1
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Kim D, Vanderbilt CM, Yang SR, Nandakumar S, Nafa K, Feratovic R, Rekhtman N, Rijo I, Casanova J, Yun A, Brannon AR, Berger MF, Ladanyi M, Lin O, Arcila ME. Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling. Nat Commun 2025; 16:116. [PMID: 39747849 PMCID: PMC11696557 DOI: 10.1038/s41467-024-55456-8] [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: 07/15/2024] [Accepted: 12/03/2024] [Indexed: 01/04/2025] Open
Abstract
Comprehensive molecular profiling by next-generation sequencing has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACTTM. Special emphasis is given to the use of residual supernatant cell-free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples are similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples have excellent performance overall, low-level cross-contamination is identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples have negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy, delivered successful results in 71% of cases where tumor tissue from CB was depleted.
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Affiliation(s)
- David Kim
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Chad M Vanderbilt
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Subhiksha Nandakumar
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rusmir Feratovic
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natasha Rekhtman
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivelise Rijo
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklyn Casanova
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita Yun
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Rose Brannon
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oscar Lin
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Heymann JJ, Pineda CM, Booth CN, Jenkins E, Menke JR, Monaco SE, Nayar R, Nishino M, Roy-Chowdhuri S, Ruiz-Cordero R, Russell DK, Saqi A, Sundling KE, Thrall MJ, Torous VF, VandenBussche CJ, VanderLaan PA, Zhang ML, Siddiqui MT. Tools, techniques, and challenges in preparing cytology specimens for ancillary studies: results of the ASC Optimizing Cytology and Small Biopsy Specimen Processing for Ancillary Studies task force survey. J Am Soc Cytopathol 2025; 14:55-63. [PMID: 39547835 DOI: 10.1016/j.jasc.2024.10.001] [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: 08/13/2024] [Revised: 09/25/2024] [Accepted: 10/09/2024] [Indexed: 11/17/2024]
Abstract
INTRODUCTION Ancillary testing on cytopathology and other small biopsy specimens is crucial for diagnosis and provides critical information to clinicians. Testing is dependent on preanalytic factors and would benefit from standardization of specimen collection protocols across laboratories. To assess institutional practices and areas of need for evidence-based standards, we surveyed current practices across cytopathology laboratories. MATERIALS AND METHODS A twelve-question electronic survey was distributed to American Society of Cytopathology (ASC) members through email, social media, and the ASC from January 8, 2024 to March 1, 2024. Survey responses were tabulated. RESULTS Of 294 respondents, 257 (87%) completed at least 10/12 questions. Formalin-fixed, paraffin-embedded cell blocks (CBs) are utilized for immunohistochemistry, molecular testing, and in situ hybridization by 89%, 84%, and 71% of respondents, respectively. For fine needle aspirations, no collection medium is utilized by a majority of respondents. In contrast, 61% utilize no collection medium for fluids; 64% predominantly utilize liquid-based preservatives for other exfoliative specimens. For CB preparation, 58% of respondents use coagulating agent; 67% use no fixative before formalin. The two most significant factors limiting clinical utility of ancillary testing in cytology specimens are low cellularity and lack of validation (49% and 23% of respondents, respectively). CONCLUSIONS There is wide variation in current practices among laboratories, reflecting lack of consensus. Although laboratories utilize different collection media for different specimen types, for CB utilization, current survey results are similar to those reported previously. ASC has convened a task force to facilitate specimen standardization and minimize variability among preanalytic factors.
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Affiliation(s)
- Jonas J Heymann
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York.
| | - Cristiana M Pineda
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | | | | | - Joshua R Menke
- Department of Pathology, Stanford University, Stanford, California
| | - Sara E Monaco
- Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Ritu Nayar
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michiya Nishino
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Sinchita Roy-Chowdhuri
- Division of Pathology and Laboratory Medicine, Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roberto Ruiz-Cordero
- Department of Pathology and Laboratory Medicine, Miller School of Medicine, University of Miami, Miami, Florida
| | | | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Kaitlin E Sundling
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Michael J Thrall
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Vanda F Torous
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - M Lisa Zhang
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Momin T Siddiqui
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, New York, New York
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Dipasquale A, Pisapia P, Reduzzi C. Liquid biopsy through non-blood fluids: The show must go on. THE JOURNAL OF LIQUID BIOPSY 2024; 6:100272. [PMID: 40027316 PMCID: PMC11863827 DOI: 10.1016/j.jlb.2024.100272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 10/15/2024] [Accepted: 10/15/2024] [Indexed: 03/05/2025]
Abstract
Image 1.
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Affiliation(s)
- Angelo Dipasquale
- IRCCS Humanitas Research Hospital, Milan, Italy
- Young Committee, International Society of Liquid Biopsy, Spain
| | - Pasquale Pisapia
- Young Committee, International Society of Liquid Biopsy, Spain
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | - Carolina Reduzzi
- Young Committee, International Society of Liquid Biopsy, Spain
- Department of Medicine, Weill Cornell Medicine, New York, USA
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Heymann JJ, D'Ambrosio D, Dombrowski KS, Desai N, Illei PB. Pulmonary Cytopathology: Current and Future Impact on Patient Care. Surg Pathol Clin 2024; 17:395-410. [PMID: 39129139 DOI: 10.1016/j.path.2024.06.002] [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] [Indexed: 08/13/2024]
Abstract
Small biopsies of lung are routinely obtained by many methods, including several that result in cytologic specimens. Because lung cancer is often diagnosed at a stage for which primary resection is not an option, it is critical that all diagnostic, predictive, and prognostic information be derived from such small biopsy specimens. As the number of available diagnostic and predictive markers expands, cytopathologists must familiarize themselves with current requirements for specimen acquisition, handling, results reporting, and molecular and other ancillary testing, all of which are reviewed here.
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Affiliation(s)
- Jonas J Heymann
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Danielle D'Ambrosio
- Department of Pathology, New York University Grossman School of Medicine, 560 First Avenue, New York, NY 10016, USA
| | - Katya S Dombrowski
- Department of Pathology, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Niyati Desai
- Department of Pathology and Cell Biology, New York-Presbyterian Hospital-Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Peter B Illei
- Department of Pathology, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
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Kim D, Vanderbilt C, Yang SR, Nandakumar S, Nafa K, Feratovic R, Rekhtman N, Rijo I, Casanova J, Yun A, Brannon AR, Berger M, Ladanyi M, Lin O, Arcila M. Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling - A report on the impact of process optimization through the analysis of 4,871 cytology samples profiled by MSK-IMPACT. RESEARCH SQUARE 2024:rs.3.rs-4746484. [PMID: 39108489 PMCID: PMC11302697 DOI: 10.21203/rs.3.rs-4746484/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Comprehensive molecular profiling by next generation sequencing (NGS) has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACT™. Special emphasis is given to the use of residual supernatant cell free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples were similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples had excellent performance overall, low-level cross-contamination was identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples had negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy delivered successful results in 71% of cases where tumor tissue from CB was depleted.
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Affiliation(s)
- David Kim
- Memorial Sloan Kettering Cancer Center
| | | | | | | | | | | | | | | | | | - Anita Yun
- Memorial Sloan Kettering Cancer Center
| | | | | | | | - Oscar Lin
- Memorial Sloan Kettering Cancer Center
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6
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Thakur S, Rathor A, Jain S, Nambirajan A, Khurana S, Malik PS, Jain D. Pleural effusion supernatant: a reliable resource for cell-free DNA in molecular testing of lung cancer. J Am Soc Cytopathol 2024; 13:291-302. [PMID: 38704351 DOI: 10.1016/j.jasc.2024.03.006] [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: 01/03/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 05/06/2024]
Abstract
INTRODUCTION DNA extracted from malignant pleural effusion (PE) sediments is the traditional source of tumor DNA for predictive biomarker molecular testing (MT). Few recent studies have proposed the utility of cell-free DNA (cfDNA) extracted from effusion cytology centrifuged supernatants (CCS) in MT. The aim of this study was to assess the feasibility and utility of molecular testing on cfDNA extracted from PE CCS in lung cancer patients. MATERIALS AND METHODS The study was of prospective design. All PE CCS were collected and stored. Subsequently, in patients confirmed as primary lung adenocarcinoma (LUAD) and where patient matched effusion sediment/tissue biopsy/plasma was being tested for EGFR mutations, cfDNA extraction and EGFR MT by real-time polymerase chain reaction (qPCR) were performed. Custom panel targeted next-generation sequencing (NGS) (Ion Torrent; Thermo Fisher, Carlsbad, CA) was also performed wherever feasible. RESULTS Out of 299 PE CCS collected, 20 CCS samples were included in the study. Concordant EGFR mutations were detected in pleural effusion CCS of 10 of 11 (91%) EGFR mutant cases as per qPCR performed on the matched sediment DNA (n = 8), lung biopsy (n = 2), and plasma (n = 1) samples. In 1 positive sample, CCS detected additional EGFR T790M mutation. Among 10 CCS samples also tested by NGS, additional EGFR mutations missed by qPCR were picked up in 2 (2 of 10). Success of mutation detection in CCS cfDNA did not correlate with cfDNA quantity or tumor fraction in sediment. CONCLUSIONS cfDNA from effusion CCS is a reliable and independent source of tumor DNA highly amenable for MT and complement results from other tumor DNA sources for comprehensive mutation profiling in LUAD patients.
