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Hawkins P, Stevenson T, Powari M. Use of cytology fluid samples for predictive biomarker testing in lung cancer patients. Cytopathology 2024; 35:242-249. [PMID: 38041234 DOI: 10.1111/cyt.13344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/19/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
OBJECTIVE To provide a method of directly using cytology fluid samples for predictive biomarker testing in lung cancer patients and to determine the efficacy of a variety of fluid sample types. METHOD A review of our in-house data from a range of cytology samples including endobronchial ultrasound (EBUS) fine-needle aspirate (FNA) needle washings (NW) and serous effusions tested on the Biocartis Idylla platform. All fluid samples were originally tested using Sanger sequencing. RESULTS Using our method for fluid samples all of our cytology samples tested for epithelial growth factor receptor (EGFR) yielded valid results on this platform and all variant cases identified. The data showed serous fluids provided the best quality DNA, and variant genotype reports were obtained within 150 minutes. CONCLUSION Cytology fluid samples can be used for predictive biomarker testing for lung cancer patients to provide in-house results with all fluids providing good-quality DNA.
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Affiliation(s)
- Paul Hawkins
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Tracey Stevenson
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Manish Powari
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
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2
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Jones M, Abendano DG, Turner M, Sullivan C, Reyes MCD. The histologic outcomes of indeterminate thyroid nodules with rat sarcoma mutations: A case series. Diagn Cytopathol 2023; 51:E332-E337. [PMID: 37583345 DOI: 10.1002/dc.25214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/17/2023]
Abstract
Molecular testing is an adjunct test for thyroid fine needle aspirations with indeterminate diagnoses, with certain mutations showing a greater risk of malignancy (ROM). Rat sarcoma (RAS) point mutations are the most common alterations in indeterminate thyroid nodules. While they can have a high ROM, they are also found in benign disease. This study describes the histologic outcomes of indeterminate nodules with RAS mutations. Bethesda III and IV thyroid nodules with ThyroSeq results showing RAS mutations (NRAS, KRAS, and HRAS) were identified between November 1, 2018 and February 28, 2023. Baseline patient characteristics, ThyroSeq results, and surgical diagnoses were collected. We identified 18 nodules with RAS mutations from 17 patients. Fourteen were NRAS (isolated NRAS in 6; NRAS with other abnormalities [NRAS+] in 8); one was isolated KRAS; and three were HRAS with other abnormalities (HRAS+). NRAS Q16R was the most common amino acid change. Twelve cases had follow-up. Two were malignant, a minimally invasive follicular carcinoma (NRAS+) and a papillary thyroid carcinoma, follicular variant (HRAS+). Three were noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP), 2 HRAS+ and 1 NRAS+. Four were follicular adenomas, one being atypical (3 NRAS+ and one isolated NRAS). One was an oncocytic adenoma (isolated NRAS). Two were nodular hyperplasias (isolated NRAS and NRAS+, respectively). Twenty-eight percent of our RAS-mutated nodules were malignant or NIFTP. All three HRAS-mutated nodules were malignant or NIFTP. The three isolated RAS mutations with follow up were benign (adenomas or nodular hyperplasia). These findings were in line with the literature.
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Affiliation(s)
- MacKenzie Jones
- Medical University of South Carolina College of Medicine, Charleston, South Carolina, USA
| | - Dorbin G Abendano
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Matthew Turner
- Medical University of South Carolina College of Medicine, Charleston, South Carolina, USA
| | - Christopher Sullivan
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Maria Cecilia D Reyes
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
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Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathol 2023; 131:289-299. [PMID: 36650408 PMCID: PMC10614161 DOI: 10.1002/cncy.22679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Rather than surgical resection, cytologic specimens are often used as first-line clinical diagnostic procedures due to higher safety, speed, and cost-effectiveness. Archival diagnostic cytology slides containing cancer can be equivalent to tissue biopsies for DNA mutation testing, but the accuracy of transcriptomic profiling by RNA sequencing (RNA-seq) is less understood. METHODS This study compares the results from whole transcriptome RNA-seq and a targeted RNA-seq assay of stained cytology smears (CS) versus matched tumor tissue samples preserved fresh-frozen (FF) and processed as formalin-fixed paraffin-embedded (FFPE) sections. Cellular cytology scrapes from all 11 breast cancers were fixed and stained using three common protocols: Carnoy's (CS_C) or 95% ethanol (CS_E) fixation and then Papanicolaou stain or air-dried then methanol fixation and DiffQuik stain (CS_DQ). Agreement between samples was assessed using Lin's concordance correlation coefficient. RESULTS Library yield for CS_DQ was too low, therefore it was not sequenced. The distributions of concordance correlation coefficient of gene expression levels in comparison to FF were comparable between CS_C and CS_E, but expression of genes enriched in stroma was lower in cytosmear samples than in FF or FFPE. Six signatures showed similar concordance to FF for all methods and two were slightly worse in CS_C and CS_E. Genomic signatures were highly concordant using targeted RNA-seq. The allele fraction of selected mutations calculated on cytosmear specimens was highly correlated with FF tissues using both RNA-seq methods. CONCLUSION RNA can be reliably extracted from cytology smears and is suitable for transcriptome profiling or mutation detection, except for signatures of tumor stroma.
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Affiliation(s)
- Michal Marczyk
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Chunxiao Fu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rosanna Lau
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lili Du
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexander J. Trevarton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bruno V. Sinn
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Rebekah E. Gould
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lajos Pusztai
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
| | - Christos Hatzis
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
| | - William Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Fielding DI, Dalley AJ, Singh M, Nandakumar L, Lakis V, Chittoory H, Fairbairn D, Patch AM, Kazakoff SH, Ferguson K, Bashirzadeh F, Bint M, Pahoff C, Son JH, Hodgson A, Sharma S, Waddell N, Lakhani SR, Hartel G, Nones K, Simpson PT. Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples. Cancer Cytopathol 2023. [PMID: 36938641 DOI: 10.1002/cncy.22690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 03/21/2023]
Abstract
BACKGROUND Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels. METHODS A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. All patients had air-dried, Diff-Quik cytology smears and formalin-fixed, paraffin-embedded cell blocks collected for cytopathology and molecular testing. One hundred eighty-five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina). RESULTS Each microscopy parameter had a significant effect on the DNA yield. An algorithm was developed that predicted a >50-ng DNA yield of a smear with an area under the curve of 0.86. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. Low-malignant-cell content (<25%) and smear area (<15%) were the main reasons for failure. All standard-of-care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Tier 1/2 mutations were discovered in two cases where standard-of-care specimens were inadequate for sequencing. Smears were scored for tumor mutation burden. CONCLUSIONS Microscopy of Diff-Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks.
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Affiliation(s)
- David I Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Andrew J Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Mahendra Singh
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Lakshmy Nandakumar
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David Fairbairn
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen H Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kaltin Ferguson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Michael Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Carl Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Queensland, Australia
| | - Jung Hwa Son
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Alan Hodgson
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- ACL Pathology, Bellavista, New South Wales, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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VanderLaan PA, Roy-Chowdhuri S, Griffith CC, Weiss VL, Booth CN. Molecular testing of cytology specimens: overview of assay selection with focus on lung, salivary gland, and thyroid testing. J Am Soc Cytopathol 2022; 11:403-414. [PMID: 36184436 PMCID: PMC10225070 DOI: 10.1016/j.jasc.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022]
Abstract
Ancillary and molecular testing of cytopathology specimens has emerged as a reliable and useful tool to provide diagnostic information and treatment-related biomarker status for the management of cancer patients. The cytology specimens obtained through minimally invasive means have proven suitable testing substrates for a variety of ancillary tests, including immunohistochemistry, fluorescence in situ hybridization, as well as polymerase chain reaction and next generation sequencing molecular techniques. By focusing specifically on the cytology specimen, this review provides an overview of basic testing considerations and assay selection in addition to updates on the ancillary testing of cytologic tumor specimens from the lung, salivary gland, and thyroid.
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Affiliation(s)
- Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Vivian L Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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Koh J, Shin SA, Lee JA, Jeon YK. Lymphoproliferative disorder involving body fluid: diagnostic approaches and roles of ancillary studies. J Pathol Transl Med 2022; 56:173-186. [PMID: 35843627 PMCID: PMC9288893 DOI: 10.4132/jptm.2022.05.16] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Lymphocyte-rich effusions represent benign reactive process or neoplastic condition. Involvement of lymphoproliferative disease in body cavity is not uncommon, and it often causes diagnostic challenge. In this review, we suggest a practical diagnostic approach toward lymphocyte-rich effusions, share representative cases, and discuss the utility of ancillary tests. Cytomorphologic features favoring neoplastic condition include high cellularity, cellular atypia/pleomorphism, monomorphic cell population, and frequent apoptosis, whereas lack of atypia, polymorphic cell population, and predominance of small T cells usually represent benign reactive process. Involvement of non-hematolymphoid malignant cells in body fluid should be ruled out first, followed by categorization of the samples into either small/medium-sized cell dominant or large-sized cell dominant fluid. Small/medium-sized cell dominant effusions require ancillary tests when either cellular atypia or history/clinical suspicion of lymphoproliferative disease is present. Large-sized cell dominant effusions usually suggest neoplastic condition, however, in the settings of initial presentation or low overall cellularity, ancillary studies are helpful for more clarification. Ancillary tests including immunocytochemistry, in situ hybridization, clonality test, and next-generation sequencing can be performed using cytologic preparations. Throughout the diagnostic process, proper review of clinical history, cytomorphologic examination, and application of adequate ancillary tests are key elements for successful diagnosis.
