1
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Lacoste-Collin L, Decaussin-Petrucci M, Buffet C. [Molecular and other ancillary tests proposed by The Bethesda system for reporting thyroid cytopathology 2023]. Ann Pathol 2024; 44:36-46. [PMID: 37953129 DOI: 10.1016/j.annpat.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023]
Abstract
For the first time the 2023 version of The Bethesda System for Reporting Thyroid Cytology dedicates a whole chapter (chapter 14) to ancillary studies almost exclusively represented by molecular testing. The latest data reported bring some evidence that molecular testing could help to optimize the diagnostic performance of « indeterminate » categories (AUS and NF). Other studies suggest a promising role to guide the management of suspicious of malignancy and malignant categories. Indeed, the recognition of prognostic and predictive biomarkers analyzed on cytological samples, regardless of how it is collected, has progressed thanks to advances in our knowledge of molecular abnormalities of thyroid tumors. The chapter 14 is presented here highlighting the current and emerging roles of « in-house » and commercialized molecular testing as presented by TSBRTC.
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Affiliation(s)
| | - Myriam Decaussin-Petrucci
- Service d'anatomie pathologique, centre hospitalier Lyon Sud, hospices civils de Lyon, EA 3738, université Lyon 1, Lyon, France
| | - Camille Buffet
- Service des pathologies thyroïdiennes et tumorales endocrines, hôpital Pitié-Salpêtrière, AP-HP, Sorbonne université, GRC n(o) 16, GRC tumeurs thyroïdiennes, 75013 Paris, France; Laboratoire d'Imagerie Biomédicale, CNRS, Inserm, 75006 Paris, France
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2
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Xu L, Haitao R, Li Z. Application of Ultrasound Shear Wave Elastography Combined With BRAFV600E Mutation for the Diagnosis of Papillary Thyroid Carcinoma. Ultrasound Q 2023; 39:199-205. [PMID: 37543733 DOI: 10.1097/ruq.0000000000000647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
ABSTRACT This prospective study aimed to investigate the combination of shear wave elastography (SWE) and BRAFV600E mutation testing for the diagnosis of papillary thyroid carcinoma (PTC). One hundred thyroid nodules with an American College of Radiology thyroid imaging reporting and data system classification of 4 or 5 were subjected to SWE measurement, BRAFV600E genotyping, fine-needle aspiration, and surgery. Nonparametric statistical tests were used to compare the differences in the elastic parameters and BRAF genotypes between benign and malignant thyroid nodules of PTC, and receiver operating characteristic curve analysis was conducted to compare the diagnostic efficacy. In addition, the correlations between elastic parameters and BRAFV600E mutation in PTC were analyzed using binary logistic regression. The SWE, BRAFV600E, and their combination exhibited sensitivities of 72.9%, 81.3%, and 85.4%, respectively, and specificities of 66.7%, 90.3%, and 86.5%, respectively, in the diagnosis of PTC ( P < 0.05). The SWE, BRAFV600E, and their combination exhibited sensitivities of 50.0%, 24.1% and 56.3%, respectively, and specificities of 89.7%, 87.5% and 82.8%, respectively, in the diagnosis of central cervical lymph node metastasis ( P < 0.05). The combined use of SWE and BRAFV600E detection had the largest area under the curve, indicating that this combination is more effective in diagnosing PTC and lymph node metastasis in the central region than either method alone. Furthermore, Emax was positively associated with the BRAFV600E genotype. In conclusion, the combination of SWE and BRAFV600E genotype detection can improve the diagnostic efficacy for PTC. Emax can predict the BRAFV600E mutation status.