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Affiliation(s)
- Shilpi Thakur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Amber Rathor
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Surabhi Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Khurana
- Department of Medical Oncology, Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Prabhat Singh Malik
- Department of Medical Oncology, Institute Rotary Cancer Hospital, 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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Kodama H, Murakami H, Mamesaya N, Kobayashi H, Omori S, Wakuda K, Ko R, Ono A, Kenmotsu H, Naito T, Matsumoto S, Goto K, Shimizu T, Gon Y, Takahashi T. Suitability of frozen cell pellets from cytology specimens for the Amoy 9-in-1 assay in patients with non-small cell lung cancer. Thorac Cancer 2024; 15:1665-1672. [PMID: 38898747 PMCID: PMC11260549 DOI: 10.1111/1759-7714.15382] [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: 03/30/2024] [Revised: 05/03/2024] [Accepted: 05/11/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND The AmoyDx Pan lung cancer PCR panel (AmoyDx PLC panel) has been approved as a companion diagnostic tool for multiple anticancer agents in patients with non-small cell lung cancer (NSCLC). However, the suitability of cytology specimens as samples for the AmoyDx PLC panel remains unclear. We evaluated the performance of frozen cell pellets from cytology specimens (FCPs) in the Amoy 9-in-1 assay, a preapproval assay of the AmoyDx PLC panel. METHODS We retrospectively collected data of NSCLC patients enrolled in LC-SCRUM-Asia from the Shizuoka Cancer Center between September 2019 and May 2021. RESULTS A total of 49 cases submitted FCPs for evaluation of oncogenic driver alterations and were assessed using Amoy 9-in-1 and next-generation sequencing (NGS) assays. The success rates of DNA and RNA analyses using the Amoy 9-in-1 were both 100%, compared with 86% and 45%, respectively, using NGS assays. Oncogenic driver alterations were detected in 27 (55%) and 23 (47%) patients using Amoy 9-in-1 and NGS, respectively. No inconsistent results were observed among 19 cases in which both assays showed successful detection. In the remaining 30 cases, 10 had inconsistent results: nine oncogenic driver alterations (3 MET, 2 ALK, 2 ROS1, and 2 KRAS) were detectable only in Amoy 9-in-1, and one epidermal growth factor receptor (EGFR) mutation was detectable only in NGS. CONCLUSION FCPs can be successfully used in the AmoyDx PLC panel, with higher success rate compared with the NGS assay. The AmoyDx PLC panel may be an option in cases when insufficient tissue sample is available for the NGS assay.
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Affiliation(s)
- Hiroaki Kodama
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | | | - Nobuaki Mamesaya
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | - Haruki Kobayashi
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | - Shota Omori
- Respiratory Medicine and Infectious DiseasesOita University Faculty of MedicineOitaJapan
| | - Kazushige Wakuda
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | - Ryo Ko
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | - Akira Ono
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | | | - Tateaki Naito
- Division of Thoracic OncologyShizuoka Cancer CenterShizuokaJapan
| | - Shingo Matsumoto
- Department of Thoracic OncologyNational Cancer Center Hospital EastKashiwaJapan
| | - Koichi Goto
- Department of Thoracic OncologyNational Cancer Center Hospital EastKashiwaJapan
| | - Tetsuo Shimizu
- Division of Respiratory Medicine, Department of Internal MedicineNihon University School of MedicineTokyoJapan
| | - Yasuhiro Gon
- Division of Respiratory Medicine, Department of Internal MedicineNihon University School of MedicineTokyoJapan
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8
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Jager L, Jennings LJ, Dittmann D, Blanco J, Choy B, Nayar R. Supernatant fluid from endobronchial ultrasound-guided transbronchial needle aspiration for rapid next-generation sequencing. J Am Soc Cytopathol 2024:S2213-2945(24)00043-7. [PMID: 38797657 DOI: 10.1016/j.jasc.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024]
Abstract
INTRODUCTION There is an increasing demand to optimize the workflow and maximize tissue available for next-generation sequencing (NGS) for non-small cell carcinoma. We looked at transbronchial needle endobronchial ultrasound-guided bronchoscopy with transbronchial needle aspiration samples and evaluated the performance of supernatant (SN) fluid processed from a dedicated aspirate collected for NGS testing. MATERIALS AND METHODS Nineteen samples were collected and processed using a new workflow. Five aspirates were collected in formalin. One additional dedicated pass was collected fresh and centrifuged. The resulting cell pellet was added to formalin for cell block (CB) processing. DNA and RNA were extracted from concentrated SN for targeted testing using the Oncomine Precision Assay (Thermo Scientific, Waltham, MA). NGS results from the corresponding CB samples were used as "controls" for comparison. RESULTS Thirty-one mutations were detected in SN (Table 1). The most frequently mutated genes were TP53 (35%), EGFR (23%), KRAS (13%), CTNNB1 (6%), and ERBB2 (6%). There was 100% concordance between the mutations detected in SN and corresponding CBs with comparable variant allele frequencies. Turnaround time of NGS results was 1 day for SN compared to 4-10 days for CB. CONCLUSIONS We were able to demonstrate the usefulness of SN for reliable rapid molecular results. We successfully incorporated the workflow for tissue handling and processing among our clinical, cytopathology, and molecular teams. Molecular results were available at the same time as the cytologic diagnosis, allowing for timely reporting of a comprehensive diagnosis. This approach is particularly useful in patients with advanced disease requiring urgent management.
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Affiliation(s)
- Lucy Jager
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois.
| | - Lawrence J Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - David Dittmann
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - Jayjay Blanco
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - Bonnie Choy
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - Ritu Nayar
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
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Arhant G, Lachkar S, Thiebaut PA, Marguet F, Lamy A, Thiberville L, Salaün M, Guisier F, Sabourin JC, Piton N. Detection of Tumor DNA in Bronchoscopic Fluids in Peripheral NSCLC: A Proof-of-Concept Study. JTO Clin Res Rep 2024; 5:100596. [PMID: 38328474 PMCID: PMC10847031 DOI: 10.1016/j.jtocrr.2023.100596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction DNA genotyping from plasma is a useful tool for molecular characterization of NSCLC. Nevertheless, the false-negative rate justifies the development of methods with higher sensitivity, especially in difficult-to-reach peripheral lung tumors. Methods We aimed at comparing molecular analysis from the supernatant of guide sheath flush fluid collected during radial-EndoBronchial UltraSound (r-EBUS) bronchoscopy with plasma sampling and tumor biopsies in patients with peripheral NSCLC. The DNA was genotyped using high-throughput sequencing or the COBAS mutation test. There were 65 patients with peripheral lung tumors subjected to concomitant sampling of guide sheath flush supernatant, plasma tumor DNA, and tumor biopsy and cytology using r-EBUS. There were 33 patients (including 24 newly diagnosed with having NSCLC) with an identifiable tumor mutation in the primary lesion selected for the comparative analysis. Results Guide sheath flush-based genotyping yielded a mutation detection rate of 61.8% (17 of 24 mutated EGFR, one of two ERBB2, one of one KRAS, one of one MAP2K, one of four MET, and zero of one STK11), compared with 33% in plasma-based genotyping (p = 0.0151). Furthermore, in eight of 34 r-EBUS without tumor cells on microscopic examination, we were able to detect the mutation in four paired guide sheath flush supernatant, compared with only two in paired plasma. Conclusion The detection of tumor DNA in the supernatant of guide sheath flush fluid collected during r-EBUS bronchoscopy represents a sensitive and complementary method for genotyping NSCLC.
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Affiliation(s)
- Gwenaëlle Arhant
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Samy Lachkar
- Department of Pneumology, CHU Rouen, Rouen, France
| | - Pierre-Alain Thiebaut
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Florent Marguet
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Aude Lamy
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Luc Thiberville
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Mathieu Salaün
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Florian Guisier
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Jean-Christophe Sabourin
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Nicolas Piton
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
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10
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Pisapia P, Malapelle U, Vielh P, Troncone G. The liquid biopsy series: A cytopathological perspective. Cytopathology 2023; 34:517-518. [PMID: 37675604 DOI: 10.1111/cyt.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/08/2023] [Indexed: 09/08/2023]
Abstract
In the modern era of personalised medicine, the correct assessment of the genomic landscape for patients affected by cancer with haematological malignancies is crucial. In this scenario, liquid biopsy represents not only an alternative but a complementary source of tumour nucleic acids to tissue in order to guarantee the best clinical management for these patients.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Philippe Vielh
- Department of Pathology, Medipath and the American Hospital of Paris, Paris, France
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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11
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Biondini D, Tinè M, Semenzato U, Daverio M, Scalvenzi F, Bazzan E, Turato G, Damin M, Spagnolo P. Clinical Applications of Endobronchial Ultrasound (EBUS) Scope: Challenges and Opportunities. Diagnostics (Basel) 2023; 13:2565. [PMID: 37568927 PMCID: PMC10417616 DOI: 10.3390/diagnostics13152565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Endobronchial Ultrasound (EBUS) has been widely used to stage lung tumors and to diagnose mediastinal diseases. In the last decade, this procedure has evolved in several technical aspects, with new tools available to optimize tissue sampling and to increase its diagnostic yield, like elastography, different types of needles and, most recently, miniforceps and cryobiopsy. Accordingly, the indications for the use of the EBUS scope into the airways to perform the Endobronchial Ultrasound-TransBronchial Needle Aspiration (EBUS-TBNA) has also extended beyond the endobronchial and thoracic boundaries to sample lesions from the liver, left adrenal gland and retroperitoneal lymph nodes via the gastroesophageal tract, performing the Endoscopic UltraSound with Bronchoscope-guided Fine Needle Aspiration (EUS-B-FNA). In this review, we summarize and critically discuss the main indication for the use of the EBUS scope, even the more uncommon, to underline its utility and versatility in clinical practice.