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Affiliation(s)
- Jiwon Koh
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sun Ah Shin
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, National Cancer Center, Goyang, Korea
| | - Ji Ae Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Corresponding Author: Yoon Kyung Jeon, MD, PhD, Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea Tel: +82-2-740-8323, Fax: +82-2-743-5530, E-mail:
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Maddox A, Smart LM. Technical aspects of the use of cytopathological specimens for diagnosis and predictive testing in malignant epithelial neoplasms of the lung. Cytopathology 2021; 33:23-38. [PMID: 34717021 DOI: 10.1111/cyt.13072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022]
Abstract
Lung cancer is a leading cause of cancer mortality worldwide but recent years have seen a rapidly rising proportion of cases of advanced non-small cell carcinoma amenable to increasingly targeted therapy, initially based on the differential response to systemic treatment of tumours of squamous or glandular differentiation. In two-thirds of the cases, where patients present with advanced disease, both primary pathological diagnosis and biomarker testing is based on small biopsies and cytopathological specimens. The framework of this article is an overview of the technical aspect of each stage of the specimen pathway with emphasis on maximising potential for success when using small cytology samples. It brings together the current literature addressing pre-analytical and analytical aspects of specimen acquisition, performing rapid onsite evaluation, and undertaking diagnostic and predictive testing using immunocytochemistry and molecular platforms. The advantages and drawbacks of performing analysis on cell block and non-cell block specimen preparations is discussed.
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Affiliation(s)
- Anthony Maddox
- Department of Cellular Pathology, West Hertfordshire Hospitals NHS Trust, Hemel Hempstead Hospital, Hemel Hempstead, UK
| | - Louise M Smart
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, UK
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Hawkins P, Stevenson T, Powari M. Use of the Idylla EGFR Mutation Test for Variant Detection in Non-Small Cell Lung Cancer Samples. Am J Clin Pathol 2021; 156:653-660. [PMID: 33877290 DOI: 10.1093/ajcp/aqab003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Stratified management of patients with non-small cell lung carcinoma (NSCLC) through epithelial growth factor receptor (EGFR) variant analysis has become standard clinical practice. The Idylla system is a fully compliant European in vitro diagnostics device, a fully automated platform designed to rapidly genotype formalin-fixed paraffin-embedded tissue samples. This retrospective study aims to validate the Idylla EGFR Mutation Test for use with extracted DNA from known NSCLC samples. METHODS In this study, 20 µL of archival extracted DNA was placed directly inside the Idylla EGFR assay single-use cartridge. Idylla results were compared with the original Sanger sequencing reference method. RESULTS The Idylla EGFR Mutation Test yielded valid results for all samples tested, confirming the variants identified by the reference method that lay within the Idylla target range. No false-positive cases were noted with the Idylla assay. Variant genotype reports were obtained within 150 minutes. CONCLUSIONS The Idylla EGFR assay is sensitive for extracted DNA and can be reliably applied to cytologic specimens, enabling its implementation as an ancillary first-line test for patients with NSCLC.
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Affiliation(s)
- Paul Hawkins
- Department of Cellular Pathology, Royal Devon and Exeter NHS Foundation Trust, DevonUK
| | - Tracey Stevenson
- Department of Cellular Pathology, Royal Devon and Exeter NHS Foundation Trust, DevonUK
| | - Manish Powari
- Department of Cellular Pathology, Royal Devon and Exeter NHS Foundation Trust, DevonUK
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Testing EGFR with Idylla on Cytological Specimens of Lung Cancer: A Review. Int J Mol Sci 2021; 22:ijms22094852. [PMID: 34063720 PMCID: PMC8125729 DOI: 10.3390/ijms22094852] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
The current standard of care for advanced non-small-cell lung cancer is based on detecting actionable mutations that can benefit from targeted therapy. Comprehensive genetic tests can have long turn-around times, and because EGFR mutations are the most prevalent actionable mutation, a quick detection would enable a prompt initiation of targeted therapy. Furthermore, the scarcity of diagnostic material means that sometimes only cytologic material is available. The Idylla™ EGFR assay is a real-time PCR–based method able to detect 51 EGFR mutations in 2.5 h. Idylla is validated for use only on FFPE sections, but some researchers described their experiences with cytological material. We reviewed the relevant literature, finding four articles describing 471 cases and many types of cytological input material: smears, cell-block sections, suspensions, and extracted DNA. The sensitivity, specificity, and limit of detection appear comparable to those obtained with histological input material, with one exception: the usage of scraped stained smears as input may reduce the accuracy of the test. In conclusion, usage of cytological material as input to the Idylla EGFR test is possible. A workflow where common mutations are tested first and fast, leaving rarer mutations for subsequent comprehensive profiling, seems the most effective approach.
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Canberk S, Engels M. Cytology samples and molecular biomarker testing in lung cancer-advantages and challenges. Virchows Arch 2021; 478:45-57. [PMID: 33389149 DOI: 10.1007/s00428-020-02995-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
This review presents an overview on molecular diagnostic in lung cancer using cytologic samples. Every patient with advanced non-small cell lung cancer (NSCLC) should be tested for targetable driver mutations and gene arrangements. If a mutation is found, this may open an option for targeted therapy. As most of the NSCLC patients in advanced stage of disease are no candidates for surgery, these tests have to be performed on small biopsies or cytology samples. The most common and treatable gene alterations should be tested in every patient: EGFR, ALK, ROS1. A growing number of other genetic changes with targetable mutations may become treatable in the near future. To find patients who might profit from inclusion into clinical studies, relevant additional markers may be tested in an appropriate context. Another important approach for treatment is immunotherapy of lung cancer, which is guided by status of PD-L1 expression on tumour cells. The use of cytology samples carries considerable advantages: often, DNA of high quality is extracted thus enabling easy and precise analysis, and samples may be easily obtained. In case of effusions, effusion fluid seldom is not aspirated for immediate patient relief, so no additional dedicated procedure is needed. Some challenges exist: If the tumour cell count is low, mutations with a low allelic frequency may be missed. In cellblocks formalin-induced DNA, damage may obviate any DNA analysis. In very cellular smears, FISH may be impossible due to massive overlapping of nuclei. Autofluorescence may impede FISH analysis. Although there is no real universal test for genomic profiling for lung cancer, the pathology laboratory must be prepared to offer different assays on different specimens in order to address turnaround time and optimise detections of difficult tumour alterations such as gene fusions. The data from the literature demonstrate that cytology show consistent results, and it is a good alternative for lung cancer molecular testing.
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Affiliation(s)
- Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen, 208 4200-135, Porto, Portugal. .,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal.
| | - Marianne Engels
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62,, 50924, Köln, Germany
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Jia J, Guo H, Zhao H, Zhao L, Ling Y, Chen L, Zhang Z. Oncogenic gene transcripts detection by FISH on liquid-based cytology slides of 338 advanced lung cancer patients. J Am Soc Cytopathol 2020; 10:270-277. [PMID: 33423957 DOI: 10.1016/j.jasc.2020.12.002] [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: 11/09/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Oncogenic gene transcripts in advanced lung cancer are a strong indication for targeted therapy. Cytology specimens are often the only materials available for oncogenic fusion analysis. This prospective study is to evaluate the feasibility of anaplastic lymphoma kinase (ALK) gene rearrangements, ROS oncogene 1 (ROS-1), and c-mesenchymal-epidermal transformation (c-MET) detected by fluorescence in situ hybridization (FISH) using liquid-based cytology (LBC) slides. MATERIALS AND METHODS Consecutive cytology specimens including fine-needle aspiration biopsy (FNAB) and serous effusions from 338 advanced lung cancer patients were collected between March 1, 2015, and July 6, 2016. The correlation between ALK, ROS-1, c-MET, and other common driver gene abnormalities and the therapeutic response to crizotinib in ALK-positive patients were also evaluated. RESULTS ALK fusion transcripts were detected in 31 of 338 patients (9.17%). Twenty-two of the 31 ALK-positive patients were treated with crizotinib at our institution (2 were lost to follow-up), and the overall response rate was 75.0 % (15 of 20); disease control rate was 90.0% (18 of 20). FISH analyses for ROS-1 and c-MET were performed on 75 and 73 patients, respectively, and showed 3 patients positive for ROS-1 and 3 positive for c-MET. These positive cases were all ALK-negative. CONCLUSION For patients with advanced lung cancer, LBC slides are suitable for detecting oncogenic gene transcripts, and the results can provide a reliable guideline for targeted therapy.
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Affiliation(s)
- Jia Jia
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - HuiQin Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huan Zhao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - LinLin Zhao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yun Ling
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Longwen Chen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, Arizona.
| | - ZhiHui Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Murphy SJ, Harris FR, Smadbeck JB, Serla V, Karagouga G, Johnson SH, Kosari F, Pierson KE, Bungum AO, Edell ES, Mansfield AS, Wigle DA, Kipp BR, Vasmatzis G, Aubry MC. Optimizing clinical cytology touch preparations for next generation sequencing. Genomics 2020; 112:5313-5323. [PMID: 33144219 DOI: 10.1016/j.ygeno.2020.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 12/26/2022]
Abstract
Intraoperative diagnosis is routinely performed on cytology touch preparations (TPs) from core needle biopsies (CNBs). Current interest promotes their utility as an important source of patient tissue for clinical genomic testing. Herein we present whole genome structural variant analysis (SVA) from mate-pair sequencing (MPseq) and whole exome sequencing (WES) mutation calling in DNA directly whole genome amplified (WGA) from TPs. Chromosomal copy changes and somatic DNA junction detection from MPseq of TPs were highly consistent with associated CNBs and bulk resected tissues in all cases. While increased frequency coverage noise from limitations of amplification of limited sample input was significant, this was effectively compensated by natural tumor enrichment during the TP process, which also enhanced variant detection and loss of heterozygosity evaluations from WES. This novel TP methodology enables expanded utility of frequently limited CNB for both clinical and research genomic testing.
