/13/2016] [Indexed: 02/07/2023]
Abstract
Local concentrations of mutations are well known in human cancers. However, their three-dimensional spatial relationships in the encoded protein have yet to be systematically explored. We developed a computational tool, HotSpot3D, to identify such spatial hotspots (clusters) and to interpret the potential function of variants within them. We applied HotSpot3D to >4,400 TCGA tumors across 19 cancer types, discovering >6,000 intra- and intermolecular clusters, some of which showed tumor and/or tissue specificity. In addition, we identified 369 rare mutations in genes including TP53, PTEN, VHL, EGFR, and FBXW7 and 99 medium-recurrence mutations in genes such as RUNX1, MTOR, CA3, PI3, and PTPN11, all mapping within clusters having potential functional implications. As a proof of concept, we validated our predictions in EGFR using high-throughput phosphorylation data and cell-line-based experimental evaluation. Finally, mutation-drug cluster and network analysis predicted over 800 promising candidates for druggable mutations, raising new possibilities for designing personalized treatments for patients carrying specific mutations.
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Affiliation(s)
- Beifang Niu
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Adam D. Scott
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Sohini Sengupta
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Matthew H. Bailey
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Prag Batra
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Jie Ning
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Matthew A. Wyczalkowski
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Wen-Wei Liang
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Qunyuan Zhang
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Department of Genetics, Washington University, St. Louis, Missouri 63108, USA
| | - Michael D. McLellan
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Sam Q. Sun
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Piyush Tripathi
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Carolyn Lou
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - Kai Ye
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Department of Genetics, Washington University, St. Louis, Missouri 63108, USA
| | - R. Jay Mashl
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
| | - John Wallis
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Michael C. Wendl
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Department of Genetics, Washington University, St. Louis, Missouri 63108, USA
- Department of Mathematics, Washington University, St. Louis, Missouri 63108, USA
| | - Feng Chen
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63108, USA
| | - Li Ding
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, Missouri 63108, USA
- Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA
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Roy-Chowdhuri S, Stewart J. Preanalytic Variables in Cytology: Lessons Learned From Next-Generation Sequencing—The MD Anderson Experience. Arch Pathol Lab Med 2016; 140:1191-1199. [DOI: 10.5858/arpa.2016-0117-ra] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
As our understanding of genomic alterations underlying solid tumor malignancies continues to evolve, molecular testing of tumor samples is increasingly used to guide therapeutic management. Next-generation sequencing (NGS) provides a novel platform for the simultaneous screening of multiple genes using small amounts of DNA. Several recent studies have described NGS mutational analysis using cytologic specimens. The cytopathologist's role in specimen assessment and triaging is critical to effectively implementing NGS in routine cytology practice.
Objectives.—
To review the NGS experience and a variety of preanalytic factors that affect NGS success rates of cytologic specimens at our institution.
Data Sources.—
To evaluate cytology specimen adequacy rates for NGS, we reviewed a 14-month period of image-guided fine-needle aspiration and core needle biopsies used for testing. In addition, we reviewed data from our previously published studies to evaluate preanalytic factors affecting NGS success in these specimens.