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Affiliation(s)
- Davide Biondini
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
- Department of Medicine, University of Padova, 35128 Padova, Italy
| | - Mariaenrica Tinè
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
| | - Umberto Semenzato
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
| | - Matteo Daverio
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
| | - Francesca Scalvenzi
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
| | - Erica Bazzan
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
| | - Graziella Turato
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
| | - Marco Damin
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy
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12
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Turner SA, Abou Shaar R, Yang Z. The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology. Diagn Cytopathol 2023; 51:83-94. [PMID: 36345929 PMCID: PMC10098847 DOI: 10.1002/dc.25067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.
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Affiliation(s)
- Scott A Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Rand Abou Shaar
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zhongbo Yang
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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13
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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: 1.3] [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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14
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Li G, Liu D, Flandrin P, Zhang Y, Lambert C, Mallouk N, Cottier M. Tumor-Derived Exosomal RNA From Fine-Needle Aspiration Supernatant as a Novel Liquid Biopsy for Molecular Diagnosis of Cancer. PATHOLOGY AND ONCOLOGY RESEARCH 2022; 28:1610344. [PMID: 35991837 PMCID: PMC9388727 DOI: 10.3389/pore.2022.1610344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/06/2022] [Indexed: 11/15/2022]
Abstract
Background: We hypothesized that the fine needle aspiration (FNA) supernatant from tumor might contain tumor-derived exosomes. The objective of this pilot study was to test if tumor-derived exosomal RNA could be found in FNA supernatants for molecular diagnosis of cancer. Methods: 10 FNA samples from pancreatic tumor were included. After the routine recuperation of cellular material by centrifugation, the cell-free Cytolyt liquid was collected instead of being discarded. 10 ml Cytolyt was used to isolate the exosomes. Transmission electronic microscopy (TEM) was used to examine the presence of exosomes. The exosomal marker CD63 was analyzed by flow cytometry. The exosomal RNA was extracted. RT-qPCR was performed to detect the GAPDH and the tumor marker of glypican 1 gene expression. Results: TEM confirmed the presence of exosomes from FNA supernatants. Flow cytometry showed a strong positive expression of exosome marker CD63. The concentration of exosomal RNA ranged from 18.81 to 354.75 ng/μl with an average of 81.76 ng/μl. The average exosomal RNA quantity was 1390.01 ng (range from 319.77 to 6030.75 ng) with an average 260/280 ratio of 2.12. GAPDH was detectable in all samples. Exosomal glypican 1 was detected in all samples of pancreatic ductal adenorcarcinomas (3/3) and absent from benign cystic samples (3/3). Furthermore, exosomal glypican 1 was positive in one sample with a non-contributive cytology and in one sample in which no malignant cell was found. Conclusion: This is the first report that the supernatants from FNA biopsy may contain tumor-derived exosomal RNA. These tumor-derived exosomes from FNA may provide a new liquid biopsy for the molecular diagnosis of cancer.
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Affiliation(s)
- Guorong Li
- Department of Digestive Surgery and Urology, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
- *Correspondence: Dongdong Liu, ; Guorong Li,
| | - Dongdong Liu
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Dongdong Liu, ; Guorong Li,
| | - Pascale Flandrin
- Laboratory of Molecular Biology, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
| | - Yang Zhang
- Guangzhou HopeTech Biological Technology Co., Ltd., Guangzhou, China
| | - Claude Lambert
- Section of Flow Cytometry, Immunology Laboratory, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
| | - Nora Mallouk
- Center of Electronic Microscopy, CMES, Faculty of Medicine, University Jean Monnet, Saint-Etienne, France
| | - Michèle Cottier
- Laboratory of Cytopathology, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
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15
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Specimen Considerations in Molecular Oncology Testing. Clin Lab Med 2022; 42:367-383. [DOI: 10.1016/j.cll.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Paulson V, Konnick EQ, Lockwood CH. When Tissue Is the Issue. Clin Lab Med 2022; 42:485-496. [DOI: 10.1016/j.cll.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Performance of Idylla KRAS assay on extracted DNA and de-stained cytology smears: Can we rescue small sample? Ann Diagn Pathol 2022; 60:152023. [DOI: 10.1016/j.anndiagpath.2022.152023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022]
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18
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Ruff HM, Lou SK, Hahn E, Grenier S, Stockley TL, Boerner SL. Molecular yield and cytomorphologic assessment of fine needle aspiration specimen supernatants. J Am Soc Cytopathol 2022; 11:142-153. [PMID: 35305954 DOI: 10.1016/j.jasc.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
INTRODUCTION Cytology samples are frequently relied upon for the diagnosis of advanced cancer such as lung cancer. As the recommendations for solid malignancies biomarker testing continue to expand, it becomes increasingly important to efficiently utilize limited specimens to minimize the need for additional sampling and its associated risks and costs. MATERIALS AND METHODS We performed molecular testing on fresh or CytoLyt-fixed supernatants derived from fine needle aspirates (FNAs) and compared its performance against the clinical specimen (including formalin-fixed paraffin-embedded cell blocks, residual PreservCyt and fresh samples). Supernatants were assessed for cellularity using Field-stained Cytospin (CS) preparations. RESULTS There was overall almost perfect agreement (41/45 cases, K = 0.822) and substantial to almost perfect agreement in molecular testing results of clinically actionable variants between fresh (20/23 cases, Κ = 0.742) and CytoLyt-fixed (21/22 cases, Κ = 0.908) and its clinical specimen counterpart. Interestingly, CS examination of the supernatants revealed viable tumor cells. Centrifugation for 1 minute at 300 rpm is optimal for overall or tumor cellularity recovery. Delayed molecular testing after 3, 4 and 7 days at 4 degrees Celsius showed identical molecular results. CONCLUSIONS We validated the use of supernatants derived from FNA cytology samples as a substrate for molecular testing using next-generation sequencing and other molecular techniques.
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Affiliation(s)
- Heather M Ruff
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Si Kei Lou
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Elan Hahn
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sylvie Grenier
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Tracy L Stockley
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Scott L Boerner
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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19
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Vigliar E, Lozano MD, Roy-Chowdhuri S. Editorial: Advances in Molecular Cytopathology. Front Med (Lausanne) 2022; 9:851949. [PMID: 35223934 PMCID: PMC8873172 DOI: 10.3389/fmed.2022.851949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
- *Correspondence: Elena Vigliar
| | - Maria D. Lozano
- Department of Pathology, Clinica University of Navarra, Pamplona, Spain
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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20
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Nikas IP, Mountzios G, Sydney GI, Ioakim KJ, Won JK, Papageorgis P. Evaluating Pancreatic and Biliary Neoplasms with Small Biopsy-Based Next Generation Sequencing (NGS): Doing More with Less. Cancers (Basel) 2022; 14:cancers14020397. [PMID: 35053560 PMCID: PMC8773813 DOI: 10.3390/cancers14020397] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Pancreatic cancer and cholangiocarcinoma are aggressive diseases mostly diagnosed at an advanced and inoperable stage. This review presents the value of next-generation sequencing (NGS) when performed on small biopsies—including fine-needle aspiration/biopsy samples, brushings, pancreatic juice and bile, and also blood—in the field of pancreatobiliary neoplasia. NGS could guide physicians while evaluating pancreatic solid and cystic lesions or suspicious biliary strictures, performing surveillance in high-risk individuals, or monitoring the disease and assessing prognosis in already diagnosed cancer patients. Evidence suggests that NGS performed on small biopsies is a robust tool for the diagnosis and pre-operative risk stratification of pancreatic and biliary lesions, whereas it also carries significant prognostic and therapeutic value. However, effective standardization of the pre-analytical and analytical assay parameters used for each clinical scenario is needed to fully implement NGS into routine practice and provide more personalized management in patients with suspected or established pancreatobiliary neoplasia. Abstract Pancreatic cancer and cholangiocarcinoma are lethal diseases mainly diagnosed at an inoperable stage. As pancreatobiliary surgical specimens are often unavailable for further molecular testing, this review aimed to highlight the diagnostic, prognostic, and therapeutic impact of next-generation sequencing (NGS) performed on distinct small biopsies, including endoscopic ultrasound fine-needle aspirations and biopsies of pancreatic solid and cystic lesions, biliary duct brushings, and also “liquid biopsies” such as the pancreatic juice, bile, and blood. NGS could clarify indeterminate pancreatic lesions or biliary strictures, for instance by identifying TP53 or SMAD4 mutations indicating high-grade dysplasia or cancer. It could also stratify pancreatic cystic lesions, by distinguishing mucinous from non-mucinous cysts and identifying high-risk cysts that should be excised in surgically fit patients, whereas the combination of cytology, elevated cystic CEA levels and NGS could improve the overall diagnostic accuracy. When NGS is performed on the pancreatic juice, it could stratify high-risk patients under surveillance. On the plasma, it could dynamically monitor the disease course and response to therapy. Notably, the circulating tumor DNA (ctDNA) levels have been associated with staging, grading, and survival. Lastly, NGS has shown potential in identifying potentially actionable molecular alterations. In conclusion, NGS applied on small biopsies could carry significant diagnostic, prognostic, and therapeutic value.
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Affiliation(s)
- Ilias P. Nikas
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (G.I.S.); (K.J.I.)
- Correspondence:
| | - Giannis Mountzios
- Fourth Department of Medical Oncology and Clinical Trials Unit, Henry Dunant Hospital Center, 11526 Athens, Greece;
| | - Guy I. Sydney
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (G.I.S.); (K.J.I.)
- Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL 62702, USA
| | - Kalliopi J. Ioakim
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (G.I.S.); (K.J.I.)
- Department of Internal Medicine, Limassol General Hospital, Limassol 4131, Cyprus
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University Hospital and College of Medicine, Seoul 03080, Korea;
| | - Panagiotis Papageorgis
- Tumor Microenvironment, Metastasis and Experimental Therapeutics Laboratory, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia 2404, Cyprus;
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21
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The storm of NGS in NSCLC diagnostic-therapeutic pathway: How to sun the real clinical practice. Crit Rev Oncol Hematol 2021; 169:103561. [PMID: 34856311 DOI: 10.1016/j.critrevonc.2021.103561] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
The increasing number of approved drugs along with next generation sequencing (NGS) technologies look out as potential revolution of biomolecular characterization of non-small-cell lung cancer (NSCLC). Nevertheless, several aspects impact on success rate of NGS in clinical practice: a multidisciplinary approach and thorough knowledge of strengths and limits of each technologic diagnostic tool are required. Crucial preliminary step is the selection of the best available sample before testing, aware of clinical condition and setting of disease. Genomic data should be than integrated in the clinical context and matched with available therapeutic options; Molecular Tumor Boards (MTB) are worldwide emerging interdisciplinary groups implemented to transfer the impact of precision medicine in clinical practice. In order to guarantee equity in treatment, these considerations should find their application widely and rapidly. Aim of this review is offering an overview of emerging biomarkers, relative upcoming targeted drugs, and new diagnostic chances with an authors' perspective about a real-life diagnostic-therapeutic algorithm useful for daily clinical practice.
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22
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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23
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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: 0.5] [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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24
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Malapelle U, Pisapia P, Addeo A, Arrieta O, Bellosillo B, Cardona AF, Cristofanilli M, De Miguel-Perez D, Denninghoff V, Durán I, Jantus-Lewintre E, Nuzzo PV, O'Byrne K, Pauwels P, Pickering EM, Raez LE, Russo A, Serrano MJ, Gandara DR, Troncone G, Rolfo C. Liquid biopsy from research to clinical practice: focus on non-small cell lung cancer. Expert Rev Mol Diagn 2021; 21:1165-1178. [PMID: 34570988 DOI: 10.1080/14737159.2021.1985468] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the current era of personalized medicine, liquid biopsy has acquired a relevant importance in patient management of advanced stage non-small cell lung cancer (NSCLC). As a matter of fact, liquid biopsy may supplant the problem of inadequate tissue for molecular testing. The term 'liquid biopsy' refers to a number of different biological fluids, but is most clearly associated with plasma-related platforms. It must be taken into account that pre-analytical processing and the selection of the appropriate technology according to the clinical context may condition the results obtained. In addition, novel clinical applications beyond the evaluation of the molecular status of predictive biomarkers are currently under investigation. AREAS COVERED This review summarizes the available evidence on pre-analytical issues and different clinical applications of liquid biopsies in NSCLC patients. EXPERT OPINION Liquid biopsy should be considered not only as a valid alternative but as complementary to tissue-based molecular approaches. Careful attention should be paid to the optimization and standardization of all phases of liquid biopsy samples management in order to determine a significant improvement in either sensitivity or specificity, while significant reducing the number of 'false negative' or 'false positive' molecular results.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, Geneva, Switzerland
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), México City, México
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar, Barcelona, Spain.,Department of Pathology, Ciberonc, Madrid, Spain
| | - Andres F Cardona
- Department of Oncology, Clinical and Translational Oncology Group, Clínica Del Country, Bogotá, Colombia.,Department of Oncology, Foundation for Clinical and Applied Cancer Research (Ficmac), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (Fox-g/oncolgroup), Universidad el Bosque, Bogotá, Colombia
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Diego De Miguel-Perez
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Valeria Denninghoff
- Department of Pathology, University of Buenos Aires - National Council for Scientific and Technical Research (Conicet), Buenos Aires, Argentina
| | - Ignacio Durán
- Department of Oncology, Hospital Universitario Marques de Valdecilla, IDIVAL, Santander, Spain
| | - Eloísa Jantus-Lewintre
- Department of Pathology, Ciberonc, Madrid, Spain.,Molecular Oncology Laboratory, Fundación Para La Investigación Del Hospital General Universitario De Valencia, Valencia, Spain.,Mixed Unit TRIAL, (Príncipe Felipe Research Centre & Fundación Para La Investigación Del Hospital General Universitario De Valencia), Valencia, Spain.,Department of Biotechnology, Universitat Politècnica De València, Valencia, Spain
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, The Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ken O'Byrne
- Medical Oncology, Princess Alexandra Hospital, Queensland University of Technology, Brisbane City, Australia
| | - Patrick Pauwels
- Center for Oncological Research Antwerp (Core), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (Uantwerp), Wilrijk, Belgium.,Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Edward M Pickering
- Divison of Pulmonary and Critical Care Medicine, Section of Interventional Pulmonology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Luis E Raez
- Thoracic Oncology Program, Memorial Cancer Institute/Memorial Health Care System, Florida International University, Miami, FL, USA
| | - Alessandro Russo
- Department of Oncology, Medical Oncology Unit, A.O. Papardo, Messina, Italy
| | - Maria José Serrano
- GENyO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Liquid Biopsy and Cancer Interception Group, Granada, Spain
| | - David R Gandara
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico Ii, Naples, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA
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Pisapia P, Pepe F, Sgariglia R, Nacchio M, Russo G, Conticelli F, Girolami I, Eccher A, Bellevicine C, Vigliar E, Malapelle U, Troncone G. Next generation sequencing in cytology. Cytopathology 2021; 32:588-595. [PMID: 33792981 PMCID: PMC8451925 DOI: 10.1111/cyt.12974] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 03/06/2021] [Indexed: 12/17/2022]
Abstract
The application of next generation sequencing (NGS) technology to cytological samples has significantly modified molecular cytopathology practice. Cytological samples represent a valid source of high-quality DNA for NGS analysis, especially for predicting patients' response to targeted treatments and for refining the risk of malignancy in indeterminate cytological diagnoses. However, several pre-analytical factors may influence the reliability of NGS clinical analysis. Here, we briefly review the challenges of NGS in cytology practice, focusing on those pre-analytical factors that may negatively affect NGS success rates and routine diagnostic applications. Finally, we address the future directions of the field.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public HealthUniversity of Naples Federico IINaplesItaly
| | - Francesco Pepe
- Department of Public HealthUniversity of Naples Federico IINaplesItaly
| | - Roberta Sgariglia
- Department of Public HealthUniversity of Naples Federico IINaplesItaly
| | | | - Gianluca Russo
- Department of Public HealthUniversity of Naples Federico IINaplesItaly
| | | | | | - Albino Eccher
- Department of Pathology and DiagnosticsUniversity and Hospital Trust of VeronaVeronaItaly
| | | | - Elena Vigliar
- Department of Public HealthUniversity of Naples Federico IINaplesItaly
| | - Umberto Malapelle
- Department of Public HealthUniversity of Naples Federico IINaplesItaly
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26
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Tafoya M, Judd A, Chiotti K, Dearen K, Jiron K, Chabot-Richards D, Broehm CJ. Performance of a 50-gene next generation sequencing panel with post-centrifuge supernatant cytology fluid in non-small-cell lung cancer. Diagn Cytopathol 2021; 49:1173-1178. [PMID: 34339108 DOI: 10.1002/dc.24844] [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: 05/23/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND Liquid based cytology (LBC) specimens are increasingly utilized for molecular analysis, as results are comparable to molecular analysis performed on traditional specimens (biopsy or cell block). However, there are few studies demonstrating the long-term viability of DNA in LBC samples. METHODS In this study, a 50-gene next generation sequencing (NGS) panel was performed on DNA isolated from post-centrifuged supernatant LBC samples of cases of non-small-cell lung carcinoma. Comparison was made to results of an identical NGS panel performed on a concurrent clinical sample (biopsy or cell block). Quality parameters including DNA concentration, total reads, amplicons with reads under 450 and 350, and variant allele fraction were also compared. For a subset of LBC samples, DNA was isolated after being held for varying extended lengths of time after collection (up to 41 days) at 5°C and results compared. RESULTS Results of NGS mutation analysis were concordant between LBC samples and clinical samples. DNA concentration was on average higher in the LBC samples compared to the clinical samples. The remaining metrics were more variable, but illustrated the adequacy of LBC samples for NGS testing. DNA isolated from LBC samples held for longer periods of time was of good concentration. NGS analysis was successfully performed on all samples, with concordance with results of clinical samples. CONCLUSION DNA isolated directly from LBC fluid is suitable for NGS analysis. DNA is also stable in LBC preservative for extended periods of time before isolation and NGS analysis can subsequently be successfully performed.