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Affiliation(s)
- Stephen J Murphy
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Faye R Harris
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - James B Smadbeck
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Vishnu Serla
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States; Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Giannoula Karagouga
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Sarah H Johnson
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Farhad Kosari
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Karlyn E Pierson
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Aaron O Bungum
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric S Edell
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Dennis A Wigle
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Benjamin R Kipp
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - George Vasmatzis
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Marie Christine Aubry
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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Arcila ME, Yang SR, Momeni A, Mata DA, Salazar P, Chan R, Elezovic D, Benayed R, Zehir A, Buonocore DJ, Rekhtman N, Lin O, Ladanyi M, Nafa K. Ultrarapid EGFR Mutation Screening Followed by Comprehensive Next-Generation Sequencing: A Feasible, Informative Approach for Lung Carcinoma Cytology Specimens With a High Success Rate. JTO Clin Res Rep 2020; 1:100077. [PMID: 33511359 PMCID: PMC7839984 DOI: 10.1016/j.jtocrr.2020.100077] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION For patients with advanced NSCLC, cytologic samples may be the only diagnostic specimen available for molecular profiling. Although both rapid and comprehensive assessment are essential in this setting, an integrated multitest approach remains an important strategy in many laboratories, despite the risks and challenges when working with scant samples. In this study, we describe our experience and high success rate in using a multitest approach, focusing on the clinical validation and incorporation of ultrarapid EGFR testing using the Idylla system followed by comprehensive next-generation sequencing (NGS). METHODS Cytology samples received for routine molecular testing were included in this study. The performance characteristics of the EGFR Idylla assay were assessed; tissue suitability parameters and interpretation criteria to supplement automated mutation calling were established. The assay performance was monitored for 1 year, comparing the results with those of concurrent NGS testing by MSK-IMPACT (primarily) or MSK-AmpliSeq and MSK-Fusion solid panel in a subset of cases. RESULTS Overall, 301 samples were studied; 83 samples were included in validation (60.2% [50 of 83] were positive for EGFR mutations). Concordance with the reference method was 96.4% (80 of 83) of the samples with excellent reproducibility. The limit of detection was variable depending on the total tissue input and the specific mutation tested. Unextracted tissue inputs that maintained total EGFR cycle of quantification at less than 23 allowed all mutations to be detected if present at greater than 5% variant allele frequency. Mutations could be detected at 1% variant allele frequency with total EGFR cycle of quantification of 18. During the clinical implementation phase, 218 NSCLC samples were tested by Idylla (24.3% [53 of 218] were EGFR mutation positive). Concurrent NGS testing was requested on 165 samples and successfully performed on 96.4% (159 of 165) of the samples. The Idylla automated results were concordant with those obtained by NGS in 96.2% (153 of 159) of cases and improved to 98.7% (157 of 159) after incorporation of manual review criteria to supplement automated calling, resulting in a diagnostic sensitivity of 95.6% (95% confidence interval: 84.9%-99.5%). In general, 9% (14 of 159) of the cases tested by NGS had EGFR mutations not covered by the Idylla assay, primarily insertions in exon 19 and 20 and minor mutations cooccurring with canonical sensitizing mutations. CONCLUSIONS Comprehensive molecular testing is feasible and has a high success rate in NSCLC cytology samples when using a multitest approach. Testing with the Idylla system enables rapid and accurate determination of the EGFR status without compromising subsequent NGS testing.
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Affiliation(s)
- Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amir Momeni
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A. Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger Chan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Elezovic
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Darren J. Buonocore
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Oscar Lin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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14
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Dong Z, Cao Z, Wu W, Zhang L, Hou L, Zhang W, Wu C. Evaluation of liquid based cytology in detection of EGFR mutation in NSCLC by large samples. J Thorac Dis 2020; 12:4941-4949. [PMID: 33145068 PMCID: PMC7578468 DOI: 10.21037/jtd-20-2750] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Cytology samples are the main resources to detect driver oncogene alterations for advanced lung cancer patients. To explore the value of liquid-based cytology in the detection of epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancer (NSCLC), we analyzed data from a large cohort of EGFR mutation-positive patients. Methods We analyzed the clinicopathological characteristics of 8,029 NSCLC cases tested for EGFR mutation by liquid-based cytology specimens and 1,934 NSCLC cases tested by formalin-fixed and paraffine-embedded (FFPE) samples in the Shanghai Pulmonary Hospital from September 2015 to December 2019. Before detection, we evaluated the number of tumor cells in the liquid-based cytology slide, and samples with more than 50 tumor cells and visible sediment were selected for DNA extraction after centrifugation. Results The positive rate of EGFR mutation in liquid-based cytology-tested cases was 47.18%, higher than the 41.37% tested through FFPE sample (P<0.01). Accordingly, the mutation rate of EGFR in adenocarcinoma (AC) and NSCLC was higher than that of the FFPE sample (60.01% vs. 54.15%, P<0.01; 30.54% vs. 21.99%, P<0.01). The positive rate of EGFR mutation in pleural effusion was 62.67%, which was the highest rate among liquid-based cytology sample t (P<0.01). Conclusions Using quality control and standard procedure, it was found that liquid-based cytology specimen testing is a convenient and reliable method of EGFR detection, as validated by analysis of a large cohort. EGFR mutation detection should also be carried out in NSCLC patients diagnosed by cytology more than in AC patients.
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Affiliation(s)
- Zhengwei Dong
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ziyang Cao
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liping Zhang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Zhang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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Satturwar S, Rekhtman N, Lin O, Pantanowitz L. An update on touch preparations of small biopsies. J Am Soc Cytopathol 2020; 9:322-331. [PMID: 32417160 DOI: 10.1016/j.jasc.2020.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/10/2020] [Accepted: 04/11/2020] [Indexed: 02/08/2023]
Abstract
Touch preparations (TPs) are being increasingly utilized in the era of personalized medicine. They fill a gap in cytopathology practice by providing a method to perform rapid onsite evaluation of small tissue samples such as core needle biopsies. However, there is a paucity of literature about how best to perform and interpret a TP. A high-quality TP can provide excellent diagnostic accuracy and good concordance with core needle biopsy histopathology findings. Although many of the cytomorphologic features of TPs overlap with fine needle aspirate smears, TP cytology is unique and differs from conventional smears in many aspects. It is important for cytologists to recognize these features, as well as potential pitfalls and artifacts in order to avoid misinterpretation. Core depletion of tumor cells is a notable drawback if TPs are performed too aggressively. TP slides are also valuable for ancillary testing because they often contain a cellular and pure population of whole tumor cells. This paper reviews all of the aspects of TPs including their clinical utility, proper slide preparation techniques, distinctive cytomorphologic characteristics, limitations, and potential pitfalls.
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Affiliation(s)
- Swati Satturwar
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Oscar Lin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liron Pantanowitz
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
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16
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Seneldir H, Kir G, Soylemez T, Girgin RB, Ozbay N, Ozen F, Ankarali H, Bas G, Alimoglu O. Diagnostic accuracy of molecular testing with three molecular markers on thyroid fine-needle aspiration cytology with abnormal category. Diagn Cytopathol 2020; 48:507-515. [PMID: 32031330 DOI: 10.1002/dc.24394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/12/2020] [Accepted: 01/30/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Cases with abnormal category, determined by thyroid fine-needle aspiration (FNA), frequently undergo surgical resection, despite the majority of cases being identified as benign after resection. Additional diagnostic markers are needed to guide the management of patients with abnormal thyroid nodules. MATERIALS AND METHODS The retrospective study enrolled 150 cases diagnosed abnormal by FNA cytology that had undergone molecular testing with three markers (BRAF V600E, NRAS, and KRAS) on the cell block. Seventy-one cases had a surgical follow-up. RESULTS When NIFTP is not considered as malignant, positive predictive values (PPVs) of cytology and combined cytology and molecular testing (CC-MT) were 67.6% (95% CI: 0.555-0.782) and 89.2% (95% CI: 0.746-0.970) (P = .004), respectively. The sensitivity of the CC-MT was 68.8%, specificity was 82.5%, and the false-positive rate was 17.4%. When NIFTP is considered as malignant, PPVs of cytology and CC-MT were 83.1% (95% CI: 0.743-0.918) and 94.6% (95% CI: 0.873-1.018) (P = .047), respectively. The sensitivity of the CC-MT was 59.3%, specificity was 83.3%, and the false-positive rate was 16.7%. CONCLUSION The addition of molecular testing with a small panel to FNA cytology may increase the PPV of cytology in abnormal categories. Small panel (BRAF V600E, KRAS, and NRAS) with high specificity and high PPVs may be used particularly for the detection of thyroid malignancy. Cell blocks can be an especially useful and straightforward method for molecular diagnostic studies.