Conclusions.—
Identifying factors that affect NGS success rates in cytology specimens is crucial for a better understanding of specimen adequacy requirements and for proper use of limited-volume tissue samples. In our practice, which uses direct smears as well as cell block sections, NGS success rates in core needle biopsy and fine-needle aspiration samples are comparable. The chance of successful testing is further increased by procuring concurrent fine-needle aspiration and core needle biopsy samples. The type of glass slides used for direct smears and the method of tissue extraction affect our DNA yield. Validating a DNA input for cytology samples that is lower than that recommended by the manufacturer has significantly increased our NGS success rate.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
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42
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Xu J, Jin B, Chu T, Dong X, Yang H, Zhang Y, Wu D, Lou Y, Zhang X, Wang H, Han B. EGFR tyrosine kinase inhibitor (TKI) in patients with advanced non-small cell lung cancer (NSCLC) harboring uncommon EGFR mutations: A real-world study in China. Lung Cancer 2016; 96:87-92. [DOI: 10.1016/j.lungcan.2016.01.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/07/2016] [Accepted: 01/26/2016] [Indexed: 01/08/2023]
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Ragazzi M, Tamagnini I, Bisagni A, Cavazza A, Pagano M, Baldi L, Boni C, Cantile F, Barbieri F, Nicoli D, Sartori G, de Biase D, Gardini G, Rossi G. Diamond: immunohistochemistry versus sequencing in EGFR analysis of lung adenocarcinomas. J Clin Pathol 2016; 69:440-7. [PMID: 26553934 DOI: 10.1136/jclinpath-2015-203348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 02/05/2023]
Abstract
AIMS Identification of epidermal growth factor receptor (EGFR) mutations in lung adenocarcinomas is the single most important predictor of clinical response and outcome using EGFR tyrosine kinase inhibitors (TKIs). EGFR E746-A750del and L858R mutations are the most common gene alterations, also predicting the best clinical response to TKIs. We evaluated the accuracy of EGFR mutation-specific antibodies in a large cohort of lung adenocarcinomas, with different molecular settings and types of tissue samples. METHODS 300 lung adenocarcinomas diagnosed on cytology (48 cell blocks), biopsy (157 cases) and surgical resections (95 cases) were selected. All cases were investigated for EGFR by sequencing and two mutation-specific antibodies (clone 6B6 for E746-A750del; clone 43B2 for L858R) were tested using an automated immunostainer. Discordant results were investigated by next-generation sequencing (NGS). RESULTS Overall sensitivity and specificity of mutant-specific antibodies were 58.6% and 98.0%, respectively, and they increased up to 84% and 100% if only tumours harbouring E746-A750del were considered. In 13 discordant cases, NGS confirmed immunohistochemistry results in eight samples. CONCLUSIONS The EGFR mutation-specific antibodies have a fair/good sensitivity and good/high specificity in identifying classic mutations, but they cannot replace molecular tests. The antibodies work equally well on biopsies and cell blocks, possibly permitting a rapid screening in cases with poor material.
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Affiliation(s)
- Moira Ragazzi
- Department of Oncology and Advanced Technologies, Operative Unit of Pathology, Azienda S Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Ione Tamagnini
- Department of Oncology and Advanced Technologies, Operative Unit of Pathology, Azienda S Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Alessandra Bisagni
- Department of Oncology and Advanced Technologies, Operative Unit of Pathology, Azienda S Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Alberto Cavazza
- Department of Oncology and Advanced Technologies, Operative Unit of Pathology, Azienda S Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Maria Pagano
- Department of Oncology and Advanced Technologies, Operative Unit of Oncology, Azienda S. Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Licia Baldi
- Department of Oncology and Advanced Technologies, Operative Unit of Oncology, Azienda S. Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Corrado Boni
- Department of Oncology and Advanced Technologies, Operative Unit of Oncology, Azienda S. Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Flavia Cantile
- Department of Oncology and Hematology, Division of Oncology, Azienda Ospedaliero-Universitaria Policlinico, Modena, Italy
| | - Fausto Barbieri
- Department of Oncology and Hematology, Division of Oncology, Azienda Ospedaliero-Universitaria Policlinico, Modena, Italy
| | - Davide Nicoli
- Department of Oncology and Advanced Technologies, Operative Unit of Molecular Biology, Azienda S. Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Giuliana Sartori
- Department of Oncology and Advanced Technologies, Cervical Screening Unit, Azienda S. Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Dario de Biase
- Department of Medicine (DIMES), Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Giorgio Gardini
- Department of Oncology and Advanced Technologies, Operative Unit of Pathology, Azienda S Maria Nuova - IRCCS, Reggio Emilia, Italy
| | - Giulio Rossi
- Integrated Department of Diagnostic Laboratories, Section of Pathologic Anatomy, Azienda Ospedaliero-Universitaria Policlinico, Modena, Italy
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Targeted sequencing with enrichment PCR: a novel diagnostic method for the detection of EGFR mutations. Oncotarget 2016; 6:13742-9. [PMID: 25915533 PMCID: PMC4537046 DOI: 10.18632/oncotarget.3807] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/18/2015] [Indexed: 01/01/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is an important mediator of tumor cell survival and proliferation. The detection of EGFR mutations can predict prognoses and indicate when treatment with EGFR tyrosine kinase inhibitors should be used. As such, the development of highly sensitive methods for detecting EGFR mutations is important. Targeted next-generation sequencing is an effective method for diagnosing mutations. We compared the abilities of enrichment PCR followed by ultra-deep pyrosequencing (UDP), UDP alone, and PNA-mediated RT-PCR clamping to detect low-frequency EGFR mutations in tumor cell lines and tissue samples. Using enrichment PCR-UDP, we were able to detect the E19del and L858R mutations at minimum frequencies of 0.01% and 0.05%, respectively, in the PC-9 and H197 tumor cell lines. We also confirmed the sensitivity of detecting the E19del mutation by performing a titration analysis in FFPE tumor samples. The lowest mutation frequency detected was 0.0692% in tissue samples. EGFR mutations with frequencies as low as 0.01% were detected using enrichment PCR-UDP, suggesting that this method is a valuable tool for detecting rare mutations, especially in scarce tissue samples or those with small quantities of DNA.