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Affiliation(s)
- Li Xu
- Department of Ultrasound, Bishan Hospital of Chongqing, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Ran Haitao
- Department of Ultrasound, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhou Li
- Department of Ultrasound, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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3
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Ly A, Balassanian R, Alperstein S, Donnelly A, McGrath C, Sohani AR, Stelow EB, Thrall MJ, Zhang ML, Pitman MB. One procedure-one report: the Re-Imagine Cytopathology Task Force position paper on small tissue biopsy triage in anatomic pathology. J Am Soc Cytopathol 2023; 12:395-406. [PMID: 37270328 DOI: 10.1016/j.jasc.2023.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Endoscopic biopsy procedures increasingly generate multiple tissue samples from multiple sites, and frequently retrieve concurrent cytologic specimens and small core needle biopsies. There is currently lack of consensus in subspecialized practices as to whether cytopathologists or surgical pathologists should review such samples, and whether the pathology findings should be reported together or separately. MATERIALS AND METHODS In December 2021, the American Society of Cytopathology convened the Re-Imagine Cytopathology Task Force to examine various workflows that would facilitate unified pathology reporting of concurrently obtained biopsies and improve clinical care. RESULTS AND CONCLUSIONS This position paper summarizes the key points and highlights the advantages, challenges, and resources available to support the implementation of such workflows that result in "one procedure-one report".
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Affiliation(s)
- Amy Ly
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
| | - Ronald Balassanian
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Susan Alperstein
- Department of Pathology, Weill Cornell Medical College, New York, New York
| | - Amber Donnelly
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska
| | - Cindy McGrath
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aliyah R Sohani
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Edward B Stelow
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Michael J Thrall
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - M Lisa Zhang
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Martha B Pitman
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
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4
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VanderLaan PA, Roy-Chowdhuri S, Griffith CC, Weiss VL, Booth CN. Molecular testing of cytology specimens: overview of assay selection with focus on lung, salivary gland, and thyroid testing. J Am Soc Cytopathol 2022; 11:403-414. [PMID: 36184436 PMCID: PMC10225070 DOI: 10.1016/j.jasc.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022]
Abstract
Ancillary and molecular testing of cytopathology specimens has emerged as a reliable and useful tool to provide diagnostic information and treatment-related biomarker status for the management of cancer patients. The cytology specimens obtained through minimally invasive means have proven suitable testing substrates for a variety of ancillary tests, including immunohistochemistry, fluorescence in situ hybridization, as well as polymerase chain reaction and next generation sequencing molecular techniques. By focusing specifically on the cytology specimen, this review provides an overview of basic testing considerations and assay selection in addition to updates on the ancillary testing of cytologic tumor specimens from the lung, salivary gland, and thyroid.
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Affiliation(s)
- Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Vivian L Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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5
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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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6
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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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7
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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: 0.5] [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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8
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Personalized Diagnosis in Differentiated Thyroid Cancers by Molecular and Functional Imaging Biomarkers: Present and Future. Diagnostics (Basel) 2022; 12:diagnostics12040944. [PMID: 35453992 PMCID: PMC9030409 DOI: 10.3390/diagnostics12040944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Personalized diagnosis can save unnecessary thyroid surgeries, in cases of indeterminate thyroid nodules, when clinicians tend to aggressively treat all these patients. Personalized diagnosis benefits from a combination of imagery and molecular biomarkers, as well as artificial intelligence algorithms, which are used more and more in our timeline. Functional imaging diagnosis such as SPECT, PET, or fused images (SPECT/CT, PET/CT, PET/MRI), is exploited at maximum in thyroid nodules, with a long history in the past and a bright future with many suitable radiotracers that could properly contribute to diagnosing malignancy in thyroid nodules. In this way, patients will be spared surgery complications, and apparently more expensive diagnostic workouts will financially compensate each patient and also the healthcare system. In this review we will summarize essential available diagnostic tools for malignant and benignant thyroid nodules, beginning with functional imaging, molecular analysis, and combinations of these two and other future strategies, including AI or NIS targeted gene therapy for thyroid carcinoma diagnosis and treatment as well.