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Affiliation(s)
- Hatice Seneldir
- Department of Pathology, Goztepe Research and Training Hospital, Istanbul Medeniyet University, Istanbul, Turkey
| | - Gozde Kir
- Department of Pathology, Goztepe Research and Training Hospital, Istanbul Medeniyet University, Istanbul, Turkey
| | - Tuce Soylemez
- Department of Pathology, Goztepe Research and Training Hospital, Istanbul Medeniyet University, Istanbul, Turkey
| | - Rabia B Girgin
- Department of Pathology, Goztepe Research and Training Hospital, Istanbul Medeniyet University, Istanbul, Turkey
| | - Nurver Ozbay
- Department of Pathology, Goztepe Research and Training Hospital, Istanbul Medeniyet University, Istanbul, Turkey
| | - Filiz Ozen
- Department of Medical Genetics, Istanbul Medeniyet University, Istanbul, Turkey
| | - Handan Ankarali
- Department of Biostatistics and Medical Informatics, Istanbul Medeniyet University, Istanbul, Turkey
| | - Gurhan Bas
- Department of General Surgery, Goztepe Research and Training Hospital, Istanbul Medeniyet University, Istanbul, Turkey
| | - Orhan Alimoglu
- Department of General Surgery, Goztepe Research and Training Hospital, Istanbul Medeniyet University, Istanbul, Turkey
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Usefulness of rapid on-site evaluation specimens from endoscopic ultrasound-guided fine-needle aspiration for cancer gene panel testing: A retrospective study. PLoS One 2020; 15:e0228565. [PMID: 31999789 PMCID: PMC6991993 DOI: 10.1371/journal.pone.0228565] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/19/2020] [Indexed: 12/27/2022] Open
Abstract
Pancreatic cancer (PC) is a highly lethal malignancy, with a 5-year survival rate of 6%. Cancer gene panel testing is expected to allow selection of suitable therapeutic drugs in individual patients with PC and improve their prognosis. Although somatic mutations can be identified in formalin-fixed, paraffin-embedded samples derived from surgical specimen, the rate of surgical indication among patients with PC is only 20%. To acquire genome information with a less invasive method, we used rapid on-site evaluation (ROSE) specimens from endoscopic ultrasound-guided fine-needle aspiration. The present study aimed to retrospectively evaluate the utility of comprehensive cancer gene panel testing with ROSE specimens. DNA was extracted from preserved ROSE specimens of 26 patients diagnosed with PC between 2011 and 2017. DNA sequences of oncogenes and cancer-related genes were determined using the Ion AmpliSeq Comprehensive Caner Panel. We compared KRAS mutations between cancer gene panel testing by next-generation sequencing (NGS) and KRAS mutation analysis by polymerase chain reaction. The mean yield of DNA per extraction from ROSE specimens was 171 ng (range, 34-478 ng). On cancer gene panel testing, we noted KRAS mutations (92%), TP53 mutations (50%), CDKN2A mutations (15%), and SMAD4 mutations (31%). The concordance rate of KRAS mutations between cancer gene panel testing by NGS using ROSE specimens and KRAS mutation analysis by the companion diagnostics using residual materials was 81%. Among five cases of KRAS discordance, three showed KRAS mutations in cancer gene panel testing but not in KRAS mutation analysis. Cancer gene panel testing with ROSE specimens can help stratify unresectable PC patients without additional invasive approaches, and it can be used for therapeutic drug selection.
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Roy-Chowdhuri S, Pisapia P, Salto-Tellez M, Savic S, Nacchio M, de Biase D, Tallini G, Troncone G, Schmitt F. Invited review-next-generation sequencing: a modern tool in cytopathology. Virchows Arch 2019; 475:3-11. [PMID: 30877381 DOI: 10.1007/s00428-019-02559-z] [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: 02/20/2019] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 02/05/2023]
Abstract
In recent years, cytopathology has established itself as an independent diagnostic modality to guide clinical management in many different settings. The application of molecular techniques to cytological samples to identify prognostic and predictive biomarkers has played a crucial role in achieving this goal. While earlier studies have demonstrated that single biomarker testing is feasible on cytological samples, currently, this provides only limited and increasingly insufficient information in an era where an increasing number of biomarkers are required to guide patient care. More recently, multigene mutational assays, such as next-generation sequencing (NGS), have gained popularity because of their ability to provide genomic information on multiple genes. The cytopathologist plays a key role in ensuring success of NGS in cytological samples by influencing the pre-analytical steps, optimizing preparation types and adequacy requirement in terms of cellularity and tumor fraction, and ensuring optimal nucleic acid extraction for DNA input requirements. General principles of the role and potential of NGS in molecular cytopathology in the universal healthcare (UHC) European environment and examples of principal clinical applications were discussed in the workshop that took place at the 30th European Congress of Pathology in Bilbao, European Society of Pathology, whose content is here comprehensively described.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Anatomic Pathology, University of Bologna Medical Center, Bologna, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
| | - Fernando Schmitt
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Department of Pathology, Medical Faculty of Porto University, Porto, Portugal
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Khoueiry P, Fakhri G, Akel R, El Assaad M, Mahfouz R, Khuri F, Chami H, Petersen J, Viet S, Davies G, Kadara H, Tfayli A. Deep targeted sequencing analysis of hot spot mutations in non-small cell lung cancer patients from the Middle Eastern population. J Thorac Dis 2019; 11:2383-2391. [PMID: 31372275 DOI: 10.21037/jtd.2019.05.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background The overall 5-year survival of lung cancer remains dismal despite the current treatment regimens. Testing for driver mutations has become routine practice for oncologists due to the presence of targeted therapy readily available for patients. Deep targeted sequencing through next generation sequencing (NGS) is an adequate methodology to detect mutations at multi-genetic levels. The molecular pathology of non-small cell lung cancer (NSCLC) is poorly understood in the Middle East and, to date, no other reports have been published on deep targeted sequencing of lung adenocarcinoma (LUAD) tissues. Methods Deep targeted sequencing using TruSeq Amplicon Cancer panel of 48 genes was performed on 85 formalin-fixed paraffin-embedded tissues from patients with LUAD who were treatment-naive at the time of the collection. Variants with an allele frequency higher than 10% were retained. Results Variant calling identified a total of 2,455 variants of which missense mutations were the most frequent (75.6%). All of our samples showed at least one mutation in one of the 10 most commonly mutated genes with FLT3 being the gene with the highest mutation rate (67%). TP53, KRAS and STK11 were the second, third and fourth most commonly mutated genes, respectively while EGFR mutation rate reached 22.4%. Conclusions To the best of our knowledge, this is the first hot spot profiling study on patients from this area. The frequencies of mutated genes presented in our study showed similarity to other reported outcomes. At least one mutation was detected in our cohort of LUAD.
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Affiliation(s)
- Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Ghina Fakhri
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Reem Akel
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Majd El Assaad
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Fadlo Khuri
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hassan Chami
- Division of Pulmonary and Critical Care, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Jason Petersen
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Sarah Viet
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Gareth Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Humam Kadara
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Arafat Tfayli
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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Yu GH, Glaser LJ, Gustafson KS. Role of Ancillary Techniques in Fluid Cytology. Acta Cytol 2019; 64:52-62. [PMID: 31018204 DOI: 10.1159/000496568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/02/2019] [Indexed: 01/11/2023]
Abstract
The cytologic evaluation of serous effusions may be challenging for a number of reasons. Distinction of benign, reactive conditions from malignancy represents the main focus when examining these specimens. The morphologic diagnosis of malignancy may be difficult due to the relative paucity of abnormal cells. In other situations, cellularity is not an issue, but the ability to confidently identify a second, foreign (i.e., tumor) population within a background mesothelial cells on the basis of cytomorphologic features alone may pose problems. Cases with definitive morphologic evidence of malignancy may require additional studies in order to determine the tumor subtype and, in the case of carcinoma, the primary site of origin. Cases in which a definitive and precise diagnosis of malignancy is made may be optimal candidates for further molecular testing in order to gain prognostic information and guide personal therapeutic decisions. Finally, while an inflammatory or infectious condition can be suggested on the basis of cellular components and associated background elements, the identification of causative agent(s) may be difficult without additional studies. In all of these situations, the use of ancillary studies and techniques is critical; their utility and appropriate application are the subject of this review.
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Affiliation(s)
- Gordon H Yu
- Hospital of the University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,
| | - Laurel J Glaser
- Hospital of the University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Karen S Gustafson
- Hospital of the University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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21
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Sussman R, Rosenbaum JN. Development and Validation of Molecular Assays for Limited Tissue Samples. Acta Cytol 2019; 64:147-154. [PMID: 30995656 DOI: 10.1159/000499109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/23/2019] [Indexed: 12/11/2022]
Abstract
As the value of molecular testing of cancer specimens increases, the number of tests imposed on tumor specimens also increases, often in tension with the amount of tumor material available. To develop and validate molecular assays for limited specimens, there are specific concerns that must be addressed, including DNA quality, quantity, and abundance; the number of targets/ability to multiplex; and the analytical sensitivity and specificity of the assay itself. Ultimately, weighing these considerations during assay validation in the overall context of clinical utility and laboratory workflow is critical for delivering the highest level of personalized care to patients.