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Roy-Chowdhuri S, Aisner DL, Allen TC, Beasley MB, Borczuk A, Cagle PT, Capelozzi V, Dacic S, da Cunha Santos G, Hariri LP, Kerr KM, Lantuejoul S, Mino-Kenudson M, Moreira A, Raparia K, Rekhtman N, Sholl L, Thunnissen E, Tsao MS, Vivero M, Yatabe Y. Biomarker Testing in Lung Carcinoma Cytology Specimens: A Perspective From Members of the Pulmonary Pathology Society. Arch Pathol Lab Med 2016; 140:1267-1272. [PMID: 27081878 DOI: 10.5858/arpa.2016-0091-sa] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The advent of targeted therapy in lung cancer has heralded a paradigm shift in the practice of cytopathology with the need for accurately subtyping lung carcinoma, as well as providing adequate material for molecular studies, to help guide clinical and therapeutic decisions. The variety and versatility of cytologic-specimen preparations offer significant advantages to molecular testing; however, they frequently remain underused. Therefore, evaluating the utility and adequacy of cytologic specimens is critical, not only from a lung cancer diagnosis standpoint but also for the myriad ancillary studies that are necessary to provide appropriate clinical management. A large fraction of lung cancers are diagnosed by aspiration or exfoliative cytology specimens, and thus, optimizing strategies to triage and best use the tissue for diagnosis and biomarker studies forms a critical component of lung cancer management. This review focuses on the opportunities and challenges of using cytologic specimens for molecular diagnosis of lung cancer and the role of cytopathology in the molecular era.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yasushi Yatabe
- From the Department of Pathology, University of Texas MD Anderson Cancer Center, Houston (Dr Roy-Chowdhuri); the Department of Pathology, University of Colorado Cancer Center, Denver (Dr Aisner); the Department of Pathology, University of Texas Medical Branch, Galveston (Dr Allen); the Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York (Dr Beasley); the Department of Pathology, Weill Cornell Medical College, New York (Drs Borczuk and Cagle); the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas (Dr Cagle); the Department of Pathology, University of Sao Paulo Medical School, Sao Paulo, Brazil (Dr Capelozzi); the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Dr Dacic); the Department of Pathology, University Health Network, Princess Margaret Cancer Centre, and the University of Toronto, Toronto, Ontario, Canada (Drs da Cunha Santos and Tsao); the Department of Pathology, Massachusetts General Hospital, and Harvard Medical School, Boston (Drs Hariri and Mino-Kenudson); the Department of Pathology, Aberdeen University Medical School, and Aberdeen Royal Infirmary, Foresterhill, Aberdeen, Scotland, United Kingdom (Dr Kerr); the Department of Biopathology, Centre Léon Bérard, Lyon, and J Fourier University, Institut National de la Santé et de la Recherche Médicale-Institut Albert Bonniot, Grenoble, France (Dr Lantuejoul); the Department of Pathology, New York University, New York (Dr Moreira); the Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois (Dr Raparia); the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York (Dr Rekhtman); the Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston (Drs Sholl and Vivero); the Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands (Dr Thunnissen); and the Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan (Dr Yatabe)
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Liu Y, Zhao Y, Qin Y, Du X, Wang Q, Lyu J. A novel microfluidic device that integrates nucleic acid extraction, amplification, and detection to identify an EGFR mutation in lung cancer tissues. RSC Adv 2016. [DOI: 10.1039/c5ra26225a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel microfluidic to detect a EGFR mutation in 40 min in an easy way for personalized medicine.