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Affiliation(s)
- Marissa Tafoya
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Andrew Judd
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Kelsey Chiotti
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Karen Dearen
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Kassandra Jiron
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Devon Chabot-Richards
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Cory J Broehm
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
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27
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Perrone ME, Alvarez R, Vo TT, Chung MW, Chhieng DC, Paulson VA, Colbert BG, Q Konnick E, Huang EC. Validating cell-free DNA from supernatant for molecular diagnostics on cytology specimens. Cancer Cytopathol 2021; 129:956-965. [PMID: 34265180 DOI: 10.1002/cncy.22491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Cytology specimens are often used for biomarker testing in the setting of neoplasia. On occasion, formalin-fixed paraffin-embedded (FFPE) cell blocks unfortunately may not yield sufficient material for testing. Recent studies have suggested that residual supernatant fluid from cell block preparation is a valuable source of DNA: both cellular and cell-free DNA (cfDNA). In the present study, the use of cfDNA from supernatant is compared against DNA from FFPE materials. METHODS cfDNA was extracted prospectively from residual supernatants of 30 cytology samples (29 neoplastic cases and 1 benign ascitic fluid from a patient with a history of melanoma). Samples were tested using clinically validated next-generation-sequencing platforms and the results were compared with data from paired FFPE cell blocks in a real-time prospective clinical setting. Thirteen samples were tested on an amplicon-based assay (Solid Tumor Hotspot), and 17 samples were tested using a comprehensive capture-based assay (UW-Oncoplex). RESULTS Neoplastic content was estimated by mutational variant allele fraction, with a mean content of 24.0% and 25.8% in supernatant and FFPE, respectively. The variant concordance between paired samples was 90%, and identical results were detected in both supernatant and FFPE samples in 74% of cases. CONCLUSIONS This study confirmed that cfDNA from supernatant is a viable alternative to FFPE cell blocks for molecular biomarker testing using both amplicon-based and capture-based assays with potential for decreasing additional tissue sampling and faster turnaround time.
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Affiliation(s)
- Marie E Perrone
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Rebeca Alvarez
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Tawnie T Vo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Moon-Wook Chung
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - David C Chhieng
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Vera A Paulson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Brice G Colbert
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Eric Q Konnick
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Eric C Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
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28
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Patel A, Hissong E, Rosado L, Burkhardt R, Cong L, Alperstein SA, Siddiqui MT, Park HJ, Song W, Velu PD, Rennert H, Heymann JJ. Next-Generation Sequencing of Cell-Free DNA Extracted From Pleural Effusion Supernatant: Applications and Challenges. Front Med (Lausanne) 2021; 8:662312. [PMID: 34195208 PMCID: PMC8236629 DOI: 10.3389/fmed.2021.662312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Cell-free DNA (cfDNA) extracted from diverse specimen types has emerged as a high quality substrate for molecular tumor profiling. Analytical and pre-analytical challenges in the utilization of cfDNA extracted from pleural effusion supernatant (PES) are herein characterized in patients with metastatic non-small cell lung carcinoma (NSCLC). Pleural effusion specimens containing metastatic NSCLC were collected prospectively. After ThinPrep® (TP) and cell block (CB) preparation, DNA was extracted from residual PES and analyzed by gel electrophoresis for quality and quantity. Libraries were prepared and sequenced with a targeted next-generation sequencing (NGS) platform and panel clinically validated for plasma specimens. Results were compared with DNA extracted from corresponding FFPE samples that were sequenced using institutional targeted NGS assays clinically validated for solid tumor FFPE samples. Tumor (TC) and overall cellularity (OC) were evaluated. Fourteen specimens were collected from 13 patients. Median specimen volume was 180 mL (range, 35–1,400 mL). Median TC and OC on TP slides and CB sections were comparable. Median extracted DNA concentration was 7.4 ng/μL (range, 0.1–58.0 ng/μL), with >5 ng/μL DNA extracted from 10/14 specimens (71%). Mutations were identified in 10/14 specimens, including 1/3 specimens with median molecular coverage <1,000 reads. The minimal detected allelic fraction was 0.6%. NGS was falsely negative for the presence of one driver mutation. No correlation was identified between sample volume or OC, quality or quantity of extracted DNA, or mutation detection. Despite analytical and pre-analytical challenges, PES represents a robust source of DNA for NGS.
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Affiliation(s)
- Ami Patel
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Erika Hissong
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Lucelina Rosado
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Robert Burkhardt
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Lin Cong
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Susan A Alperstein
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Momin T Siddiqui
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Hyeon Jin Park
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Wei Song
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Priya D Velu
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Hanna Rennert
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Jonas J Heymann
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
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29
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Russo A, Incorvaia L, Del Re M, Malapelle U, Capoluongo E, Gristina V, Castiglia M, Danesi R, Fassan M, Giuffrè G, Gori S, Marchetti A, Normanno N, Pinto C, Rossi G, Santini D, Sartore-Bianchi A, Silvestris N, Tagliaferri P, Troncone G, Cinieri S, Beretta GD. The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM-SIAPEC-IAP-SIBioC-SIC-SIF Italian Scientific Societies. ESMO Open 2021; 6:100164. [PMID: 34091263 PMCID: PMC8182269 DOI: 10.1016/j.esmoop.2021.100164] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023] Open
Abstract
The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and other blood derivatives, such as circulating tumor cells, circulating tumor RNA, microRNAs, platelets, extracellular vesicles, as well as other biofluids such as urine and cerebrospinal fluid, may be adopted in the near future. Despite the evident advantages compared with tissue biopsy, LB still presents some limitations due to both biological and technological issues. In this context, the absence of harmonized procedures corresponds to an unmet clinical need, ultimately affecting the rapid implementation of LB in clinical practice. In this position paper, based on experts' opinions, the AIOM-SIAPEC-IAP-SIBIOC-SIF Italian Scientific Societies critically discuss the most relevant technical issues of LB, the current and emerging evidences, with the aim to optimizing the applications of LB in the clinical setting.
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Affiliation(s)
- A Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy.
| | - L Incorvaia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - U Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - E Capoluongo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - V Gristina
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Castiglia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - R Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - M Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy; Veneto Institute of Oncology (IOV-IRCCS), Padua, Italy
| | - G Giuffrè
- Department of Human Pathology in Adult and Developmental Age 'Gaetano Barresi', Section of Pathology, University of Messina, Messina, Italy
| | - S Gori
- Department of Oncology, IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - A Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Chieti, Italy
| | - N Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - C Pinto
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS-AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - G Rossi
- Pathology Unit, Ospedale Santa Maria Delle Croci, Ravenna, Italy
| | - D Santini
- Department of Medical Oncology, University Campus Biomedico, Rome, Italy
| | - A Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - N Silvestris
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori 'Giovanni Paolo II' of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - P Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - G Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - S Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
| | - G D Beretta
- Department of Oncology, Humanitas Gavazzeni, Bergamo, Italy
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30
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Pisapia P, Pepe F, Iaccarino A, Sgariglia R, Nacchio M, Conticelli F, Salatiello M, Tufano R, Russo G, Gragnano G, Girolami I, Eccher A, Malapelle U, Troncone G. Next Generation Sequencing in Cytopathology: Focus on Non-Small Cell Lung Cancer. Front Med (Lausanne) 2021; 8:633923. [PMID: 33644101 PMCID: PMC7904874 DOI: 10.3389/fmed.2021.633923] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular cytopathology is a rapidly evolving field embracing both conventional microscopy and molecular pathology. Its growing popularity stems from the fact that in many types of advanced cancers, including non small cell lung cancer (NSCLC), cytological samples often constitute the only available specimens for morphomolecular analysis. Indeed, non formalin fixed and paraffin embedded (FFPE) cytological samples feature a higher quality of extracted nucleic acids than histological specimens. However, because of the growing complexity of molecular testing, several efforts should be made to validate the analytical performance of the wide array of currently available molecular technologies, including next generation sequencing (NGS). This technology has the terrific advantage of allowing simultaneous detection of scores of predictive biomarkers even in low-input DNA/RNA specimens. Here, we briefly review the role of the modern cytopathologist in the morphomolecular diagnosing of advanced stage NSCLC and the adoption of NGS in conventional cytopreparations (cell blocks, direct smears, and liquid-based cytology) and supernatants.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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31
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Durin L, Pradines A, Basset C, Ulrich B, Keller L, Dongay V, Favre G, Mazieres J, Guibert N. Liquid Biopsy of Non-Plasma Body Fluids in Non-Small Cell Lung Cancer: Look Closer to the Tumor! Cells 2020; 9:cells9112486. [PMID: 33207539 PMCID: PMC7698102 DOI: 10.3390/cells9112486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/19/2022] Open
Abstract
Liquid biopsy is a rapidly emerging field due to an increasing number of oncogenic drivers and a better understanding of resistance mechanisms to targeted therapies in non-small cell lung cancer (NSCLC). The sensitivity of the most widely used blood-based assays is, however, limited in particular in cases of low tumor volume where shed of tumor-derived material can be limited. A negative result thus requires biopsy confirmation using minimally invasive sampling procedures that can result in small specimens, which are often not suitable for genotyping. Liquid biopsy is not limited to plasma, and tumor DNA circulating in other body fluids such as urine, pleural fluid, cerebrospinal fluid, or cytology specimen-derived supernatant can be exploited. In comparison to cell blocks, these fluids in close contact to the tumor may contain a more abundant and less analytically demanding tumor DNA. In this review, we discuss the potential applications of circulating tumor DNA derived from cytology samples in NSCLC, from early stage (screening, nodule characterization) to metastatic disease.
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Affiliation(s)
- Lucile Durin
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
| | - Anne Pradines
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
| | - Céline Basset
- Cytology Department, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France;
| | - Bryan Ulrich
- Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Laura Keller
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
| | - Vincent Dongay
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
| | - Gilles Favre
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
| | - Julien Mazieres
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
| | - Nicolas Guibert
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
- Correspondence: ; Tel.: +33-567771836
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32
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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: 0.8] [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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Ruiz-Cordero R, Ng DL. Neurotrophic receptor tyrosine kinase (NTRK) fusions and their role in cancer. Cancer Cytopathol 2020; 128:775-779. [PMID: 33002320 DOI: 10.1002/cncy.22350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Neurotrophic receptor tyrosine kinase (NTRK) fusions are rare, therapeutically actionable, and, in some cases, diagnostic oncogenic events that can occur in a variety of adult and pediatric cancers. Cytopathologists need to be a familiar with the types of tumors that can harbor NTRK fusions to triage specimens accordingly for testing.