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Affiliation(s)
- Robyn Sussman
- Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason N Rosenbaum
- Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,
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22
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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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23
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Engels M, Michael C, Dobra K, Hjerpe A, Fassina A, Firat P. Management of cytological material, pre-analytical procedures and bio-banking in effusion cytopathology. Cytopathology 2019; 30:31-38. [PMID: 30430668 DOI: 10.1111/cyt.12654] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/27/2018] [Accepted: 10/31/2018] [Indexed: 12/18/2022]
Abstract
Serous effusion fluid is one of the most commonly encountered specimens in routine cytopathology practice. It provides invaluable information about the patient and the clinical status; but to get the most of it, specimen handling and processing must be carried out properly. Cytomorphology is the basis of a successful analysis which should complemented by ancillary tests when needed. A wide spectrum of ancillary techniques - ranging from immunocytochemistry and flow cytometry to different assays of molecular pathology - can be applied to serous effusions. This article describes the acquisition and management of serous effusion fluids, methods for preservation and transportation, different techniques of cytopreparation, application of immunocytochemistry, flow cytometry, and fluorescence in-situ hybridization (FISH), as well as DNA extraction for polymerase chain reaction (PCR) and next generation sequencing (NGS). Principles of bio-banking of effusion samples are also discussed which is getting more important in correlation with the developments in personalized medicine.
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Affiliation(s)
- Marianne Engels
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Claire Michael
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Health Center, Cleveland, Ohio
| | - Katalin Dobra
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anders Hjerpe
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ambrogio Fassina
- Department of Medicine, Surgical Pathology & Cytopathology Unit, University of Padova, Padova, Italy
| | - Pinar Firat
- Department of Pathology, Koc University School of Medicine, Istanbul, Turkey
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Kang A, Miranda A, de Boer B. Manufactured Cell Blocks: Turning Smears into Sections. Acta Cytol 2019; 63:28-34. [PMID: 30612123 DOI: 10.1159/000493907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/19/2018] [Indexed: 11/19/2022]
Abstract
Whilst cytological smears are still the basis of cytodiagnosis, there is an increasing role for ancillary testing. Specimens obtained are not always optimal, often with limited material for ancillary studies. Several reports have described the utility of scraping material from cytological smears to manufacture cell blocks to provide material for ancillary studies. Our objective was a retrospective review of the PathWest (QE2) experience with manufactured cell blocks (mCB) over the last 10 years. A total of 178 fine-needle aspiration cases with mCB were extracted from the PathWest database. Data were subdivided into: lymph node (89), breast (31), thyroid (23), soft tissue (13), liver (11), and other sites (11) and were analysed. All available material was reviewed. Diagnostic material was identified in 163 mCB (91.6%). Immunohistochemistry (IHC) was performed on 149 cases. Positive IHC staining was seen in 139 cases (93.3%) and advanced the diagnosis in 119 cases (79.9%). Molecular studies were performed on 38 mCB with adequate DNA obtained in 37 cases (97.3%). Our review has demonstrated that cellular material scraped from air-dried or prefixed smears can be made into cell blocks. Antigen preservation is adequate to provide diagnostically useful results with IHC whilst DNA integrity is preserved to allow molecular analysis.
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Affiliation(s)
- Alexandra Kang
- PathWest Laboratory Medicine, QE2 Medical Centre, Nedlands, Washington, Australia
| | - Alina Miranda
- PathWest Laboratory Medicine, QE2 Medical Centre, Nedlands, Washington, Australia
- School of Biomedical Sciences, Curtin University, Bentley, Washington, Australia
| | - Bastiaan de Boer
- PathWest Laboratory Medicine, QE2 Medical Centre, Nedlands, Washington, Australia,
- School of Pathology and Laboratory Medicine, UWA, Nedlands, Washington, Australia,
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Young K, da Cunha Santos G, Card P, Leighl N. The role of cytology in molecular testing and personalized medicine in lung cancer: A clinical perspective. Cancer Cytopathol 2018; 127:72-78. [DOI: 10.1002/cncy.22085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/21/2018] [Accepted: 11/01/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Kelvin Young
- Department of Hematology/Oncology St. Michael’s Hospital Toronto Ontario Canada
| | - Gilda da Cunha Santos
- Division of Medical Oncology, Princess Margaret Cancer Center University of Toronto Toronto Ontario Canada
| | - Paul Card
- Kaleidoscope Strategic, Inc Toronto Ontario Canada
| | - Natasha Leighl
- Division of Medical Oncology, Princess Margaret Cancer Center University of Toronto Toronto Ontario Canada
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26
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Balla A, Hampel KJ, Sharma MK, Cottrell CE, Sidiropoulos N. Comprehensive Validation of Cytology Specimens for Next-Generation Sequencing and Clinical Practice Experience. J Mol Diagn 2018; 20:812-821. [DOI: 10.1016/j.jmoldx.2018.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/21/2018] [Indexed: 12/29/2022] Open
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27
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Nambirajan A, Jain D. Cell blocks in cytopathology: An update. Cytopathology 2018; 29:505-524. [DOI: 10.1111/cyt.12627] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Aruna Nambirajan
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
| | - Deepali Jain
- Department of Pathology; All India Institute of Medical Sciences; New Delhi India
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28
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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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Roy-Chowdhuri S, Mehrotra M, Bolivar AM, Kanagal-Shamanna R, Barkoh BA, Hannigan B, Zalles S, Ye W, Duose D, Broaddus R, Staerkel G, Wistuba I, Medeiros LJ, Luthra R. Salvaging the supernatant: next generation cytopathology for solid tumor mutation profiling. Mod Pathol 2018; 31:1036-1045. [PMID: 29463880 DOI: 10.1038/s41379-018-0006-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/27/2017] [Accepted: 12/03/2017] [Indexed: 12/25/2022]
Abstract
With the expanding role of targeted therapy in patients with solid tumors, pathologists face the daunting task of having to maximize limited volume tissue obtained by fine needle aspiration for a variety of molecular tests. While most molecular studies on fine needle aspiration samples have been reported using cellular material, recent studies have shown that a substantial amount of DNA can be retrieved from the supernatant fluid of aspirate needle rinses after cell pelleting for cytospin or cell block preparations. In routine clinical workflow, the supernatant is discarded; however this fluid may provide a complementary source of DNA for tumor mutational profiling. In this study, we evaluated the post-centrifuged supernatant from 25 malignant and 10 benign fine needle aspiration needle rinses. The mean and median DNA yields from the supernatants were 445 ng and 176.4 ng (range, 15.1-2958 ng), respectively. Next generation sequencing using the Ion AmpliSeq Cancer Hotspot Panel v2 detected somatic mutations in all 25 malignant samples. No mutations were detected in any of the benign samples tested. When available, mutations detected in the supernatant fluid were compared to the next generation sequencing analysis performed on a prior or concurrent surgical specimen from the same patient and showed 100% concordance. In a subset of cases (n = 19) mutations in EGFR, KRAS, BRAF, PIK3CA, and NRAS were successfully confirmed by droplet digital PCR, providing an orthogonal platform for mutation analysis. In summary, in this study we show that post centrifuged supernatants from fine needle aspiration needle rinses can provide a robust substrate for expanded mutation profiling by next generation sequencing, as well as hotspot mutation testing by droplet digital PCR. The ability to detect somatic mutations from otherwise discarded supernatant fluids offers the ability to triage and effectively utilize limited volume fine needle aspiration samples when multiple molecular tests are requested, without the need to re-biopsy for additional tissue samples.
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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, TX, USA.
| | - Meenakshi Mehrotra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Maria Bolivar
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bedia A Barkoh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brette Hannigan
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie Zalles
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenrui Ye
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dzifa Duose
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell Broaddus
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gregg Staerkel
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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30
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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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31
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Kiura K, Yoh K, Katakami N, Nogami N, Kasahara K, Takahashi T, Okamoto I, Cantarini M, Hodge R, Uchida H. Osimertinib in patients with epidermal growth factor receptor T790M advanced non-small cell lung cancer selected using cytology samples. Cancer Sci 2018; 109:1177-1184. [PMID: 29363250 PMCID: PMC5891183 DOI: 10.1111/cas.13511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/11/2018] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
Osimertinib is a potent, irreversible epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) selective for EGFR‑TKI sensitizing (EGFRm) and T790M resistance mutations. The primary objective of the cytology cohort in the AURA study was to investigate safety and efficacy of osimertinib in pretreated Japanese patients with EGFR T790M mutation‐positive non‐small cell lung cancer (NSCLC), with screening EGFR T790M mutation status determined from cytology samples. The cytology cohort was included in the Phase I dose expansion component of the AURA study. Patients were enrolled based on a positive result of T790M by using cytology samples, and received osimertinib 80 mg in tablet form once daily until disease progression or until clinical benefit was no longer observed at the discretion of the investigator. Primary endpoint for efficacy was objective response rate (ORR) by investigator assessment. Twenty‐eight Japanese patients were enrolled into the cytology cohort. At data cut‐off (February 1, 2016), 12 (43%) were on treatment. Investigator‐assessed ORR was 75% (95% confidence interval [CI] 55, 89) and median duration of response was 9.7 months (95% CI 3.8, not calculable [NC]). Median progression‐free survival was 8.3 months (95% CI 4.2, NC) and disease control rate was 96% (95% CI 82, 100). The most common all‐causality adverse events were paronychia (46%), dry skin (46%), diarrhea (36%) and rash (36%). Osimertinib provided clinical benefit with a manageable safety profile in patients with pretreated EGFR T790M mutation‐positive NSCLC whose screening EGFR T790M mutation‐positive status was determined from cytology samples. (ClinicalTrials.gov number NCT01802632).