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9
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Tarabichi M, Demetter P, Craciun L, Maenhaut C, Detours V. Thyroid cancer under the scope of emerging technologies. Mol Cell Endocrinol 2022; 541:111491. [PMID: 34740746 DOI: 10.1016/j.mce.2021.111491] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023]
Abstract
The vast majority of thyroid cancers originate from follicular cells. We outline outstanding issues at each step along the path of cancer patient care, from prevention to post-treatment follow-up and highlight how emerging technologies will help address them in the coming years. Three directions will dominate the coming technological landscape. Genomics will reveal tumoral evolutionary history and shed light on how these cancers arise from the normal epithelium and the genomics alteration driving their progression. Transcriptomics will gain cellular and spatial resolution providing a full account of intra-tumor heterogeneity and opening a window on the microenvironment supporting thyroid tumor growth. Artificial intelligence will set morphological analysis on an objective quantitative ground laying the foundations of a systematic thyroid tumor classification system. It will also integrate into unified representations the molecular and morphological perspectives on thyroid cancer.
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Affiliation(s)
- Maxime Tarabichi
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium.
| | - Pieter Demetter
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Ligia Craciun
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Carine Maenhaut
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium.
| | - Vincent Detours
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium.
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10
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Gokozan HN, Dilcher TL, Alperstein SA, Qiu Y, Mostyka M, Scognamiglio T, Solomon JP, Song W, Rennert H, Beg S, Stern E, Goyal A, Siddiqui MT, Heymann JJ. Combining molecular testing and the Bethesda category III:VI ratio for thyroid fine‐needle aspirates: A quality‐assurance metric for evaluating diagnostic performance in a cytopathology laboratory. Cancer Cytopathol 2021; 130:259-274. [DOI: 10.1002/cncy.22542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023]
Affiliation(s)
- Hamza N. Gokozan
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
- Division of Head and Neck Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Thomas L. Dilcher
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Susan A. Alperstein
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Yuqing Qiu
- Department of Population Health Sciences New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Maria Mostyka
- Division of Head and Neck Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Theresa Scognamiglio
- Division of Head and Neck Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - James P. Solomon
- Clinical Genomics Laboratory 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
| | - Hanna Rennert
- Division of Molecular and Genomic Pathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Shaham Beg
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Evan Stern
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Abha Goyal
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Momin T. Siddiqui
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
| | - Jonas J. Heymann
- Division of Cytopathology New York‐Presbyterian Hospital–Weill Cornell Medical College New York New York
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11
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Agrawal T, Xi L, Navarro W, Raffeld M, Patel SB, Roth MJ, Klubo‐Gwiezdzinska J, Filie AC. An Effective Approach for
BRAF V600E
Mutation Analysis of Routine Thyroid Fine Needle Aspirates. Cytopathology 2021; 33:344-349. [DOI: 10.1111/cyt.13093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/30/2021] [Accepted: 12/22/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Tanupriya Agrawal
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
- Department of Pathology University of Rochester Medical Center Rochester
| | - Liqiang Xi
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Winnifred Navarro
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Mark Raffeld
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Snehal B. Patel
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
- Snehal B. Patel ‐ HeloGenika LLC Dexter
| | - Mark J. Roth
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Joanna Klubo‐Gwiezdzinska
- National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 9000 Rockville Pike Bethesda MD 20892 USA
| | - Armando C. Filie
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
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12
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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: 37] [Impact Index Per Article: 12.3] [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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13
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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: 14] [Impact Index Per Article: 4.7] [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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14
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Akahane T, Kitazono I, Kobayashi Y, Nishida-Kirita Y, Yamaguchi T, Yanazume S, Tabata K, Kobayashi H, Tanimoto A. Direct next-generation sequencing analysis using endometrial liquid-based cytology specimens for rapid cancer genomic profiling. Diagn Cytopathol 2021; 49:1078-1085. [PMID: 34319014 DOI: 10.1002/dc.24841] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Genomic examination of cytology specimens is often performed on cell blocks or conventional smears rather than on liquid-based cytology (LBC) specimens. Since LBC specimens preserve high-quality DNA, cancer genome profiling using next-generation sequencing (NGS) is also attainable from residual LBC specimens. One of the advantages of using LBC specimens for NGS is that it allows direct extraction of DNA from residual specimens, avoiding a sacrifice of smear slides and minimizing genomic profiling processing time. METHODS Endometrial LBC specimens were subjected to NGS analysis to validate the practicality of rapid cancer genomic profiling in a pathology laboratory. The extracted DNA was subjected to NGS using a customized cancer gene panel comprising 56 genes and 17 microsatellite regions. The workflow strategy was defined, and the processing time estimated for specimen sampling, cell counting, NGS run, and genome profiling. RESULTS NGS analysis of most LBC specimens revealed somatic mutations, tumor mutation burden, and microsatellite instability, which were almost identical to those obtained from formalin-fixed paraffin-embedded tissues. The processing time for direct NGS analysis and cancer genomic profiling of the residual LBC specimens was approximately 5 days. CONCLUSION The residual LBC specimens collected using endometrial cytology were verified to carry a high tumor fraction for NGS analysis and could serve as an alternate source for rapid molecular classification and diagnosis of endometrial cancers, as a routine process in a pathology laboratory.
