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FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:jpm12050750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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2
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Xu C, Qin L, Lei W, Jiang J, Ni C, Huang J. The role of endobronchial ultrasound-guided transbronchial needle aspiration liquid-based cytology in the diagnosis of mediastinal lymphadenopathy. Diagn Cytopathol 2019; 48:316-321. [PMID: 31883315 PMCID: PMC7079241 DOI: 10.1002/dc.24374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive, reliable technique for sampling mediastinal lymph nodes (LNs). Liquid-based cytology (LBC) is widely used for cervical cancer screening because it provides reliable and feasible results. The present study aimed to evaluate effectiveness of the combination of EBUS-TBNA and LBC in the diagnosis of mediastinal lymphadenopathy. METHODS A total of 602 LNs that were retrospectively analyzed were sampled in 442 patients who underwent EBUS-TBNA between January 2014 and December 2016. The histopathological result of TBNA tissue or cell blocks was considered as the gold standard to evaluate diagnostic utility of LBC and conventional smears (CS) for the diagnosis of mediastinal lymphadenopathy. RESULTS Of the 602 LNs, 265 were mediastinal LN metastases from lung cancer, four were lymphoma, and 333 were benign. The sensitivity of LBC and CS in the diagnosis of mediastinal LN metastases from lung cancer was 72.8% and 63%, respectively, and the specificity was 98.5% and 97%, respectively. The positive predictive values for LBC and CS were 97.5% and 94.4%, respectively, whereas the negative predictive values were 82.2% and 76.9%, respectively. The accuracy of LBC and CS was 88% and 83.7%, respectively. The diagnostic value of LBC was significantly higher than that of CS (P = .001). CONCLUSIONS The combination of EBUS-TBNA and LBC is a highly reliable and feasible procedure that optimizes diagnostic utility for the diagnosis of lung cancer and mediastinal LN staging.
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Affiliation(s)
- Chuancai Xu
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lingyan Qin
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wei Lei
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Junhong Jiang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chongjun Ni
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian'an Huang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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3
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da Cunha Santos G, Saieg MA, Troncone G, Zeppa P. Cytological preparations for molecular analysis: A review of technical procedures, advantages and limitations for referring samples for testing. Cytopathology 2019; 29:125-132. [PMID: 29575423 DOI: 10.1111/cyt.12534] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Abstract
Minimally invasive procedures such as endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) must yield not only good quality and quantity of material for morphological assessment, but also an adequate sample for analysis of molecular markers to guide patients to appropriate targeted therapies. In this context, cytopathologists worldwide should be familiar with minimum requirements for refereeing cytological samples for testing. The present manuscript is a review with comprehensive description of the content of the workshop entitled Cytological preparations for molecular analysis: pre-analytical issues for EBUS TBNA, presented at the 40th European Congress of Cytopathology in Liverpool, UK. The present review emphasises the advantages and limitations of different types of cytology substrates used for molecular analysis such as archival smears, liquid-based preparations, archival cytospin preparations and FTA (Flinders Technology Associates) cards, as well as their technical requirements/features. These various types of cytological specimens can be successfully used for an extensive array of molecular studies, but the quality and quantity of extracted nucleic acids rely directly on adequate pre-analytical assessment of those samples. In this setting, cytopathologists must not only be familiar with the different types of specimens and associated technical procedures, but also correctly handle the material provided by minimally invasive procedures, ensuring that there is sufficient amount of material for a precise diagnosis and correct management of the patient through personalised care.
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Affiliation(s)
- G da Cunha Santos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - M A Saieg
- Department of Pathology, Santa Casa Medical School, São Paulo, Brazil.,Department of Pathology, AC Camargo Cancer Center, São Paulo, Brazil
| | - G Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - P Zeppa
- Department of Medicine and Surgery, University of Salerno, Salerno, Italy
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4
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The utilization of cytologic and small biopsy samples for ancillary molecular testing. Mod Pathol 2019; 32:77-85. [PMID: 30600323 DOI: 10.1038/s41379-018-0138-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/22/2018] [Indexed: 11/09/2022]
Abstract
There has recently been an increased emphasis on the utilization of cytologic samples and small biopsies for not only diagnostic purposes but also for ancillary testing. In some instances, the ancillary tests contribute to the diagnosis and in other scenarios, they provide prognostic and theranostic information for the management of patients with advanced stage cancer. These ancillary tests include immunohistochemical biomarker analysis, molecular mutation analysis, and cytogenetic tests. Despite the finite nature of the cellular material procured in cytologic and small tissue biopsies, pathologists are tasked with ordering an increasing number of tests using these limited samples. This requires the pathologists to utilize and triage these samples in an optimal fashion so that as much information can be gleaned from a given specimen. This review will focus on the pre-analytic requirements for ancillary molecular and cytogenetic tests in the context of a discussion of the various preparation methods for cytologic and small biopsy specimens. The goal will be to provide the reader with the necessary concepts that can be utilized to develop optimal specimen selection and triage strategies to maximize the chances of effectively utilizing these samples for comprehensive diagnostic and relevant ancillary testing purposes.