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Fulmer CG, Park K, Dilcher T, Ho M, Mirabelli S, Alperstein S, Hissong EM, Pittman M, Siddiqui M, Heymann JJ, Yantiss RK, Borczuk AC, Fernandes H, Sigel C, Song W, Mosquera JM, Rao R. Next-generation sequencing of residual cytologic fixative preserved DNA from pancreatic lesions: A pilot study. Cancer Cytopathol 2020; 128:840-851. [PMID: 32598087 PMCID: PMC9285651 DOI: 10.1002/cncy.22315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/01/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a sensitive and specific tool in the risk stratification of pancreatic lesions, including cysts. The sensitivity and specificity of EUS-FNA has been shown to improve when cytology is combined with next-generation sequencing (NGS). Ideally, fresh cyst fluid is used for NGS. In this pilot study, we explore the possibility of sequencing DNA derived from residual alcohol-fixed pancreatic aspirates. METHODS Residual cytologic fixatives (n = 42) from 39 patients who underwent EUS-FNA for pancreatic lesions were collected along with demographics, imaging, and laboratory studies. Samples were designated as nonneoplastic/nonmucinous benign (NB), mucinous cyst (MC), pancreatic ductal adenocarcinoma (PDAC), or well-differentiated neuroendocrine tumor (NET) on the basis of cytopathologic evaluation and sequenced on the Oncomine platform (ThermoFisher Scientific, Waltham, Massachusetts). RESULTS Ten of 14 (71.4%) MCs exhibited clinically significant variants, including KRAS, GNAS, and TP53. Ten of 15 (66.7%) PDACs had KRAS alterations, and 9 of 15 (60%) showed variants in TP53. No variants were detected in any NETs. Only 1 of 9 (11.1%) NB aspirates showed variants in KRAS and MAP2K. Sequencing of formalin-fixed, paraffin-embedded tissue revealed variants identical to those detected in fixative-derived DNA in 4 of 5 cases (80%). CONCLUSION Residual DNA from alcohol-fixed aspirates are an underutilized source for NGS. Sequencing residual fixative-derived DNA has the potential to be integrated into the workup of pancreatic aspirates, possibly impacting management.
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Affiliation(s)
- Clifton G Fulmer
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, The Cleveland Clinic, Cleveland, OH
| | - Kyung Park
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Dilcher
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mai Ho
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Susanna Mirabelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Susan Alperstein
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Erika M. Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Meredith Pittman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Momin Siddiqui
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jonas J. Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rhonda K. Yantiss
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alain C. Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carlie Sigel
- Department of Pathology, The Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Song
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rema Rao
- The Leopold G. Koss Division of Cytology, The Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA
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Cecchini MJ, Yi ES. Liquid biopsy is a valuable tool in the diagnosis and management of lung cancer. J Thorac Dis 2020; 12:7048-7056. [PMID: 33282410 PMCID: PMC7711358 DOI: 10.21037/jtd.2020.04.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid biopsy refers to the use of various body fluids to test for circulating biological elements derived from the tumor. Liquid biopsy has taken on an increasingly important role in lung cancer diagnosis, molecular characterization, surveillance, monitoring, and determining mechanisms of resistance. These assays can utilize various sources of cell-free DNA (cfDNA) including blood, pleural fluid, urine, and others to detect tumor associated alterations. With the increasing power of next-generation sequencing technologies and the development of assays such as digital droplet PCR, rare tumor alleles can be detected in cfDNA to determine key characteristics of the tumor. Current assays, while effective, are still challenged by limited sensitivity and capacity to single genes or small panels of genes, though this is rapidly expanding. Nevertheless, testing of cfDNA has been shown to be valuable in detecting resistance to targeted inhibitors, particularly for detection of T790M in EGFR and monitoring response to therapy. With the continued development of more powerful and sensitive assays, these techniques will empower clinicians to better characterize early stage disease and can be used in the screening of high-risk patients, which may eliminate the requirement for tissue diagnosis in some settings. That said, since the majority of these alterations are not specific to lung cancer, there will continue to be a need for tissue in at least the initial diagnosis. Used in conjugation with tissue sampling, these assays will assist the treating clinician and the pathologist to better characterize individual tumors, even in the setting of limited tissue.
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Affiliation(s)
- Matthew J Cecchini
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
| | - Eunhee S Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Rochester, MN, USA
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Grigoriadou GΙ, Esagian SM, Ryu HS, Nikas IP. Molecular Profiling of Malignant Pleural Effusions with Next Generation Sequencing (NGS): Evidence that Supports Its Role in Cancer Management. J Pers Med 2020; 10:jpm10040206. [PMID: 33139621 PMCID: PMC7712846 DOI: 10.3390/jpm10040206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
Malignant pleural effusions (MPEs) often develop in advanced cancer patients and confer significant morbidity and mortality. In this review, we evaluated whether molecular profiling of MPEs with next generation sequencing (NGS) could have a role in cancer management, focusing on lung cancer. We reviewed and compared the diagnostic performance of pleural fluid liquid biopsy with other types of samples. When applied in MPEs, NGS may have comparable performance with corresponding tissue biopsies, yield higher DNA amount, and detect more genetic aberrations than blood-derived liquid biopsies. NGS in MPEs may also be preferable to plasma liquid biopsy in advanced cancer patients with a MPE and a paucicellular or it could be difficult to obtain tissue/fine-needle aspiration biopsy. Of interest, post-centrifuge supernatant NGS may exhibit superior results compared to cell pellet, cell block or other materials. NGS in MPEs can also guide clinicians in tailoring established therapies and identifying therapy resistance. Evidence is still premature regarding the role of NGS in MPEs from patients with cancers other than lung. We concluded that MPE processing could provide useful prognostic and theranostic information, besides its diagnostic role.
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Affiliation(s)
- Georgia Ι. Grigoriadou
- 1st Department of Medical Oncology, Theageneio Anticancer Hospital, 54007 Thessaloniki, Greece;
| | - Stepan M. Esagian
- Department of Medicine, School of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea;
| | - Ilias P. Nikas
- School of Medicine, European University of Cyprus, 2404 Nicosia, Cyprus
- Correspondence:
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Harbhajanka A, Michael CW, Janaki N, Gokozan HN, Wasman J, Bomeisl P, Yoest J, Sadri N. Tiny but mighty: use of next generation sequencing on discarded cytocentrifuged bile duct brushing specimens to increase sensitivity of cytological diagnosis. Mod Pathol 2020; 33:2019-2025. [PMID: 32457409 DOI: 10.1038/s41379-020-0577-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/15/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
Bile duct brushing (BDB) is used to evaluate pancreatobiliary lesions as it widely samples lesions with a low complication rate. Cytological evaluation of BDB is a specific but insensitive test. There is limited literature on the use of post-cytocentrifuged (PCC) samples, which are usually discarded, for next-generation sequencing (NGS) as an adjunct to cytological diagnosis of BDB. In this study we investigate whether molecular analysis by NGS of PCC specimens improves the sensitivity of diagnosis. PCC samples from 100 consecutive BDB specimens spanning 93 unique patients were retained. DNA was extracted and mutational analysis was performed agnostic of morphologic or clinical findings. Each BDB specimen was characterized as negative, atypical or positive based on morphological analysis by trained cytopathologists. Performance characteristics for mutational profiling and morphological analysis were calculated on the basis of clinicopathologic follow-up. There was sufficient clinicopathologic follow-up to classify 94 of 100 cases as either malignant (n = 43) or benign (n = 51). Based on morphologic analysis of cytology, these 94 cases were classified as either benign (n = 55), atypical (n = 18), or as at least suspicious or positive for malignancy (n = 21). Morphologic analysis of cytology showed a sensitivity of 49% and a specificity of 100% if atypical cases were considered negative. NGS revealed oncogenic alterations in 40/43 (93%) of malignant cases based on clinicopathologic follow-up. The most common alterations were in KRAS and TP53, observed in 77% and 49% of malignant cases respectively. No alterations were observed in the 51 benign cases classified based on clinicopathologic follow-up. Supplementing cytomorphologic analysis with molecular profiling of PCC by targeted NGS analysis increased the sensitivity to 93% and maintained specificity at 100%. This study provides evidence for the utility of NGS molecular profiling of PCC specimens to increase the sensitivity of BDB cytology samples, although studies with larger cohorts are needed to verify these findings.