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Affiliation(s)
- 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, Japan
| | - Ikumi Kitazono
- Unit of Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Yusuke Kobayashi
- Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | | | - Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Shintaro Yanazume
- Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroaki Kobayashi
- Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 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, Japan.,Unit of Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
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15
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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: 2.3] [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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16
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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: 2] [Impact Index Per Article: 0.7] [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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17
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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: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [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 Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- 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
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- 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
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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18
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Sgariglia R, Nacchio M, Migliatico I, Vigliar E, Malapelle U, Pisapia P, De Luca C, Iaccarino A, Salvatore D, Masone S, Troncone G, Bellevicine C. Moving towards a local testing solution for undetermined thyroid fine-needle aspirates: validation of a novel custom DNA-based NGS panel. J Clin Pathol 2021; 75:465-471. [PMID: 33789920 DOI: 10.1136/jclinpath-2021-207429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 01/04/2023]
Abstract
AIMS In thyroid cytopathology, the undetermined diagnostic categories still pose diagnostic challenges. Although next-generation sequencing (NGS) is a promising technique for the molecular testing of thyroid fine-needle aspiration (FNA) specimens, access to such technology can be difficult because of its prohibitive cost and lack of reimbursement in countries with universal health coverage. To overcome these issues, we developed and validated a novel custom NGS panel, Nexthyro, specifically designed to target 264 clinically relevant mutations involved in thyroid tumourigenesis. Moreover, in this study, we compared its analytical performance with that of our previous molecular testing strategy. METHODS The panel, which includes 15 genes (BRAF, EIF1AX, GNAS, HRAS, IDH1, KRAS, NF2, NRAS, PIK3CA, PPM1D, PTEN, RET, DICER1, CHEK2, TERT promoter), was validated with a cell-line derived reference standard and 72 FNA archival samples previously tested with the 7-gene test. RESULTS Nexthyro yielded 100% specificity and detected mutant alleles at levels as low as 2%. Moreover, in 5/72 (7%) FNAs, it detected more clinically relevant mutations in BRAF and RAS genes compared with the 7-gene test. Nexthyro also revealed better postsequencing metrics than the previously adopted commercial 'generic' NGS panel. CONCLUSION Our comparative analysis indicates that Nexthyro is a reliable NGS panel. The study also implies that a custom-based solution for routine thyroid FNA is sustainable at the local level, allowing patients with undetermined thyroid nodules affordable access to NGS.