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5
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Abstract
There has been a paradigm shift in the practice of cytopathology with the advent of highly sensitive molecular tests using small amounts of tissue that can provide diagnostic, prognostic, and predictive information for clinical management. The cytopathologist plays a key role in providing a timely and accurate diagnosis as well as ensuring appropriate processing and handling of the specimen and judicious triaging of the tissue for molecular testing that guide therapeutic decisions. As the era of "precision medicine" continues to evolve and expand, cytopathology remains a dynamic field with advances in the practice of molecular cytopathology providing new paradigms in clinical care.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard Unit 85, Houston, TX 77030, USA.
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6
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Aisner DL. The Revised College of American Pathologists/International Association for the Study of Lung Cancer/Association for Molecular Pathology Guideline: A Step Forward for Molecular Cytopathology. Arch Pathol Lab Med 2018; 142:684-685. [PMID: 29595315 DOI: 10.5858/arpa.2018-0081-ed] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dara L Aisner
- From the Department of Pathology, University of Colorado School of Medicine, Aurora
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7
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Fassan M. Molecular Diagnostics in Pathology: Time for a Next-Generation Pathologist? Arch Pathol Lab Med 2018; 142:313-320. [DOI: 10.5858/arpa.2017-0269-ra] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Context.—Comprehensive molecular investigations of mainstream carcinogenic processes have led to the use of effective molecular targeted agents in most cases of solid tumors in clinical settings.Objective.—To update readers regarding the evolving role of the pathologist in the therapeutic decision-making process and the introduction of next-generation technologies into pathology practice.Data Sources.—Current literature on the topic, primarily sourced from the PubMed (National Center for Biotechnology Information, Bethesda, Maryland) database, were reviewed.Conclusions.—Adequate evaluation of cytologic-based and tissue-based predictive diagnostic biomarkers largely depends on both proper pathologic characterization and customized processing of biospecimens. Moreover, increased requests for molecular testing have paralleled the recent, sharp decrease in tumor material to be analyzed—material that currently comprises cytology specimens or, at minimum, small biopsies in most cases of metastatic/advanced disease. Traditional diagnostic pathology has been completely revolutionized by the introduction of next-generation technologies, which provide multigene, targeted mutational profiling, even in the most complex of clinical cases. Combining traditional and molecular knowledge, pathologists integrate the morphological, clinical, and molecular dimensions of a disease, leading to a proper diagnosis and, therefore, the most-appropriate tailored therapy.
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Affiliation(s)
- Matteo Fassan
- From the Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
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8
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da Cunha Santos G, Saieg MA. Preanalytic specimen triage: Smears, cell blocks, cytospin preparations, transport media, and cytobanking. Cancer Cytopathol 2017; 125:455-464. [PMID: 28609003 DOI: 10.1002/cncy.21850] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/27/2017] [Accepted: 02/07/2017] [Indexed: 12/20/2022]
Abstract
With increasing requests for the evaluation of prognostic and predictive molecular biomarkers, great attention must be paid to the preanalytical issues regarding sample quality and DNA/RNA yield from all different types of cytological preparations. The objectives of this review were: 1) to provide an update regarding the importance of specimen triage as well as specimen handling and collection; 2) to discuss the different cell preparations that can be used for molecular testing, their advantages and limitations; and 3) to highlight the strategies for biobanking cytology samples. Good-quality DNA/RNA can be harvested from fresh cells in cell suspensions, formalin-fixed paraffin-embedded cell blocks, archival stained smears, archival unstained cytospin preparations, liquid-based cytology slides, FTA cards, and cryopreserved cells. In contrast to formalin-fixed paraffin-embedded tissue specimens (small biopsies and surgical resections), the multitude of types of sample preparations as well as the diversity in sample collection and processing procedures make cytology an ideal specimen for most genomic platforms, with less DNA and RNA degradation and a purer sample, usually with a higher concentration of tumor cells. The broad incorporation of cytological specimens into clinical practice. A should increase the number of samples potentially available for molecular tests and avoid repeat invasive procedures for tissue procurement, thereby increasing patient safety. In this context, it is of utmost importance that cytopathologists become familiar with the variables that can affect test results and embrace the goal of excellence in sample quality. Cancer Cytopathol 2017;125(6 suppl):455-64. © 2017 American Cancer Society.