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Affiliation(s)
- Katsuyuki Kiura
- Department of Allergy and Respiratory Medicine, Okayama University Hospital, Okayama, Japan
| | - Kiyotaka Yoh
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Nobuyuki Katakami
- Division of Integrated Oncology, Institute of Biomedical Research and Innovation, Kobe, Japan
| | | | - Kazuo Kasahara
- Department of Respiratory Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | | | - Isamu Okamoto
- Graduate School of Medical Sciences, Research Institute for Diseases of the Chest, Kyushu University, Fukuoka, Japan
| | | | - Rachel Hodge
- Biostatistics and Informatics, AstraZeneca, Cambridge, UK
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32
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Doxtader EE, Cheng YW, Zhang Y. Molecular Testing of Non-Small Cell Lung Carcinoma Diagnosed by Endobronchial Ultrasound-Guided Transbronchial Fine-Needle Aspiration: The Cleveland Clinic Experience. Arch Pathol Lab Med 2018; 143:670-676. [PMID: 29372844 DOI: 10.5858/arpa.2017-0184-ra] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Given the increasing demand for molecular testing of non-small cell lung carcinoma specimens to guide therapeutic decision-making and the trend toward minimally invasive techniques for obtaining diagnostic tissue, cytopathology laboratories must devise strategies to maximize DNA yield for necessary molecular testing. OBJECTIVE.— To describe our experience at Cleveland Clinic with epidermal growth factor receptor (EGFR) mutation testing by next-generation sequencing and anaplastic lymphoma kinase (ALK) gene rearrangement testing by fluorescence in situ hybridization of non-small cell lung carcinomas diagnosed by cytology, with an emphasis on specimens obtained by endobronchial ultrasound-guided transbronchial fine-needle aspiration. DATA SOURCES.— Data sources include a review of the current literature, including published articles from our institution. CONCLUSIONS.— At our institution, liquid-based cytology specimens are the primary resource used for molecular testing of non-small cell lung carcinomas; in most instances, adequate DNA can be extracted from the residual cell pellet for next-generation sequencing, and ThinPrep slides can be used reliably for fluorescence in situ hybridization testing for ALK gene rearrangements. In occasional cases where the cell pellet material is not adequate for molecular testing, cell blocks and/or surgical pathology specimens are secondary options. The cytopathologist's role in specimen handling and triage is essential to ensure that molecular testing can be carried out successfully.
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Affiliation(s)
- Erika E Doxtader
- From the Departments of Pathology (Drs Doxtader and Zhang) and Laboratory Medicine (Dr Cheng), Cleveland Clinic, Cleveland, Ohio
| | - Yu-Wei Cheng
- From the Departments of Pathology (Drs Doxtader and Zhang) and Laboratory Medicine (Dr Cheng), Cleveland Clinic, Cleveland, Ohio
| | - Yaxia Zhang
- From the Departments of Pathology (Drs Doxtader and Zhang) and Laboratory Medicine (Dr Cheng), Cleveland Clinic, Cleveland, Ohio
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33
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Guseva NV, Jaber O, Stence AA, Sompallae K, Bashir A, Sompallae R, Bossler AD, Jensen CS, Ma D. Simultaneous detection of single-nucleotide variant, deletion/insertion, and fusion in lung and thyroid carcinoma using cytology specimen and an RNA-based next-generation sequencing assay. Cancer Cytopathol 2018; 126:158-169. [DOI: 10.1002/cncy.21963] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/03/2017] [Accepted: 10/17/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Natalya V. Guseva
- Department of Pathology; University of Iowa Hospitals and Clinics; Iowa City Iowa
| | - Omar Jaber
- Department of Pathology; King Hussein Cancer Center; Amman Jordan
| | - Aaron A. Stence
- Department of Pathology; University of Iowa Hospitals and Clinics; Iowa City Iowa
| | | | - Amani Bashir
- Department of Pathology; University of Iowa Hospitals and Clinics; Iowa City Iowa
| | | | - Aaron D. Bossler
- Department of Pathology; University of Iowa Hospitals and Clinics; Iowa City Iowa
| | - Chris S. Jensen
- Department of Pathology; University of Iowa Hospitals and Clinics; Iowa City Iowa
| | - Deqin Ma
- Department of Pathology; University of Iowa Hospitals and Clinics; Iowa City Iowa
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34
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Moussavou-Boundzanga P, Koumakpayi IH, Labouba I, Leroy EM, Belembaogo E, Berthet N. Human papillomavirus detection using the Abbott RealTime high-risk HPV tests compared with conventional nested PCR coupled to high-throughput sequencing of amplification products in cervical smear specimens from a Gabonese female population. Virol J 2017; 14:241. [PMID: 29268766 PMCID: PMC5740888 DOI: 10.1186/s12985-017-0906-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/04/2017] [Indexed: 11/16/2022] Open
Abstract
Background Cervical cancer is the fourth most common malignancy in women worldwide. However, screening with human papillomavirus (HPV) molecular tests holds promise for reducing cervical cancer incidence and mortality in low- and middle-income countries. The performance of the Abbott RealTime High-Risk HPV test (AbRT) was evaluated in 83 cervical smear specimens and compared with a conventional nested PCR coupled to high-throughput sequencing (HTS) to identify the amplicons. Results The AbRT assay detected at least one HPV genotype in 44.57% of women regardless of the grade of cervical abnormalities. Except for one case, good concordance was observed for the genotypes detected with the AbRT assay in the high-risk HPV category determined with HTS of the amplicon generated by conventional nested PCR. Conclusions The AbRT test is an easy and reliable molecular tool and was as sensitive as conventional nested PCR in cervical smear specimens for detection HPVs associated with high-grade lesions. Moreover, sequencing amplicons using an HTS approach effectively identified the genotype of the hrHPV identified with the AbRT test.
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Affiliation(s)
- Pamela Moussavou-Boundzanga
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon
| | | | - Ingrid Labouba
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon.,Institut de Recherches et de Développement (IRD), Maladies Infectieuses et vecteurs : Ecologie, Génétique, Evolution et Contrôle (IRD 224 - CNRS 5290 6 UM1- UM2), Montpellier, France
| | | | - Nicolas Berthet
- Centre International de Recherches Médicales de Franceville (CIRMF), Department of Zoonosis and Emerging Diseases, 769, Franceville, BP, Gabon. .,Centre National de Recherche Scientifique (CNRS), UMR3569, 25 rue du docteur Roux, 75724, Paris, France. .,Institut Pasteur, Unité Environnement et risques infectieux, Cellule d'Intervention Biologique d'Urgence, 25 rue du Docteur Roux, 75724, Paris, France.
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35
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Asaka S, Yoshizawa A, Nakata R, Negishi T, Yamamoto H, Shiina T, Shigeto S, Matsuda K, Kobayashi Y, Honda T. Utility of bronchial lavage fluids for epithelial growth factor receptor mutation assay in lung cancer patients: Comparison between cell pellets, cell blocks and matching tissue specimens. Oncol Lett 2017; 15:1469-1474. [PMID: 29399190 PMCID: PMC5774526 DOI: 10.3892/ol.2017.7464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/01/2017] [Indexed: 12/27/2022] Open
Abstract
The detection of epidermal growth factor receptor (EGFR) mutations is necessary for the selection of suitable patients with non-small cell lung cancer (NSCLC) for treatment with EGFR tyrosine kinase inhibitors. Cytology specimens are known to be suitable for EGFR mutation detection, although tissue specimens should be prioritized; however, there are limited studies that examine the utility of bronchial lavage fluid (BLF) in mutation detection. The purpose of the present study was to investigate the utility of BLF specimens for the detection of EGFR mutations using a conventional quantitative EGFR polymerase chain reaction (PCR) assay. Initially, quantification cycle (Cq) values of cell pellets, cell-free supernatants and cell blocks obtained from three series of 1% EGFR mutation-positive lung cancer cell line samples were compared for mutation detection. In addition, PCR analysis of BLF specimens obtained from 77 consecutive NSCLC patients, detecting EGFR mutations was validated, and these results were compared with those for the corresponding formalin-fixed paraffin-embedded (FFPE) tissue specimens obtained by surgical resection or biopsy of 49 of these patients. The Cq values for mutation detection were significantly lower in the cell pellet group (average, 29.58) compared with the other groups, followed by those in cell-free supernatants (average, 34.15) and in cell blocks (average, 37.12) for all three series (P<0.05). Mutational status was successfully analyzed in 77 BLF specimens, and the results obtained were concordant with those of the 49 matching FFPE tissue specimens. Notably, EGFR mutations were even detected in 10 cytological specimens that contained insufficient tumor cells. EGFR mutation testing with BLF specimens is therefore a useful and reliable method, particularly when sufficient cancer cells are not obtained.