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Affiliation(s)
| | | | | | - Elena Vigliar
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | | | | | | | - Stefania Masone
- Clinical Medicine and Surgery, General Surgery Unit, University of Naples Federico II, Naples, Italy
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19
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Ultrasound-guided Fine Needle Aspiration Cytological Examination of Thyroid Nodules: A Practical Guideline (2019 edition). ADVANCED ULTRASOUND IN DIAGNOSIS AND THERAPY 2021. [DOI: 10.37015/audt.2021.200068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
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20
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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: 9] [Impact Index Per Article: 2.3] [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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21
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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: 32] [Impact Index Per Article: 8.0] [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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22
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Tural S, Yuce M, K Polat A, Tekcan E, Celik BZ, Karabacak U, Kara N. Novel RET Proto-oncogene variants identified in Turkish patients with thyroid carcinoma. Gene 2020; 746:144611. [PMID: 32240776 DOI: 10.1016/j.gene.2020.144611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 12/23/2022]
Abstract
Thyroid cancer is one of the few malignancies whose incidence is increasing in the last decades. Advances in understanding the molecular mechanisms lead to provide opportunity for prevention, effective early identification and targeted therapies for management. A total of 63 patients with participated in this study Genomic DNA samples were obtained from the samples formalin- embedded tissue and peripheral blood. Following polymerase chain reaction amplification of the 6 RET key exons (10, 11, 13, 14, 15, and 16) were applied and PCR products were subjected to next generation DNA sequencing (ABI 3730). Results revealed that; genotype frequencies were for rs1800961 (G > T) , GG 6 (%9.5), GT 17 (%27) TT40 (%63.5) for rs2472732 (G > A), GG31 (%49.2) GA29 (%46) AA3 (%4.8,) for rs1799939, (G > A) GG42 (%66.7) GA19 (%30.2) AA2 (%3.2), for rs1800962, (C > T) CC54 (%85.7) CT9 (%14.3), for rs1800863 (C > G), CC39 (%61.9) CG22 (%34.9) GG2 (%3.2), for rs3026272 (C > G) CC 13 (%20.6) CG 50 (%79.4). Additionally 15 potential novel genetic variants were identified in these key exons. Detailed information was given both known and new detected variants in supplementary table. Genetic variants distribution frequencies and new variants represented in Turkish thyroid cancer patients for RET proto-oncogene and that results would provide contribution to the literature.
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Affiliation(s)
- Sengul Tural
- Ondokuz Mayis University Faculty of Medicine, Department of Medical Biology, Section of Medical Genetics, Samsun, Turkey.
| | - Melek Yuce
- Ondokuz Mayis University Health Services of Vocational School, Samsun, Turkey
| | - Ayfer K Polat
- Ondokuz Mayis University Faculty of Medicine, Department of General Surgery, Samsun, Turkey
| | - Esra Tekcan
- Ondokuz Mayis University Faculty of Medicine, Department of Medical Biology, Section of Medical Genetics, Samsun, Turkey
| | - Betul Z Celik
- Ondokuz Mayis University Faculty of Medicine, Department of Medical Biology, Section of Medical Genetics, Samsun, Turkey
| | - Ufuk Karabacak
- Ondokuz Mayis University Faculty of Medicine, Department of General Surgery, Samsun, Turkey
| | - Nurten Kara
- Ondokuz Mayis University Faculty of Medicine, Department of Medical Biology, Section of Medical Genetics, Samsun, Turkey
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23
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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: 4.3] [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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24
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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: 11] [Impact Index Per Article: 2.8] [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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25
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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: 1.0] [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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26
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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: 1.8] [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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27
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Abstract
Abstract
It is well documented that in the chain from sample to the result in a clinical laboratory, the pre-analytical phase is the weakest and most vulnerable link. This also holds for the use and analysis of extracellular nucleic acids. In this short review, we will summarize and critically evaluate the most important steps of the pre-analytical phase, i.e. the choice of the best control population for the patients to be analyzed, the actual blood draw, the choice of tubes for blood drawing, the impact of delayed processing of blood samples, the best method for getting rid of cells and debris, the choice of matrix, i.e. plasma vs. serum vs. other body fluids, and the impact of long-term storage of cell-free liquids on the outcome. Even if the analysis of cell-free nucleic acids has already become a routine application in the area of non-invasive prenatal screening (NIPS) and in the care of cancer patients (search for resistance mutations in the EGFR gene), there are still many unresolved issues of the pre-analytical phase which need to be urgently tackled.