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Affiliation(s)
- Gilda da Cunha Santos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Mauro A Saieg
- Department of Pathology, Santa Casa Medical School, Sao Paulo, Brazil
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9
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Pisapia P, Lozano MD, Vigliar E, Bellevicine C, Pepe F, Malapelle U, Troncone G. ALK and ROS1 testing on lung cancer cytologic samples: Perspectives. Cancer Cytopathol 2017; 125:817-830. [DOI: 10.1002/cncy.21899] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health; University of Naples Federico II; Naples Italy
| | - Maria D. Lozano
- Department of Pathology; University Clinic of Navarra; Pamplona Spain
| | - Elena Vigliar
- Department of Public Health; University of Naples Federico II; Naples Italy
| | | | - Francesco Pepe
- Department of Public Health; University of Naples Federico II; Naples Italy
| | - Umberto Malapelle
- Department of Public Health; University of Naples Federico II; Naples Italy
| | - Giancarlo Troncone
- Department of Public Health; University of Naples Federico II; Naples Italy
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10
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Bellevicine C, Malapelle U, Vigliar E, Pisapia P, Vita G, Troncone G. How to prepare cytological samples for molecular testing. J Clin Pathol 2017; 70:819-826. [DOI: 10.1136/jclinpath-2017-204561] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 12/21/2022]
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11
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Concurrent fine needle aspirations and core needle biopsies: a comparative study of substrates for next-generation sequencing in solid organ malignancies. Mod Pathol 2017; 30:499-508. [PMID: 28084342 DOI: 10.1038/modpathol.2016.228] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 01/04/2023]
Abstract
Minimally invasive procedures, such as fine needle aspiration and core needle biopsy, are commonly used for the diagnosis in solid organ malignancies. In the era of targeted therapy, it is crucial for molecular testing to be performed on these limited volume specimens. Although several recent studies have demonstrated the utility of small biopsy specimens for molecular testing, there remains debate as to whether core needle biopsy specimens are more reliable than fine needle aspiration for molecular studies. In this study, we reviewed concurrently acquired fine needle aspiration and core needle biopsy samples (n=24), and compared overall cellularity, tumor fraction, and the results of next-generation sequencing. All somatic mutations detected in core needle biopsy samples were also detected in fine needle aspiration samples. The estimated tumor fraction was significantly higher in fine needle aspiration smears than core needle biopsy samples (P=0.003), whereas the overall DNA yield from smears was significantly lower than that obtained from the core needle biopsy specimens (P=0.01). The normalized average amplicon coverage for the genes analyzed was significantly higher in cytology smears than paired core needle biopsy samples, with lower numbers of failed amplicons and higher overall mutation allelic frequencies seen in the former. We further evaluated 100 malignant fine needle aspiration and core needle biopsy samples, acquired concurrently, for overall cellularity and tumor fraction. Overall cellularity and tumor fraction of fine needle aspiration samples was significantly higher than concurrently acquired core needle biopsy samples (P<0.001). In conclusion, we show that fine needle aspiration samples frequently provide better cellularity, higher tumor fraction, and superior sequencing metrics than concurrently acquired core needle biopsy samples. Cytologic specimens, therefore, should be better integrated into routine molecular diagnostics workflow to maximize limited tissues for clinically relevant genomic testing.
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12
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Zito Marino F, Rossi G, Brunelli M, Malzone MG, Liguori G, Bogina G, Morabito A, Rocco G, Franco R, Botti G. Diagnosis of anaplastic lymphoma kinase rearrangement in cytological samples through a fluorescence in situ hybridization-based assay: Cytological smears versus cell blocks. Cancer Cytopathol 2017; 125:303-312. [PMID: 28195686 DOI: 10.1002/cncy.21835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022]
Abstract
Anaplastic lymphoma kinase (ALK) status analysis of lung cytological specimens should be successfully encouraged in routine practice because biopsy specimens are not always available. To date, the US Food and Drug Administration has approved both fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) as diagnostic tests for identifying ALK-positive patients eligible for treatment with crizotinib. Although ALK IHC is an optimal diagnostic tool, FISH becomes mandatory in equivocal cases. ALK FISH of paraffin-embedded tissue material is still the gold standard, whereas the cytological specimen assay has not yet been completely standardized. Many controversial data have been reported on the adequacy of cytology cell blocks (CBs) versus conventional smears for FISH testing. This review discusses some critical issues related to ALK FISH of cytological samples, including the triaging of collected specimens to optimize the material, the use of CBs versus conventional smears, and alternative methods for an ALK rearrangement diagnosis. Conventional smears have the advantages of an immediate evaluation, no probe tissue-related artifactual loss, no fixation-related alterations, and usually sufficient material for an analytic preparation. On the other hand, CBs have several advantages, including the appropriate conservation of the tissue architecture, an absence of problems related to cell overlapping, and the ability to evaluate neoplastic cells in a dark field. Cancer Cytopathol 2017;125:303-312. © 2017 American Cancer Society.