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Affiliation(s)
- Shiho Asaka
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Akihiko Yoshizawa
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan.,Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Rie Nakata
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Tatsuya Negishi
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Hiroshi Yamamoto
- First Department of Internal Medicine, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Shiina
- Department of Thoracic Surgery, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Shohei Shigeto
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Kazuyuki Matsuda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Yukihiro Kobayashi
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
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36
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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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37
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Cytology Preparations of Formalin Fixative Aid Detection of Giardia in Duodenal Biopsy Samples. Am J Surg Pathol 2017; 41:570-574. [PMID: 28177963 DOI: 10.1097/pas.0000000000000817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Giardiasis is the most common intestinal parasitic infection in the United States. The organism elicits no, or minimal, inflammatory changes in duodenal biopsy samples, so it can be easily overlooked. We performed this study to determine whether Giardia could be isolated from the formalin fixative of biopsy samples, and to evaluate the value of fluid analysis in the assessment for potential infection. We prospectively evaluated duodenal biopsy samples from 92 patients with a clinical suspicion of giardiasis or symptoms compatible with that diagnosis (ie, diarrhea, bloating, or abdominal pain) Biopsy samples were routinely processed and stained with hematoxylin and eosin. Histologic diagnoses included giardiasis (5 cases, 4%), normal findings (64 cases, 70%), peptic injury/active duodenitis (12 cases, 13%), and intraepithelial lymphocytosis with villous blunting (10 cases, 12%). Fifteen cases (13%) showed detached degenerated epithelial cells or mucus droplets in the intervillous space that resembled Giardia. Cytology slides were prepared from formalin in the biopsy container using the standard Cytospin protocol and reviewed by a cytopathologist blinded to the biopsy findings. Cytologic evaluation revealed Giardia spp. in all 5 biopsy-proven cases, and identified an additional case that was not detected by biopsy analysis. Organisms were significantly more numerous (mean: 400 trophozoites; range, 120 to 810) and showed better morphologic features in cytology preparations compared with tissue sections (mean: 129 trophozoites; range, 37 to 253 organisms; P=0.05). Our findings suggest that cytology preparations from formalin fixative can resolve diagnostically challenging cases and even enhance Giardia detection in some cases.
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38
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Hwang DH, Garcia EP, Ducar MD, Cibas ES, Sholl LM. Next-generation sequencing of cytologic preparations: An analysis of quality metrics. Cancer Cytopathol 2017; 125:786-794. [DOI: 10.1002/cncy.21897] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/25/2017] [Accepted: 06/26/2017] [Indexed: 01/08/2023]
Affiliation(s)
- David H. Hwang
- Department of Pathology; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Elizabeth P. Garcia
- Center for Advanced Molecular Diagnostics; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Matthew D. Ducar
- Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston Massachusetts
| | - Edmund S. Cibas
- Department of Pathology; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Lynette M. Sholl
- Department of Pathology; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
- Center for Advanced Molecular Diagnostics; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
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Baum JE, Zhang P, Hoda RS, Geraghty B, Rennert H, Narula N, Fernandes HD. Accuracy of next-generation sequencing for the identification of clinically relevant variants in cytology smears in lung adenocarcinoma. Cancer Cytopathol 2017; 125:398-406. [PMID: 28272845 DOI: 10.1002/cncy.21844] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Minimally invasive diagnostic procedures such as needle-core biopsy and fine-needle aspiration provide adequate material for molecular analyses. Advances in precision oncology are trending toward the interrogation of limited amounts of genomic material to guide clinical and therapeutic decisions. The aim of this study was to investigate the minimum cellularity needed on cytologic smears for the identification of clinically relevant variants with next-generation sequencing (NGS). METHODS Thirty cases of cytologically diagnosed, resection-proven primary lung adenocarcinoma were identified. Nineteen of the 30 cases were known to harbor actionable variants. One Diff-Quik (DQ)-stained slide and 1 Papanicolaou (Pap)-stained slide were selected from each case. Cases were categorized as containing fewer than 100 tumor cells, 100 to 500 tumor cells, or more than 500 tumor cells. NGS was performed on the Ion Torrent platform. RESULTS NGS was successfully performed on all cell blocks and on 90% of the smears. Paired DQ and Pap smears showed similar cellularity, and cases that differed in cellularity were within 1 category of each other. The cases with more than 100 tumor cells had a 93% success rate; this was significantly different from the situation for cases with fewer than 100 tumor cells, which were successfully sequenced only 67% of the time. Overall, NGS was able to provide clinically relevant information for 83% of DQ smears and for 90% of Pap smears tested. CONCLUSIONS The data show a significantly higher likelihood of successful NGS with cytologic smears with more than 100 tumor cells. There was a trend for a higher NGS success rate with Pap smears versus DQ smears. Cancer Cytopathol 2017;125:398-406. © 2017 American Cancer Society.
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Affiliation(s)
- Jordan E Baum
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Pan Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Rana S Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Brian Geraghty
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Navneet Narula
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Helen D Fernandes
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
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de Abreu FB, Peterson JD, Amos CI, Wells WA, Tsongalis GJ. Effective quality management practices in routine clinical next-generation sequencing. Clin Chem Lab Med 2017; 54:761-71. [PMID: 26872315 DOI: 10.1515/cclm-2015-1190] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/14/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Molecular technologies have allowed laboratories to detect and establish the profiles of human cancers by identifying a variety of somatic variants. In order to improve personalized patient care, we have established a next-generation sequencing (NGS) test to screen for somatic variants in primary or advanced cancers. In this study, we describe the laboratory quality management program for NGS testing, and also provide an overview of the somatic variants identified in over 1000 patient samples as well as their implications in clinical practice. METHODS Over the past one-and-a-half years, our laboratory received a total of 1028 formalin-fixed, paraffin-embedded (FFPE) tumor tissues, which consisted of non-small-cell lung carcinomas (NSCLCs), colon adenocarcinomas, glioma/glioblastomas, melanomas, breast carcinomas, and other tumor types. During this time period, we implemented a series of quality control (QC) checks that included (1) pre-DNA extraction, (2) DNA quantification, (3) DNA quality, (4) library quantification, (5) post-emulsification PCR, and (6) post-sequencing metrics. At least 10 ng of genomic DNA (gDNA) were used to prepare barcoded libraries using the AmpliSeq CHPv2. Samples were multiplexed and sequenced on Ion Torrent 318 chips using the Ion PGM System. Variants were identified using the Variant Caller Plugin, and annotation and functional predictions were performed using the Golden Helix SVS. RESULTS A total of 1005 samples passed QC1-3, and following additional library preparation QC checkpoints, 877 samples were sequenced. Samples were classified into two categories: wild-type (127) and positive for somatic variants (750). Somatic variants were classified into clinically actionable (60%) and non-actionable (40%). CONCLUSIONS The use of NGS in routine clinical laboratory practice allowed for the detection of tumor profiles that are essential for the selection of targeted therapies and identification of applicable clinical trials, contributing to the improvement of personalized patient care in oncology.
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Han Y, Li J. Sample types applied for molecular diagnosis of therapeutic management of advanced non-small cell lung cancer in the precision medicine. ACTA ACUST UNITED AC 2017; 55:1817-1833. [DOI: 10.1515/cclm-2017-0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/07/2017] [Indexed: 12/17/2022]
Abstract
AbstractIn this era of precision medicine, molecular biology is becoming increasingly significant for the diagnosis and therapeutic management of non-small cell lung cancer. The specimen as the primary element of the whole testing flow is particularly important for maintaining the accuracy of gene alteration testing. Presently, the main sample types applied in routine diagnosis are tissue and cytology biopsies. Liquid biopsies are considered as the most promising alternatives when tissue and cytology samples are not available. Each sample type possesses its own strengths and weaknesses, pertaining to the disparity of sampling, preparation and preservation procedures, the heterogeneity of inter- or intratumors, the tumor cellularity (percentage and number of tumor cells) of specimens, etc., and none of them can individually be a “one size to fit all”. Therefore, in this review, we summarized the strengths and weaknesses of different sample types that are widely used in clinical practice, offered solutions to reduce the negative impact of the samples and proposed an optimized strategy for choice of samples during the entire diagnostic course. We hope to provide valuable information to laboratories for choosing optimal clinical specimens to achieve comprehensive functional genomic landscapes and formulate individually tailored treatment plans for NSCLC patients that are in advanced stages.
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Reynolds JP, Zhou Y, Jakubowski MA, Wang Z, Brainard JA, Klein RD, Farver CF, Almeida FA, Cheng YW. Next-generation sequencing of liquid-based cytology non-small cell lung cancer samples. Cancer Cytopathol 2017; 125:178-187. [PMID: 28085233 DOI: 10.1002/cncy.21812] [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: 08/26/2016] [Revised: 10/18/2016] [Accepted: 11/04/2016] [Indexed: 12/25/2022]
Abstract
BACKGROUND The detection of mutated epidermal growth factor receptor (EGFR) in non-small cell lung cancer (NSCLC) with residual cell pellets derived from liquid-based cytology (LBC) samples (eg, endoscopic ultrasound-guided fine-needle aspiration) has been validated with allele-specific polymerase chain reaction. The aim of this study was to validate next-generation sequencing (NGS) technology for detecting gene mutations with residual cell pellets from LBC. METHODS Archived DNA extracted from LBC samples of adenocarcinoma stored in PreservCyt with a known EGFR mutation status was retrieved. Genomic DNA was multiplex-amplified and enriched with Ion AmpliSeq Cancer Hotspot Panel v2 chemistry and the OneTouch 2 instrument; this was followed by semiconductor sequencing on the Ion Personal Genome Machine platform. The mutation hotspots of 6 NSCLC-related genes (BRAF, EGFR, ERBB2, KRAS, MET, and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α [PIK3CA]) were analyzed with NextGENe and Torrent Suite bioinformatics tools. RESULTS The commonly identified EGFR sequence changes, including 4 L858R mutations, 3 exon 19 deletions, and 1 exon 20 insertion, were in 100% concordance between the assay platforms. Less common NSCLC variants were also found in the mutation hotspots of ERBB2, KRAS, MET, and PIK3CA genes. CONCLUSIONS NSCLC mutation analysis using NGS can be successfully performed on residual cell pellets derived from LBC samples. This approach allows the simultaneous examination of multiple mutation hotspots in a timely manner to improve patient care. Cancer Cytopathol 2017;125:178-187. © 2016 American Cancer Society.