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Affiliation(s)
- Aparna Harbhajanka
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Claire W Michael
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nafiseh Janaki
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School Boston, Boston, MA, USA
| | - Hamza N Gokozan
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jay Wasman
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Philip Bomeisl
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jennifer Yoest
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Navid Sadri
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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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: 20] [Impact Index Per Article: 4.0] [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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Hannigan B, Ye W, Mehrotra M, Lam V, Bolivar A, Zalles S, Barkoh BA, Duose D, Hu PC, Broaddus R, Stewart J, Heymach J, Medeiros LJ, Wistuba I, Luthra R, Roy-Chowdhuri S. Liquid biopsy assay for lung carcinoma using centrifuged supernatants from fine-needle aspiration specimens. Ann Oncol 2020; 30:963-969. [PMID: 30887015 DOI: 10.1093/annonc/mdz102] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Tumor mutation profiling is standard-of-care in lung carcinoma patients. However, comprehensive molecular profiling of small specimens, including core needle biopsy (CNB) and fine-needle aspiration (FNA) specimens, may often be inadequate due to limited tissue. Centrifuged FNA supernatants, which are typically discarded, have emerged recently as a novel liquid-based biopsy for molecular testing. In this study, we evaluate the use of lung carcinoma FNA supernatants for detecting clinically relevant mutations. METHODS Supernatants from lung carcinoma FNA samples (n = 150) were evaluated. Samples were further analyzed using next-generation sequencing (NGS) and ultrasensitive droplet digital PCR (ddPCR). Mutation profiles in a subset of samples were compared with results derived from paired tissue samples from the same patient (n = 67) and available plasma liquid biopsy assay (n = 45). RESULTS All 150 samples yielded adequate DNA and NGS were carried out successfully on 104 (90%) of 116 selected samples. Somatic mutations were detected in 82% of the samples and in 50% of these patients a clinically relevant mutation was identified that would qualify them for targeted therapy or a clinical trial. There was high overall concordance between the mutation profiles of supernatants and the corresponding tissue samples, with 100% concordance with concurrent FNA and 96% with concurrent CNB samples. Comparison of actionable driver mutations detected in supernatant versus plasma samples showed 84% concordance. CONCLUSIONS FNA supernatants can provide a valuable specimen source for genotyping lung carcinoma especially in patients with insufficient tumor tissue, thereby reducing multigene mutation profiling failure rates, improving turnaround times, and avoiding repeat biopsies.
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Affiliation(s)
- B Hannigan
- Graduate Program in Diagnostic Genetics, School of Health Professions
| | - W Ye
- Graduate Program in Diagnostic Genetics, School of Health Professions
| | - M Mehrotra
- Departments of Hematopathology, Division of Pathology and Laboratory Medicine
| | - V Lam
- Thoracic/Head and Neck Medical Oncology
| | - A Bolivar
- Graduate Program in Diagnostic Genetics, School of Health Professions
| | - S Zalles
- Graduate Program in Diagnostic Genetics, School of Health Professions
| | - B A Barkoh
- Departments of Hematopathology, Division of Pathology and Laboratory Medicine
| | - D Duose
- Translational Molecular Pathology, Division of Pathology and Laboratory Medicine
| | - P C Hu
- Graduate Program in Diagnostic Genetics, School of Health Professions
| | - R Broaddus
- Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Stewart
- Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Heymach
- Thoracic/Head and Neck Medical Oncology
| | - L J Medeiros
- Departments of Hematopathology, Division of Pathology and Laboratory Medicine
| | - I Wistuba
- Translational Molecular Pathology, Division of Pathology and Laboratory Medicine
| | - R Luthra
- Departments of Hematopathology, Division of Pathology and Laboratory Medicine
| | - S Roy-Chowdhuri
- Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA.
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40
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Gokozan H, Harbhajanka A, Bomeisl P, Michael CW, Sadri N. Use of cytology centrifuged supernatants improves cost and turnaround time for targeted next generation sequencing. Diagn Cytopathol 2020; 48:1167-1172. [PMID: 32697040 DOI: 10.1002/dc.24548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Molecular testing is an essential step in providing patients with advanced non-small-cell lung cancer (NSCLC), the most appropriate front-line targeted therapies. We recently implemented targeted NGS on previously discarded cytology centrifuged supernatant (CCS). METHODS In this study, we reviewed our implementation process to evaluate its performance. Performance and turnaround time (TAT) of molecular testing on all cytology NSCLC cases submitted for targeted NGS from June 2018 to September 2019 were evaluated, which included 46 and 62 cytology cases before and after implementation of CCS, respectively. Associated cost savings using CCS was also analyzed. RESULTS The mean TAT defined as the time of collection to time of reporting was 8.5 ± 1.8 days in CCS cohort (range 5-13) as compared with 12.2 ± 5.3 days in the (FFPE) cell block (CB) cohort (range: 6-27). The success rate of sequencing was similar for both cohorts (100% in CCS and 96% in FFPE CB). CONCLUSION Our results demonstrate that NGS using CCS improves TAT, preserves FFPE CB for other testing, and results in cost savings of $50 per case.
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Affiliation(s)
- HamzaN Gokozan
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Aparna Harbhajanka
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Philip Bomeisl
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Claire W Michael
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Navid Sadri
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Yamaguchi T, Akahane T, Harada O, Kato Y, Aimono E, Takei H, Tasaki T, Noguchi H, Nishihara H, Kamata H, Tanimoto A. Next-generation sequencing in residual liquid-based cytology specimens for cancer genome analysis. Diagn Cytopathol 2020; 48:965-971. [PMID: 32511899 DOI: 10.1002/dc.24511] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cancer genome profiling of cytology specimens using next-generation sequencing (NGS) requires adequate and good-quality DNA. Genomic examination of cytology samples was conventionally performed on cell block (CB) or smear specimens than on residual liquid-based cytology (LBC) specimens, which are high-quality DNA sources even after long-term storage. METHODS We estimated tumor fractions of 37 residual LBC specimens, including 30 fine needle aspiration (FNA) samples from the thyroid (12 papillary thyroid carcinomas and two malignant lymphomas), lymph node (13 metastatic carcinomas and one malignant lymphoma), and breast cancer (one phyllodes tumor and one invasive ductal carcinoma), two pancreatic carcinoma samples, and five liquid (ascites, pleural effusion, and cerebrospinal fluid) samples. The DNA was extracted from all samples and subjected to NGS using a customized cancer gene panel comprising 28 cancer-related genes. RESULTS NGS analysis revealed somatic mutations corresponding to pathological diagnosis with adequate variant allele frequency (VAF) in 24 LBC specimens, which had significantly higher tumor fraction (72.5% ± 4.9%). Ten cases, including the five fluid samples, had very small tumor fractions (7.5% ± 2.3%) to obtain sufficient VAF. Other two samples had high tumor fractions but showed very low VAF, indicating the presence of fusion genes. The remaining one sample yielded no DNA recovery. CONCLUSION The residual LBC specimens collected by FNA from the thyroid gland and lymph node were verified to carry high tumor fraction and could serve as an alternate source for molecular testing to screen and diagnose cancers without the use of CB or smears.
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Affiliation(s)
- Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Ohi Harada
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Yasutaka Kato
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Eriko Aimono
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hidehiro Takei
- Department of Diagnostic Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Takashi Tasaki
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hirotsugu Noguchi
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroshi Nishihara
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan.,Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hajime Kamata
- Department of Neurosurgery, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
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Sung S, Heymann JJ, Crapanzano JP, Moreira AL, Shu C, Bulman WA, Saqi A. Lung cancer cytology and small biopsy specimens: diagnosis, predictive biomarker testing, acquisition, triage, and management. J Am Soc Cytopathol 2020; 9:332-345. [PMID: 32591241 DOI: 10.1016/j.jasc.2020.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
In the 21st century, there has been a dramatic shift in the management of advanced-stage lung carcinoma, and this has coincided with an increasing use of minimally invasive tissue acquisition methods. Both have had significant downstream effects on cytology and small biopsy specimens. Current treatments require morphologic, immunohistochemical, and/or genotypical subtyping of non-small cell lung carcinoma. To meet these objectives, standardized classification of cytology and small specimen diagnoses, immunohistochemical algorithms, and predictive biomarker testing guidelines have been developed. This review provides an overview of current classification, biomarker testing, methods of small specimen acquisition and triage, clinical management strategies, and emerging technologies.
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Affiliation(s)
- Simon Sung
- Columbia University Medical Center, Department of Pathology & Cell Biology, New York, New York.
| | - Jonas J Heymann
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - John P Crapanzano
- Columbia University Medical Center, Department of Pathology & Cell Biology, New York, New York
| | - Andre L Moreira
- Department of Pathology, New York University Langone Health, New York, New York
| | - Catherine Shu
- Department of Medicine, Hematology & Oncology, Columbia University Medical Center, New York, New York
| | - William A Bulman
- Department of Medicine, Pulmonary, Columbia University Medical Center, New York, New York
| | - Anjali Saqi
- Columbia University Medical Center, Department of Pathology & Cell Biology, New York, New York
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43
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Small but powerful: the promising role of small specimens for biomarker testing. J Am Soc Cytopathol 2020; 9:450-460. [PMID: 32507626 DOI: 10.1016/j.jasc.2020.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 12/22/2022]
Abstract
Emphasis on the use of small specimens for biomarker testing to provide prognostic and predictive information for guiding clinical management for patients with advanced-stage cancer has been increasing. These biomarker tests include molecular analysis, cytogenetic tests, and immunohistochemical assays. Owing to the limited nature of the cellular material procured in these small specimens, which are collected using minimally invasive techniques (ie, fine needle aspiration and core needle biopsy), pathologists have been required to triage these samples judiciously and provide the clinically relevant genomic information required for patient care. Awareness of the advantages and limitations of these specimen preparations and the specific preanalytic requirements for the testing methods will help pathologists to develop optimal strategies to maximize the chances of effectively using these samples for comprehensive diagnostic and relevant biomarker testing.