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Affiliation(s)
- Federica Zito Marino
- Pathology Unit, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy.,Pathology Unit, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Giulio Rossi
- Unit of Pathologic Anatomy, Azienda USL Valle d'Aosta, Aosta, Italy
| | - Matteo Brunelli
- Anatomic Pathology Section Department of Pathology, University of Verona, Verona, Italy
| | | | - Giuseppina Liguori
- Pathology Unit, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy
| | - Giuseppe Bogina
- Section of Pathologic Anatomy, Sacro Cuore Don Calabria Hospital, Negrar, Italy
| | - Alessandro Morabito
- Medical Oncology Unit, Department of Thoracic Surgical and Medical Oncology, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy
| | - Gaetano Rocco
- Division of Thoracic Surgery, Department of Thoracic Surgical and Medical Oncology, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy
| | - Renato Franco
- Pathology Unit, Luigi Vanvitelli University of Campania, Naples, Italy
| | - Gerardo Botti
- Pathology Unit, Istituto Nazionale Tumori Fondazione G. Pascale, Naples, Italy
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13
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Roy-Chowdhuri S, Roy S, Monaco SE, Routbort MJ, Pantanowitz L. Big data from small samples: Informatics of next-generation sequencing in cytopathology. Cancer Cytopathol 2016; 125:236-244. [PMID: 27918649 DOI: 10.1002/cncy.21805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 12/12/2022]
Abstract
The rapid adoption of next-generation sequencing (NGS) in clinical molecular laboratories has redefined the practice of cytopathology. Instead of simply being used as a diagnostic tool, cytopathology has evolved into a practice providing important genomic information that guides clinical management. The recent emphasis on maximizing limited-volume cytology samples for ancillary molecular studies, including NGS, requires cytopathologists not only to be more involved in specimen collection and processing techniques but also to be aware of downstream testing and informatics issues. For the integration of molecular informatics into the clinical workflow, it is important to understand the computational components of the NGS workflow by which raw sequence data are transformed into clinically actionable genomic information and to address the challenges of having a robust and sustainable informatics infrastructure for NGS-based testing in a clinical environment. Adapting to needs ranging from specimen procurement to report delivery is crucial for the optimal utilization of cytology specimens to accommodate requests from clinicians to improve patient care. This review presents a broad overview of the various aspects of informatics in the context of NGS-based testing of cytology specimens. Cancer Cytopathol 2017;125:236-244. © 2016 American Cancer Society.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Somak Roy
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sara E Monaco
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mark J Routbort
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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14
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Layfield LJ, Roy-Chowdhuri S, Baloch Z, Ehya H, Geisinger K, Hsiao SJ, Lin O, Lindeman NI, Roh M, Schmitt F, Sidiropoulos N, VanderLaan PA. Utilization of ancillary studies in the cytologic diagnosis of respiratory lesions: The papanicolaou society of cytopathology consensus recommendations for respiratory cytology. Diagn Cytopathol 2016; 44:1000-1009. [PMID: 27561242 DOI: 10.1002/dc.23549] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/06/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022]
Abstract
The Papanicolaou Society of Cytopathology has developed a set of guidelines for respiratory cytology including indications for sputum examination, bronchial washings and brushings, CT-guided FNA and endobronchial ultrasound guided fine needle aspiration (EBUS-FNA), as well as recommendations for classification and criteria, ancillary testing and post-cytologic diagnosis management and follow-up. All recommendation documents are based on the expertise of committee members, an extensive literature review, and feedback from presentations at national and international conferences. The guideline documents selectively present the results of these discussions. The present document summarizes recommendations for ancillary testing of cytologic samples. Ancillary testing including microbiologic, immunocytochemical, flow cytometric, and molecular testing, including next-generation sequencing are discussed. Diagn. Cytopathol. 2016;44:1000-1009. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lester J Layfield
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zubair Baloch
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hormoz Ehya
- Department of Pathology, Fox Chase Cancer Center, Temple University, Philadelphia, Pennsylvania
| | - Kim Geisinger
- Department of Pathology, University of Mississippi, Jackson, Mississippi
| | - Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Oscar Lin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal I Lindeman
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Michael Roh
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Fernando Schmitt
- Département de Médecine, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Nikoletta Sidiropoulos
- Department of Pathology and Laboratory Medicine, The University of Vermont, Burlington, Vermont
| | - Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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15
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De Luca C, Gragnano G, Pisapia P, Vigliar E, Malapelle U, Bellevicine C, Troncone G. EGFR mutation detection on lung cancer cytological specimens by the novel fully automated PCR-based Idylla EGFR Mutation Assay. J Clin Pathol 2016; 70:295-300. [PMID: 27543600 DOI: 10.1136/jclinpath-2016-203989] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 11/03/2022]
Abstract
AIMS In everyday practice, epidermal growth factor receptor (EGFR) testing is centralised in referral laboratories that receive paucicellular cytological specimens. Ideally, EGFR testing should be carried out in the centre where the patient is diagnosed such that the most cellular slide can be selected from in-house collected cytological material. However, available techniques are little standardised and difficult to be implemented in settings with little expertise in molecular testing. The Idylla EGFR prototype assay is a rapid and fully automated test which may easily be adopted by a wider number of pathological centres. This study assessed whether an Idylla EGFR prototype assay can be reliably applied to cytological lung cancer specimens. METHODS The limit of detection (LOD) of the Idylla EGFR prototype assay was assessed by cell line dilution studies. A total of 10 ng was directly placed inside an Idylla EGFR prototype assay cartridge. Idylla results were compared with fragment length (exon 19 del) and Taqman assays. RESULTS The Idylla EGFR prototype assay showed an LOD of 1% mutant allele and yielded valid results in 74/76 (97.3%) samples, detecting all the mutant cases (n=32) identified by standard techniques; in addition, Idylla detected two low abundance EGFR exon 19 deletions and two G719X exon 18 point mutations, not covered by our standard reference method. CONCLUSIONS Idylla EGFR prototype assay is sensitive on extracted DNA and can reliably be applied on cytological samples, enabling implementation of EGFR testing even in less experienced diagnostic units.