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Affiliation(s)
- Yuanbin Liu
- Key Laboratory of Laboratory Medicine
- Ministry of Education
- Zhejiang Provincial Key Laboratory of Medical Genetics
- Wenzhou Medical University
- Wenzhou
| | - Yang Zhao
- Department of Respiratory Medicine
- The Second Hospital
- Dalian Medical University
- Dalian 116023
- China
| | - Yongxin Qin
- Emergency Department
- The First Hospital
- Dalian Medical University
- Dalian 116011
- China
| | - Xiaohui Du
- Scientific Research Center
- The Second Hospital
- Dalian Medical University
- Dalian 116023
- China
| | - Qi Wang
- Department of Respiratory Medicine
- The Second Hospital
- Dalian Medical University
- Dalian 116023
- China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine
- Ministry of Education
- Zhejiang Provincial Key Laboratory of Medical Genetics
- Wenzhou Medical University
- Wenzhou
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Wei S, Lieberman D, Morrissette JJD, Baloch ZW, Roth DB, McGrath C. Using "residual" FNA rinse and body fluid specimens for next-generation sequencing: An institutional experience. Cancer Cytopathol 2015; 124:324-9. [PMID: 26682952 DOI: 10.1002/cncy.21666] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/17/2023]
Abstract
BACKGROUND Tissue specimens are typically considered optimal for molecular testing; however, in the current era of personalized medicine, cytopathology specimens are increasingly recognized as potential sources for molecular testing. This is often accomplished by using cell block specimens and/or fine-needle aspiration (FNA) smear preparations. In this study, the authors investigated the feasibility, performance, and quality of "residual" FNA rinse and body effusion fluids used for next-generation sequencing (NGS). METHODS Sequence data were generated from 17 malignancies in 16 patients from 13 FNA (10 lymph nodes, 1 lung, and 2 bone lesions) and 4 effusion (3 pleural and 1 pericardial) specimens. Malignancies included carcinomas (lung, breast, ovarian, and unknown primary), melanoma, and myeloma. Paired NGS testing was performed in 7 patients who had surgical biopsy or cell block specimens available. Routinely processed residual FNA rinse material and body fluids were used for DNA extraction and NGS (targeted gene panel). RESULTS NGS was successfully performed on all 17 specimens. A significant amount of DNA was obtained from the residual FNA rinse (176.3 ng/μL) compared with the paired cell block slides (10.6 ng/μL). Two of the 10 lung adenocarcinomas (20%) demonstrated epidermal growth factor receptor (EGFR) mutations, including 1 leucine-to-arginine substitution at codon 858 (L858R) in exon 21 and 1 codon 2235_2249 deletion (resulting in an in-frame deletion of 5 amino acids from position 746 to 750 [glutamic acid, leucine, arginine, glutamic acid, and alanine]; E746_A750del) in exon 19. Three KRAS [Kirsten rat sarcoma viral oncogene homolog] mutations, 1 BRAF (v-Raf murine sarcoma viral oncogene homolog B1) mutation, and 1 NRAS (neuroblastoma RAS viral oncogene homolog) mutation were identified in the remaining lung adenocarcinomas. Patients who underwent paired testing demonstrated 100% concordant mutations. CONCLUSIONS Targeted NGS can be performed on residual FNA rinse and body fluid specimens. This approach is particularly important when a paucicellular cell block or biopsy specimen is encountered. Cancer Cytopathol 2016;124:324-29. © 2015 American Cancer Society.