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Affiliation(s)
- Michael Fleischhacker
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Drontheimer Str. 39 – 40 , 13359 Berlin , Germany
| | - Bernd Schmidt
- DRK Kliniken Berlin Mitte , Klinik für Innere Medizin – Pneumologie und Schlafmedizin , Berlin , Germany
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28
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Trimboli P, Scappaticcio L, Treglia G, Guidobaldi L, Bongiovanni M, Giovanella L. Testing for BRAF (V600E) Mutation in Thyroid Nodules with Fine-Needle Aspiration (FNA) Read as Suspicious for Malignancy (Bethesda V, Thy4, TIR4): a Systematic Review and Meta-analysis. Endocr Pathol 2020; 31:57-66. [PMID: 31811566 DOI: 10.1007/s12022-019-09596-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In patients with thyroid fine-needle aspiration (FNA) report of suspicious for malignancy (SFM), both lobectomy and thyroidectomy might be considered. BRAF mutation analysis could guide towards accurate surgical therapy. The primary outcome was the reliability of BRAF (V600E) in detecting malignancy in nodules with FNA reading of SFM. The secondary outcome was to analyze its positive predictive value (PPV) and negative predictive value (NPV) considering the surgical histology as gold standard. A literature search of online databases was performed in June 2019. BRAF prevalence among thyroid nodules with FNA read as SFM according to the most popular classification systems (i.e., Bethesda V, Thy4, TIR4 category) was searched. The random-effects model was used. Three hundred sixty original articles were identified and 34 were finally included in the study. There were 1428 thyroid nodules with FNA read as SFM and 1287 (90.1%) lesions underwent surgery with a cancer rate 89.6%. The pooled prevalence of BRAF (V600E) mutation among all nodules with SFM cytology was 47% (95% CI = 40 to 54, I2 = 85.5%). Pooled PPV and NPV of BRAF testing were 99% (95% CI, 97-99) and 24% (95% CI, 16-32), respectively. BRAF (V600E) mutation was found in about one in two nodules with thyroid FNA read as SFM, its PPV to detect cancers was excellent, and its NPV was very poor. The routine BRAF testing in FNA read as SFM cannot be recommended. BRAF (V600E) test may be useful to extend surgical approach in selected cases with further suspicious clinical/ultrasound features.
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Affiliation(s)
- Pierpaolo Trimboli
- Department of Nuclear Medicine and Thyroid Centre, Ente Ospedaliero Cantonale, Bellinzona, Switzerland.
| | - Lorenzo Scappaticcio
- Department of Nuclear Medicine and Thyroid Centre, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Unit of Endocrinology and Metabolic Diseases, University of Campania "L. Vanvitelli", Naples, Italy
| | - Giorgio Treglia
- Department of Nuclear Medicine and Thyroid Centre, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Leo Guidobaldi
- Azienda Sanitaria Unità Sanitaria Locale Roma 2, Rome, Italy
| | - Massimo Bongiovanni
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Luca Giovanella
- Department of Nuclear Medicine and Thyroid Centre, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Medical School Zürich, University of Zürich, Zürich, Switzerland
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29
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Ylli D, Patel A, Jensen K, Li ZZ, Mendonca-Torres MC, Costello J, Gomes-Lima CJ, Wartofsky L, Burman KD, Vasko VV. Microfluidic Droplet Digital PCR Is a Powerful Tool for Detection of BRAF and TERT Mutations in Papillary Thyroid Carcinomas. Cancers (Basel) 2019; 11:cancers11121916. [PMID: 31810221 PMCID: PMC6966523 DOI: 10.3390/cancers11121916] [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: 11/11/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/15/2022] Open