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Affiliation(s)
- Jordan P Reynolds
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Yaolin Zhou
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Maureen A Jakubowski
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Zhen Wang
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Jennifer A Brainard
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Roger D Klein
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Carol F Farver
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
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Krasowski MD, Ford BA, Klutts JS, Jensen CS, Briggs AS, Robinson RA, Bruch LA, Karandikar NJ. Using Focused Laboratory Management and Quality Improvement Projects to Enhance Resident Training and Foster Scholarship. Acad Pathol 2017; 4:2374289517722152. [PMID: 28913416 PMCID: PMC5590695 DOI: 10.1177/2374289517722152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 11/22/2022] Open
Abstract
Training in patient safety, quality, and management is widely recognized as an important element of graduate medical education. These concepts have been intertwined in pathology graduate medical education for many years, although training programs face challenges in creating explicit learning opportunities in these fields. Tangibly involving pathology residents in management and quality improvement projects has the potential to teach and reinforce key concepts and further fulfill Accreditation Council for Graduate Medical Education goals for pursuing projects related to patient safety and quality improvement. In this report, we present our experience at a pathology residency program (University of Iowa) in engaging pathology residents in projects related to practical issues of laboratory management, process improvement, and informatics. In this program, at least 1 management/quality improvement project, typically performed during a clinical chemistry/management rotation, was required and ideally resulted in a journal publication. The residency program also initiated a monthly management/informatics series for pathology externs, residents, and fellows that covers a wide range of topics. Since 2010, all pathology residents at the University of Iowa have completed at least 1 management/quality improvement project. Many of the projects involved aspects of laboratory test utilization, with some projects focused on other areas such as human resources, informatics, or process improvement. Since 2012, 31 peer-reviewed journal articles involving effort from 26 residents have been published. Multiple projects resulted in changes in ongoing practice, particularly within the hospital electronic health record. Focused management/quality improvement projects involving pathology residents can result in both meaningful quality improvement and scholarly output.
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Affiliation(s)
- Matthew D. Krasowski
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Bradley A. Ford
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - J. Stacey Klutts
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
- Department of Pathology and Laboratory Medicine, Iowa City VA Health Care System, Iowa City, IA, USA
| | - Chris S. Jensen
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Angela S. Briggs
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Robert A. Robinson
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Leslie A. Bruch
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Nitin J. Karandikar
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
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Gleeson FC, Kerr SE, Kipp BR, Voss JS, Minot DM, Tu ZJ, Henry MR, Vasmatzis G, Cheville JC, Lazaridis KN, Levy MJ. Molecular cytology genotyping of primary and metastatic GI stromal tumors by using a custom two-gene targeted next-generation sequencing panel with therapeutic intent. Gastrointest Endosc 2016; 84:950-958.e3. [PMID: 27118626 DOI: 10.1016/j.gie.2016.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 04/15/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS In an era of precision medicine, customized genotyping of GI stromal tumors by screening for driver mutations will become the standard of care. The fidelity of genotype concordance between paired cytology smears and surgical pathology specimens is unknown. In patients with either primary or metastatic sporadic disease, we sought to determine the frequency of KIT and PDGFRA pathogenic alterations within such specimens, imatinib sensitivity, and the concordance of pathogenic alterations between paired specimens. METHODS DNA obtained from cytology smears from 36 patients, 24 of whom had paired surgical pathology specimens, underwent targeted next-generation sequencing by using a custom panel to evaluate somatic mutations within KIT (exon 2, 9, 10, 11, 13, 14, 15, 17, 18) and PDGFRA (exon 12, 14, 15, 18) genes. Patients with KIT and PDGRFA wild-type genes completed the Qiagen Human Comprehensive Cancer GeneRead DNAseq Targeted Array V2. RESULTS Genotyping revealed KIT and PDGFRA mutations in 68% and 15% of patients. The wild-type population did not harbor mutations in BRAF, RAS family, SDHB, SETD2, or NF1. Imatinib sensitivity based on the oncogenic kinase mutation prevalence was estimated to be 68%. Mutational concordance between paired cytology and surgical pathology specimens was 96%. CONCLUSIONS Our data have demonstrated the ability to stratify either primary or metastatic gastrointestinal stromal tumors by mutational subtype using a targeted next-generation sequencing 2 gene mutation panel. We highlight the ability to use cytology specimens obtained via minimally invasive techniques as a surrogate to surgical specimens given the high mutational landscape concordance between paired specimens.
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Affiliation(s)
- Ferga C Gleeson
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas M Minot
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Zheng Jin Tu
- Division of Biomedical Statics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael R Henry
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - John C Cheville
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Konstantinos N Lazaridis
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael J Levy
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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Bellevicine C, Sgariglia R, Malapelle U, Vigliar E, Nacchio M, Ciancia G, Eszlinger M, Paschke R, Troncone G. Young investigator challenge: Can the Ion AmpliSeq Cancer Hotspot Panel v2 be used for next-generation sequencing of thyroid FNA samples? Cancer Cytopathol 2016; 124:776-784. [DOI: 10.1002/cncy.21780] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Claudio Bellevicine
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Roberta Sgariglia
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Umberto Malapelle
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Elena Vigliar
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Mariantonia Nacchio
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Giuseppe Ciancia
- Department of Advanced Biomedical Sciences; University of Naples “Federico II,”; Naples Italy
| | - Markus Eszlinger
- Department of Oncology, Cumming School of Medicine; University of Calgary; Calgary Alberta Canada
| | - Ralf Paschke
- Department of Endocrinology, Cumming School of Medicine; University of Calgary; Calgary Alberta Canada
- Department of Oncology, Cumming School of Medicine; University of Calgary; Calgary Alberta Canada
| | - Giancarlo Troncone
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
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Aisner DL, Rumery MD, Merrick DT, Kondo KL, Nijmeh H, Linderman DJ, Doebele RC, Thomas N, Chesnut PC, Varella-Garcia M, Franklin WA, Camidge DR. Do More With Less: Tips and Techniques for Maximizing Small Biopsy and Cytology Specimens for Molecular and Ancillary Testing: The University of Colorado Experience. Arch Pathol Lab Med 2016; 140:1206-1220. [PMID: 27610643 DOI: 10.5858/arpa.2016-0156-ra] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Context .- In an era in which testing of patient tumor material for molecular and other ancillary studies is of increasing clinical importance for selection of therapy, the ability to test on small samplings becomes critical. Often, small samplings are rapidly depleted in the diagnostic workup or are insufficient for multiple ancillary testing approaches. Objective .- To describe technical methodologies that can be implemented to preserve and maximize tissue for molecular and other ancillary testing. Data Sources .- Retrospective analysis of a case cohort from the University of Colorado, description of techniques used at the University of Colorado, and published literature. Conclusions .- Numerous techniques can be deployed to maximize molecular and other ancillary testing, even when specimens are from small samplings. A dedicated process for molecular prioritization has a high success rate, but also increases workload, which must be factored into establishing such a process. Additionally, establishing high-fidelity communication strings is critical for success of dedicated molecular prioritization of samples. Numerous approaches can be deployed for alternative specimen types, and several technical approaches can also aid in maximizing small specimens.
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Technical and US regulatory issues in triaging material for the molecular laboratory. Cancer Cytopathol 2016; 125:83-90. [DOI: 10.1002/cncy.21774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 07/24/2016] [Accepted: 07/27/2016] [Indexed: 12/31/2022]
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Tian SK, Killian JK, Rekhtman N, Benayed R, Middha S, Ladanyi M, Lin O, Arcila ME. Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience. Arch Pathol Lab Med 2016; 140:1200-1205. [PMID: 27588332 DOI: 10.5858/arpa.2016-0108-ra] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The value and suitability of cytology specimens for molecular diagnosis has been demonstrated by numerous studies. In practice, however, the success rates vary widely across institutions depending on the disease setting, institutional practices of acquisition, handling/processing, and testing methodologies. As the number of clinically relevant biomarkers continues to increase, more laboratories are turning to next-generation sequencing platforms for testing. Although amplicon-based next-generation sequencing assays, interrogating a limited genomic territory, can be performed with minimal input material, broader-based next-generation sequencing assays have higher DNA input requirements that may not be met if the small tissue samples are not acquired and handled appropriately. We briefly describe some of the process changes we have instituted in our laboratories when handling cytologic material to maximize the tissue available for broad hybrid-capture-based next-generation sequencing assays. Among the key changes established were the consolidation and preservation of previously discarded supernatant material in cytologic samples, the introduction of mineral oil for deparaffinization of cell blocks, and adjustments in the molecular laboratory process and bioinformatics pipelines. We emphasize that even minimal changes can have broad implications for test performance, highlighting the importance of a cohesive group-based approach among clinical, cytopathology, surgical pathology, molecular, and bioinformatics teams.
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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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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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