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Affiliation(s)
- Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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16
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Ozluk Y, Firat P, Yegen G, Hocaoglu J, Tas S, Yilmazbayhan D. EGFR mutation testing using archival-stained smears in non-small cell lung carcinoma. Cytopathology 2016; 28:35-45. [PMID: 27389045 DOI: 10.1111/cyt.12357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have shown benefits regarding progression-free and overall survival in patients whose tumours show EGFR mutations. Most patients' lung cancer is metastatic when detected. Small tissue samples and cytological materials are widely used in diagnosis. The aim of the present study was to compare the EGFR mutation analysis results between cytology, small biopsies and resections. METHODS Archival material for EGFR testing was reviewed. Cell blocks and/or stained smears and tissue blocks were used where appropriate. The tumour cell count and percentage were recorded as well as the DNA content. The influence of TTF-1 immunoreactivity on EGFR testing was also investigated. RESULTS The study cohort included 300 unpaired specimens of 84 resections, 83 small biopsies and 133 cytological materials. EGFR mutation rates did not differ significantly for cytology, small biopsy and resections (P > 0.05). The higher tumour cell percentage in FNAs than in exfoliative cytology did not affect the EGFR mutation status. EGFR mutation rates were similar when either slides or cell blocks were used. Cytology slides revealed a higher tumour cell content and DNA concentration than the cell blocks. May-Grünwald-Giemsa (MGG)-stained smears had higher rates of the EGFR mutation than the Papanicolaou (Pap)-stained slides (P < 0.05). Tumours with negative immunoreactivity for TTF-1 are less likely to have an EGFR mutation (P < 0.05). CONCLUSIONS Cytological materials can be used successfully for mutation analysis in lung cancer.
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Affiliation(s)
- Y Ozluk
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - P Firat
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - G Yegen
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - J Hocaoglu
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - S Tas
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - D Yilmazbayhan
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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17
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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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18
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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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19
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Roy-Chowdhuri S, Chow CW, Kane MK, Yao H, Wistuba II, Krishnamurthy S, Stewart J, Staerkel G. Optimizing the DNA yield for molecular analysis from cytologic preparations. Cancer Cytopathol 2015; 124:254-60. [PMID: 26630358 DOI: 10.1002/cncy.21664] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/21/2023]
Abstract
BACKGROUND Cytology smears and cytospin preparations are increasingly being used for molecular testing. With these limited samples, optimizing tissue extraction to maximize the DNA yield is, therefore, critical. This study examined 2 common methods of tissue extraction and compared DNA yields from different types of glass slides. METHODS The H226 lung cancer cell line and 5 clinical samples of cellular effusions were used to prepare Diff-Quik-stained cytospins on 4 types of glass slides: fully frosted (FF), nonfrosted (NF), positively charged (PC), and silane-coated (SC). Tissue extraction was performed by either scalpel-blade scraping or cell lifting with the Pinpoint Slide DNA Isolation System (Zymo Research). DNA was extracted with the QIAamp DNA Mini Kit (Qiagen) and was quantified with the Quant-iT PicoGreen Kit (Life Technologies). RESULTS The DNA yield in cell-line cytospins was significantly lower from FF slides versus NF, PC, and SC slides with both scraping and cell-lifting methods. In addition, scraping yielded significantly more DNA than cell lifting (P = .005). DNA yields from 5 clinical effusion cases with FF and NF slides showed results similar to the results for cell-line samples, with scraping consistently yielding more DNA than cell lifting and with NF slides outperforming FF slides. CONCLUSIONS Optimizing the DNA yield extracted from cytology specimens maximizes the chances of successful molecular testing and is critical in cases of low or marginal cellularity. This study demonstrates the following: 1) scraping yields more DNA than cell lifting, and 2) NF slides yield more DNA than FF slides.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Cytopathology Section, Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mary K Kane
- Cytopathology Section, Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Yao
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Savitri Krishnamurthy
- Cytopathology Section, Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Stewart
- Cytopathology Section, Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregg Staerkel
- Cytopathology Section, Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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20
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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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21
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Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies. Cancers (Basel) 2015; 7:1699-715. [PMID: 26343728 PMCID: PMC4586792 DOI: 10.3390/cancers7030859] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 01/28/2023] Open
Abstract
Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.