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Kunimasa K, Hirotsu Y, Amemiya K, Nagakubo Y, Goto T, Miyashita Y, Kakizaki Y, Tsutsui T, Otake S, Kobayashi H, Higuchi R, Inomata K, Kumagai T, Mochizuki H, Nakamura H, Nakatsuka SI, Nishino K, Imamura F, Kumagai T, Oyama T, Omata M. Genome analysis of peeling archival cytology samples detects driver mutations in lung cancer. Cancer Med 2020; 9:4501-4511. [PMID: 32351019 PMCID: PMC7333826 DOI: 10.1002/cam4.3089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTIONS When tumor tissue samples are unavailable to search for actionable driver mutations, archival cytology samples can be useful. We investigate whether archival cytology samples can yield reliable genomic information compared to corresponding formalin-fixed paraffin-embedded (FFPE) tumor samples. PATIENTS AND METHODS Pretreatment class V archival cytology samples with adequate tumor cells were selected from 172 lung cancer patients. The genomic profiles of the primary lung tumors have been analyzed through whole-exome regions of 53 genes. We compared the genomic profiles based on the oncogenicity and variant allele frequency (VAF) between the archival cytology and the corresponding primary tumors. We also analyzed the genomic profiles of serial cytological samples during the treatment of EGFR-TKI. RESULTS A total of 43 patients were analyzed with the paired samples for DNA mutations and other three patients were analyzed for their fusion genes. A total of 672 mutations were detected. Of those, 106 mutations (15.8%) were shared with both samples. Sixty of seventy-seven (77.9%) shared mutations were oncogenic or likely oncogenic mutations with VAF ≧10%. As high as 90% (9/10) actionable driver mutations and ALK and ROS1 fusion genes were successfully detected from archival cytology samples. Sequential analysis revealed the dynamic changes in EGFR-TKI-resistant mutation (EGFR p.T790M) during the course of treatment. CONCLUSION Archival cytology sample with adequate tumor cells can yield genetic information compared to the primary tumors. If tumor tissue samples are unavailable, we can use archival cytology samples to search for actionable driver mutations.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan.,Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuki Nagakubo
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Taichiro Goto
- Department of Surgery, School of Medicine, Keio University, Tokyo, Japan.,Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Sotaro Otake
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hiroaki Kobayashi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Rumi Higuchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Kie Inomata
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Takashi Kumagai
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Harumi Nakamura
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Shin-Ichi Nakatsuka
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Fumio Imamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan.,The University of Tokyo, Tokyo, Japan
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45
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Wu W, Huang Y, Guo J, Xie X, Li H, Cao Z, Wei H, Wu C. Detection and comparison of EGFR mutations from supernatants that contain cell-free DNA and cell pellets from FNA non-small cell lung cancer specimens. Cancer Cytopathol 2020; 128:545-552. [PMID: 32286726 DOI: 10.1002/cncy.22273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) is an important marker for targeted therapy in patients with advanced non-small cell lung cancer (NSCLC). The samples obtained with minimally invasive biopsy techniques are usually small, and this limits their application in tissue subtyping or molecular profiling. The supernatants obtained after centrifugation of fine-needle aspiration (FNA) samples are typically discarded. However, these fractions might contain cell-free DNA that could be tested for EGFR mutations by genotyping methods that are normally used for plasma analysis. METHODS In this study, 214 patients with known or suspected NSCLC who underwent FNA were enrolled. The workflow of the supernatants before molecular detection was as follows. The discarded FNA samples (15 mL) were stored in CytoLyt, a cleaning, fixation solution, and 10 mL of each sample was placed in a preservation solution for separation by low-speed centrifugation. The primary supernatants (8 mL) were then separated by high-speed centrifugation to obtain secondary supernatants. DNA was extracted from the supernatants with QIAamp circulating nucleic acid kits (Qiagen) and circulating DNA kits (AmoyDx), and EGFR mutations were assessed with Super-ARMS EGFR detection kits (AmoyDx). The DNA was then extracted from corresponding cell pellets with tissue DNA kits (AmoyDx), and the EGFR status was analyzed with the amplification refractory mutation system and next-generation sequencing methods. RESULTS All 214 samples yielded an adequate amount of cell-free DNA for EGFR detection. The use of different DNA commercial extraction kits and the DNA contents of tumor cells did not affect the yield of DNA from the supernatants. The external controlled cycle threshold value of the EGFR test was affected by the concentration of the DNA in the supernatants (P < .05). However, the difference in the concentrations of the DNA in the supernatants did not affect the EGFR mutation status. The EGFR-positive rate was 57.5% (123 of 214) in both the supernatants and the pellets from the 214 FNA samples. The concordance between EGFR variants in the supernatants and the corresponding pellets was 97.2%. EGFR mutations were also detected in 3 pellets but not in their corresponding supernatants and in 3 supernatants but not in their corresponding pellets. The supernatants of FNA biopsy samples might represent a new source for gaining information regarding the molecular characteristics of patients for targeted therapy. CONCLUSIONS Discarded supernatants provided an adequate amount of cell-free DNA for EGFR detection, and this means that the pellets can be reserved for additional morphological and molecular analyses or to avoid repeat biopsies. Analyzing the EGFR status in cell supernatants and pellets might improve detection sensitivity and confer benefits to patients.
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Affiliation(s)
- Wei Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yan Huang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Junhong Guo
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Xiaofeng Xie
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Hui Li
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Ziyang Cao
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Haiting Wei
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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Heymann JJ, Yoxtheimer LM, Park HJ, Fernandez EM, Facey KE, Alperstein SA, Tran HV, Baek I, Scognamiglio T, Rennert H, Siddiqui MT, Song W. Preanalytic variables in quality and quantity of nucleic acids extracted from FNA specimens of thyroid gland nodules collected in CytoLyt: Cellularity and storage time. Cancer Cytopathol 2020; 128:656-672. [PMID: 32267620 DOI: 10.1002/cncy.22270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Morphologic and genetic analysis of thyroid nodules may be performed from a single vial. Preanalytic variables that affect nucleic acid extracted from a single vial are evaluated. METHODS Thyroid fine-needle aspiration (FNA) specimens collected in CytoLyt were evaluated. A ThinPrep slide was prepared. Extracted nucleic acids were analyzed using Oncomine Comprehensive Panel, version 2, after Ion AmpliSeq library preparation. A pathologist and a cytotechnologist enumerated specimen cellularity. RESULTS Fifty-six samples were collected from 55 nodules in 53 patients. Bethesda category correlated with cellularity (P = .01), and storage time (median, 43 days; range, 7-77 days) was longer for specimens in categories II and III than for those in categories IV and VI (P = .01). The mean specimen DNA concentration was 4.5 ng/µL (range, 0-23.8 ng/µL), and 25 (45%) had concentrations >3.3 ng/µL. The mean specimen RNA concentration was 4.8 ng/µL (range, 0-42.4 ng/µL), and 31 (55%) had concentrations >1.4 ng/µL. Nucleic acid quantity increased with epithelial cellularity. Storage time weakly correlated with the quantity of extracted DNA, independent of cellularity, but not extracted RNA. Greater proportions of cell-free DNA and lesser proportions of long, intact RNA fragments were extracted from a subset of samples with longer storage time. Among 15 single nucleotide variants, the median mutant allelic fraction was 15.1%. One false-negative result was identified. Five specimens subsequently determined to harbor a genetic alteration failed quality metrics. CONCLUSIONS Cellularity and storage time affect the quantity and quality of nucleic acid extracted from thyroid FNA specimens collected in CytoLyt. Further investigation will serve to quantify the magnitude of such effects and to elucidate other contributing factors.
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Affiliation(s)
- Jonas J Heymann
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Lorene M Yoxtheimer
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Hyeon Jin Park
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Evan M Fernandez
- Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Kirk E Facey
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Susan A Alperstein
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Hung V Tran
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Inji Baek
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Theresa Scognamiglio
- Division of Head and Neck Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Hanna Rennert
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Momin T Siddiqui
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Wei Song
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
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47
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Yang SR, Mooney KL, Libiran P, Jones CD, Joshi R, Lau HD, Stehr H, Berry GJ, Zehnder JL, Long SR, Kong CS, Kunder CA. Targeted deep sequencing of cell-free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology. Cancer Cytopathol 2019; 128:43-56. [PMID: 31751001 DOI: 10.1002/cncy.22205] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/15/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Liquid biopsy using cell-free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored. METHODS We evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture-based next-generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty-one serous effusions from pleural (n = 15), peritoneal (n = 5), and pericardial (n = 1) cavity were analyzed. RESULTS The supernatants provided a median cfDNA concentration of 10.3 ng/µL. Notably, all effusions were sequenced successfully to a median depth >1000×, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin-fixed, paraffin-embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration (P = .5), depth of coverage (P = .6), or allele frequency of pathogenic mutations (P = .7). CONCLUSION cfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kelly L Mooney
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Paolo Libiran
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carol D Jones
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Rohan Joshi
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Hubert D Lau
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Steven R Long
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christina S Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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48
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Roy-Chowdhuri S. Tumor-derived cell-free DNA in body cavity effusion supernatants: A promising alternative for genomic profiling. Cancer Cytopathol 2019; 128:14-16. [PMID: 31750996 DOI: 10.1002/cncy.22206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Sinchita Roy-Chowdhuri
- Division of Pathology and Laboratory Medicine, Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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49
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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: 4.2] [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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50
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Pisapia P, Bellevicine C, Malapelle U, De Luca C, Vigliar E, Troncone G. Bird’s eye view of modern cytopathology: Report from the seventh international Molecular Cytopathology Meeting in Naples, Italy, 2018. Cancer Cytopathol 2019; 127:350-357. [DOI: 10.1002/cncy.22118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health University of Naples Federico II Naples Italy
| | | | - Umberto Malapelle
- Department of Public Health University of Naples Federico II Naples Italy
| | - Caterina De Luca
- Department of Public Health University of Naples Federico II Naples Italy
| | - Elena Vigliar
- Department of Public Health University of Naples Federico II Naples Italy
| | - Giancarlo Troncone
- Department of Public Health University of Naples Federico II Naples Italy
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