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Affiliation(s)
- Shuanzeng Wei
- Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Lieberman
- Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zubair W Baloch
- Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - David B Roth
- Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Cindy McGrath
- Department of Pathology and Laboratory Medicine, Center for Personalized Diagnostics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
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48
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Zhang AK. Chromogenic Assay for Lung Cancer-Related EGFR Exon 19 Hotspot Deletion Mutations. Genet Test Mol Biomarkers 2015; 20:18-23. [PMID: 26544543 DOI: 10.1089/gtmb.2015.0197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) deletion mutations are associated with the development of nonsmall-cell lung cancer (NSCLC) and can serve as useful biomarkers. AIM In the present study, a novel assay for the detection of EGFR hotspot mutations was designed to be highly sensitive and practically false-positive-free to harness the potential of detecting such mutations as biomarkers early in the diagnosis of NSCLC. The new assay draws from the polymerase chain reaction (PCR) for amplification, blue-white screening for initial allele discrimination, and Sanger sequencing for mutation confirmation. RESULTS Mutant plasmids were mixed with wild-type DNA in ratios from 1:10 to 1:1000, followed by PCR amplification, blue-white screening, and sequencing. Mutants were successfully sequence confirmed for mixtures at ratios of 1:300 and 1:1000, highlighting the assay's high sensitivity and low risk of false-positives due to confirmation by Sanger sequencing. CONCLUSION With high sensitivity and low false positives, the present assay is appealing as an aid in the early diagnosis of NSCLC through liquid biopsy. The highly customizable nature of the assay provides the possibility of applications in the early diagnosis of other cancer-related genes through nonsense-transformable mutations.
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Affiliation(s)
- Andy K Zhang
- Department of Molecular Diagnostics, Genotheramics, Inc. , San Diego, California
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Lin CC, Huang WL, Wei F, Su WC, Wong DT. Emerging platforms using liquid biopsy to detect EGFR mutations in lung cancer. Expert Rev Mol Diagn 2015; 15:1427-40. [PMID: 26420338 DOI: 10.1586/14737159.2015.1094379] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Advances in target therapies for lung cancer have enabled detection of gene mutations, specifically those of EGFR. Assays largely depend on the acquisition of tumor tissue biopsy, which is invasive and may not reflect the genomic profile of the tumor at treatment due to tumor heterogeneity or changes that occur during treatment through acquired resistance. Liquid biopsy, a blood test that detects evidence of cancer cells or tumor DNA, has generated considerable interest for its ability to detect EGFR mutations. However, its clinical application is limited by complicated collection methods and the need for technique-dependent platforms. Recently, simpler techniques for EGFR mutant detection in urine or saliva samples have been developed. This review focuses on advances in liquid biopsy and discusses its potential for clinical implementation in lung cancer.
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Affiliation(s)
- Chien-Chung Lin
- a 1 Department of Internal Medicine, Institute of Clinical Medicine, National Cheng Kung University, Hospital, College of Medicine , Tainan, Taiwan
| | - Wei-Lun Huang
- a 1 Department of Internal Medicine, Institute of Clinical Medicine, National Cheng Kung University, Hospital, College of Medicine , Tainan, Taiwan
| | - Fang Wei
- b 2 UCLA - Dentistry, 73-034 CHS UCLA School of Dentistry , 10833 Le Conte Avenue, Los Angeles, California 90095, USA
| | - Wu-Chou Su
- a 1 Department of Internal Medicine, Institute of Clinical Medicine, National Cheng Kung University, Hospital, College of Medicine , Tainan, Taiwan
| | - David T Wong
- b 2 UCLA - Dentistry, 73-034 CHS UCLA School of Dentistry , 10833 Le Conte Avenue, Los Angeles, California 90095, USA
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50
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Vigliar E, Malapelle U, de Luca C, Bellevicine C, Troncone G. Challenges and opportunities of next-generation sequencing: a cytopathologist's perspective. Cytopathology 2015; 26:271-83. [DOI: 10.1111/cyt.12265] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 01/14/2023]
Affiliation(s)
- E. Vigliar
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - U. Malapelle
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - C. de Luca
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - C. Bellevicine
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
| | - G. Troncone
- Pathology Division; Department of Public Health; University of Naples Federico II; Naples Italy
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