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22
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Roy-Chowdhuri S, Goswami RS, Chen H, Patel KP, Routbort MJ, Singh RR, Broaddus RR, Barkoh BA, Manekia J, Yao H, Medeiros LJ, Staerkel G, Luthra R, Stewart J. Factors affecting the success of next-generation sequencing in cytology specimens. Cancer Cytopathol 2015; 123:659-68. [PMID: 26230354 DOI: 10.1002/cncy.21597] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND The use of cytology specimens for next-generation sequencing (NGS) is particularly challenging because of the unconventional substrate of smears and the often limited sample volume. An analysis of factors affecting NGS testing in cytologic samples may help to increase the frequency of successful testing. METHODS This study reviewed variables associated with all in-house cytology cases (n = 207) that were analyzed by NGS with the Ion Torrent platform during a 10-month interval. A statistical analysis was performed to measure the effects of the DNA input threshold, specimen preparation, slide type, tumor fraction, DNA yield, and cytopathologist bias. RESULTS One hundred sixty-four of 207 cases (79%) were successfully sequenced by NGS; 43 (21%) failed because of either a low DNA yield or a template/library preparation failure. The median estimated tumor fraction and DNA concentration for the successfully sequenced cases were 70% and 2.5 ng/μL, respectively, whereas they were 60% and 0.2 ng/μL, respectively, for NGS failures. Cell block sections were tested in 91 cases, and smears were used in 116 cases. NGS success positively correlated with the DNA yield but not the tumor fraction. Cell block preparations showed a higher success rate than smears. Frosted-tip slides yielded significantly more DNA than fully frosted slides. Lowering the input DNA concentration below the manufacturer's recommended threshold of 10 ng (>0.85 ng/μL) resulted in a marked increase in the NGS success rate from 58.6% to 89.8%. CONCLUSIONS The failure of NGS with cytology samples is usually a result of suboptimal DNA due to multiple pre-analytical factors. Knowledge of these factors will allow better selection of cytology material for mutational analysis.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rashmi S Goswami
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Chen
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur P Patel
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark J Routbort
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajesh R Singh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Russell R Broaddus
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bedia A Barkoh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jawad Manekia
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregg Staerkel
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Stewart
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Roh MH. The Utilization of Cytologic Fine-Needle Aspirates of Lung Cancer for Molecular Diagnostic Testing. J Pathol Transl Med 2015; 49:300-9. [PMID: 26076721 PMCID: PMC4508567 DOI: 10.4132/jptm.2015.06.16] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 01/10/2023] Open
Abstract
In this era of precision medicine, our understanding and knowledge of the molecular landscape associated with lung cancer pathogenesis continues to evolve. This information is being increasingly exploited to treat advanced stage lung cancer patients with tailored, targeted therapy. During the management of these patients, minimally invasive procedures to obtain samples for tissue diagnoses are desirable. Cytologic fine-needle aspirates are often utilized for this purpose and are important not only for rendering diagnoses to subtype patients’ lung cancers, but also for ascertaining molecular diagnostic information for treatment purposes. Thus, cytologic fine-needle aspirates must be utilized and triaged judiciously to achieve both objectives. In this review, strategies in utilizing fine-needle aspirates will be discussed in the context of our current understanding of the clinically actionable molecular aberrations underlying non-small cell lung cancer and the molecular assays applied to these samples in order to obtain treatment-relevant molecular diagnostic information.
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Affiliation(s)
- Michael H Roh
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA
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24
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Malapelle U, Vatrano S, Russo S, Bellevicine C, de Luca C, Sgariglia R, Rocco D, de Pietro L, Riccardi F, Gobbini E, Righi L, Troncone G. EGFR mutant allelic-specific imbalance assessment in routine samples of non-small cell lung cancer. J Clin Pathol 2015; 68:739-41. [PMID: 26047622 DOI: 10.1136/jclinpath-2015-203101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/18/2015] [Indexed: 11/03/2022]
Abstract
In non-small cell lung cancer (NSCLC), the epidermal growth factor receptor (EGFR) gene may undergo both mutations and copy number gains. EGFR mutant allele-specific imbalance (MASI) occurs when the ratio of mutant-to-wild-type alleles increases significantly. In this study, by using a previously validated microfluidic-chip-based technology, EGFR-MASI occurred in 25/67 mutant cases (37%), being more frequently associated with EGFR exon 19 deletions (p=0.033). In a subset of 49 treated patients, we assessed whether MASI is a modifier of anti-EGFR treatment benefit. The difference in progression-free survival and overall survival between EGFR-MASI-positive and EGFR-MASI-negative groups of patients did not show a statistical significance. In conclusion, EGFR-MASI is a significant event in NSCLC, specifically associated with EGFR exon 19 deletions. However, EGFR-MASI does not seem to play a role in predicting the response to first-generation EGFR small molecules inhibitors.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Simona Vatrano
- Department of Oncology, University of Turin at San Luigi Hospital, Turin, Italy
| | - Stefania Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Caterina de Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Danilo Rocco
- Department of Oncology, Azienda Ospedaliera dei Colli, Naples, Italy
| | - Livia de Pietro
- Department of Oncology, Azienda Ospedaliera dei Colli, Naples, Italy
| | - Fernando Riccardi
- Department of Oncology, Antonio Cardarelli-Azienda Ospedaliera di Rilievo Nazionale, Naples, Italy
| | - Elisa Gobbini
- Department of Oncology, University of Turin at San Luigi Hospital, Turin, Italy
| | - Luisella Righi
- Department of Oncology, University of Turin at San Luigi Hospital, Turin, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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25
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Vigliar E, Malapelle U, Bellevicine C, Troncone G. EGFR testing and the CAP/IASLC/AMP lung cancer biomarker testing guidelines: knowledge gaps and future directions. Lung Cancer Manag 2015. [DOI: 10.2217/lmt.15.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY Developments in predictive molecular testing and personalized therapy of lung cancer have recently called for a major change in the histological and cytological activity requiring the pathologist to strictly connect with pulmonologists, oncologists and molecular biologists to improve patient management. Different clinical trials established that tyrosine kinase inhibitor therapy is superior to chemotherapy, when patients harbor EGFR mutations. Similarly, the patients whose lung carcinoma carries ALK fusion genes consistently respond to ALK inhibitors. These improvements have led to the understanding that the morphological diagnosis of lung adenocarcinoma requires a multidisciplinary approach; even more recently the College of American Pathologists, the International Association for the Study of Lung Cancer and the Association for Molecular Pathology encouraged to develop international guidelines for lung cancer biomarker testing. This paper summarizes the practical impact of these guidelines, focusing on the pathologist's role in daily EGFR testing practice.
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Affiliation(s)
- Elena Vigliar
- Dipartimento di Sanità Pubblica, Università di Napoli Federico II, Naples, Italy
| | - Umberto Malapelle
- Dipartimento di Sanità Pubblica, Università di Napoli Federico II, Naples, Italy
| | - Claudio Bellevicine
- Dipartimento di Sanità Pubblica, Università di Napoli Federico II, Naples, Italy
| | - Giancarlo Troncone
- Dipartimento di Sanità Pubblica, Università di Napoli Federico II, Naples, Italy
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26
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Vigliar E, Malapelle U, Bellevicine C, de Luca C, Troncone G. Outsourcing cytological samples to a referral laboratory for EGFR testing in non-small cell lung cancer: does theory meet practice? Cytopathology 2014; 26:312-7. [PMID: 25376259 DOI: 10.1111/cyt.12221] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2014] [Indexed: 01/24/2023]
Abstract
OBJECTIVE Guidelines from the College of American Pathologists (CAP), the International Association for the Study of Lung Cancer (IASLC) and the Association for Molecular Pathology (AMP) consider cytology suitable for testing epidermal growth factor receptor (EGFR) mutations in lung adenocarcinoma. The guidelines recommend that cytopathologists first discuss the possibility of testing squamous cell carcinomas (SqCC) in multidisciplinary meetings. Second, cell blocks should be analysed rather than smear preparations and, third, specimens should be sent to external molecular laboratories within three working days of receiving requests. This study monitored how these recommendations are met in practice. METHODS Our laboratory received 596 requests from cytologists from 13 different institutions. For each case, the cytological diagnosis, cytopreparation type, and time between the request and sample mailing were compared with the recommendations. RESULTS Of the 596 samples, 32 (5.4%) had been reported as SqCC. Three of these (9.4%) showed EGFR mutation. Cytological slides, either ThinPrep(™) (51.2%) or direct smears (43.2%), were more frequently received than cell blocks (5.7%). The mean time between the oncologist's request and specimen dispatching was 5.8 working days. CONCLUSIONS The occurrence of mutations in samples reported as SqCC was higher than expected. This questions the reliability of the original diagnosis, which reinforced the recommendation to evaluate the opportunity for testing non-adenocarcinoma cytology on a case-by-case basis. In spite of CAP/IASLC/AMP recommendations, cell blocks were underutilized for EGFR testing, but cytological slides were suitable for DNA analyses. Significant efforts are needed to avoid delays in outsourcing cytological samples for EGFR testing.
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Affiliation(s)
- E Vigliar
- Pathology Division, Department of Public Health, University of Naples, Naples, Italy
| | - U Malapelle
- Pathology Division, Department of Public Health, University of Naples, Naples, Italy
| | - C Bellevicine
- Pathology Division, Department of Public Health, University of Naples, Naples, Italy
| | - C de Luca
- Pathology Division, Department of Public Health, University of Naples, Naples, Italy
| | - G Troncone
- Pathology Division, Department of Public Health, University of Naples, Naples, Italy
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27
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Bellevicine C, Bianco A, Malapelle U, De Luca C, Vigliar E, Cacciola NA, Pallante P, Troncone G. Performance of EGFR mutant-specific antibodies in different cytological preparations: a validation study. Cytopathology 2014; 26:99-105. [DOI: 10.1111/cyt.12155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2014] [Indexed: 11/30/2022]
Affiliation(s)
- C. Bellevicine
- Dipartimento di Salute Pubblica; Universita Federico II; Naples Italy
| | - A. Bianco
- Dipartimento di Salute Pubblica; Universita Federico II; Naples Italy
| | - U. Malapelle
- Dipartimento di Salute Pubblica; Universita Federico II; Naples Italy
| | - C. De Luca
- Dipartimento di Salute Pubblica; Universita Federico II; Naples Italy
| | - E. Vigliar
- Dipartimento di Salute Pubblica; Universita Federico II; Naples Italy
| | - N. A. Cacciola
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Bioteconologie Mediche; Università degli Studi di Napoli “Federico II”; Naples Italy
| | - P. Pallante
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Bioteconologie Mediche; Università degli Studi di Napoli “Federico II”; Naples Italy
| | - G. Troncone
- Dipartimento di Salute Pubblica; Universita Federico II; Naples Italy
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28
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Bellevicine C, Malapelle U, Vigliar E, de Luca C, Troncone G. Epidermal growth factor receptor test performed on liquid-based cytology lung samples: experience of an academic referral center. Acta Cytol 2014; 58:589-94. [PMID: 25428205 DOI: 10.1159/000369756] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 11/19/2022]
Abstract
OBJECTIVES In this study we reviewed our practice of lung cancer epidermal growth factor receptor (EGFR) mutational testing in an academic centralized laboratory setting, where direct smears and liquid-based cytology (LBC) slides represent the most frequent cytological specimens received. The aim was to assess the differences, if any, between these sample types in terms of DNA yield, adequacy rates and overall EGFR testing performance. STUDY DESIGN A total of 362 cases were retrieved - received from January 2012 to January 2014 for EGFR testing - including 204 LBC specimens and 158 smears. Exon 19 deletions and the L858R point mutation in exon 21, detected by fragment assay and TaqMan assay, respectively, were confirmed by direct sequencing or by high-resolution melting. RESULTS Although the direct smears showed a higher DNA yield (60.94 vs. 23.07 ng/µl) and were more frequently cell-rich (54%) than the LBC slides (31.4%), the differences in adequacy (direct smears: 97.4%; LBCs: 94.1%) and in mutant rate (direct smears: 10.3%; LBCs: 14.0%) between the two sample types did not reach statistical significance. CONCLUSIONS Not only direct smears but also LBC slides represent an effective preparation and storage medium for cytological material to be used for EGFR molecular testing.
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Affiliation(s)
- Claudio Bellevicine
- Pathology Section, Department of Public Health, University of Naples Federico II, Naples, Italy
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29
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Ceresa BP, Peterson JL. Cell and molecular biology of epidermal growth factor receptor. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 313:145-78. [PMID: 25376492 DOI: 10.1016/b978-0-12-800177-6.00005-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The epidermal growth factor receptor (EGFR) has been one of the most intensely studied cell surface receptors due to its well-established roles in developmental biology, tissue homeostasis, and cancer biology. The EGFR has been critical for creating paradigms for numerous aspects of cell biology, such as ligand binding, signal transduction, and membrane trafficking. Despite this history of discovery, there is a continual stream of evidence that only the surface has been scratched. New ways of receptor regulation continue to be identified, each of which is a potential molecular target for manipulating EGFR signaling and the resultant changes in cell and tissue biology. This chapter is an update on EGFR-mediated signaling, and describes some recent developments in the regulation of receptor biology.
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Affiliation(s)
- Brian P Ceresa
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Joanne L Peterson
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
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