Abstract
We examined the utility of microfluidic digital PCR (dPCR) for detection of BRAF and TERT mutations in thyroid tumors. DNA extracted from 100 thyroid tumors (10 follicular adenomas, 10 follicular cancers, 5 medullary cancers, and 75 papillary thyroid cancer (PTC) were used for detection of BRAF and TERT mutations. Digital PCRs were performed using rare mutation SNP genotyping assays on QuantStudio 3D platform. In PTCs, BRAFV600E was detected by dPCR and Sanger sequencing in 42/75 (56%) and in 37/75 (49%), respectively. BRAFV600E was not detected in other tumors. The ratio of mutant/total BRAF alleles varied from 4.7% to 47.5%. These ratios were higher in classical PTCs (27.1%) as compared to follicular variant PTCs (9.4%) p = 0.001. In PTCs with and without metastases, the ratios of mutant/total BRAF alleles were 27.6% and 18.4%, respectively, (p = 0.03). In metastatic lesions percentages of mutant/total BRAF alleles were similar to those detected in primary tumors. TERTC228T and TERTC250T were found in two and one cases, respectively, and these tumors concomitantly harbored BRAFV600E. These tumors exhibited gross extra-thyroidal extension, metastases to lymph nodes, and pulmonary metastases (one case). Our results showed that dPCR allows quantitative assessment of druggable targets in PTCs and could be helpful in a molecular-based stratification of prognosis in patients with thyroid cancer.
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Affiliation(s)
- Dorina Ylli
- Thyroid Cancer Research Center, MedStar Health Research Institute, 100 Irving St NW, Washington, DC 2010, USA; (D.Y.); (C.J.G.-L.); (L.W.); (K.D.B.)
- Division of Endocrinology, Department of Internal Medicine, MedStar Washington Hospital Center, 110 Irving St NW, Washington, DC 2010, USA
- Department of Imaging and Clinical Semeiotic, Faculty of Medicine, University of Medicine Tirana, 371 Dibra St, 1005 Tirana, Albania
| | - Aneeta Patel
- Department of Pediatrics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge, Bethesda, MD 20814, USA; (A.P.); (K.J.); (M.C.M.-T.); (J.C.)
| | - Kirk Jensen
- Department of Pediatrics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge, Bethesda, MD 20814, USA; (A.P.); (K.J.); (M.C.M.-T.); (J.C.)
| | - Zhao-Zhang Li
- Biomedical instrumentation center, Uniformed Services University of the Health Sciences, 4301 Jones Bridge, Bethesda, MD 20814, USA;
| | - Maria Cecilia Mendonca-Torres
- Department of Pediatrics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge, Bethesda, MD 20814, USA; (A.P.); (K.J.); (M.C.M.-T.); (J.C.)
| | - John Costello
- Department of Pediatrics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge, Bethesda, MD 20814, USA; (A.P.); (K.J.); (M.C.M.-T.); (J.C.)
| | - Cristiane Jeyce Gomes-Lima
- Thyroid Cancer Research Center, MedStar Health Research Institute, 100 Irving St NW, Washington, DC 2010, USA; (D.Y.); (C.J.G.-L.); (L.W.); (K.D.B.)
- Division of Endocrinology, Department of Internal Medicine, MedStar Washington Hospital Center, 110 Irving St NW, Washington, DC 2010, USA
| | - Leonard Wartofsky
- Thyroid Cancer Research Center, MedStar Health Research Institute, 100 Irving St NW, Washington, DC 2010, USA; (D.Y.); (C.J.G.-L.); (L.W.); (K.D.B.)
- Division of Endocrinology, Department of Internal Medicine, MedStar Washington Hospital Center, 110 Irving St NW, Washington, DC 2010, USA
| | - Kenneth Dale Burman
- Thyroid Cancer Research Center, MedStar Health Research Institute, 100 Irving St NW, Washington, DC 2010, USA; (D.Y.); (C.J.G.-L.); (L.W.); (K.D.B.)
- Division of Endocrinology, Department of Internal Medicine, MedStar Washington Hospital Center, 110 Irving St NW, Washington, DC 2010, USA
| | - Vasyl V. Vasko
- Department of Pediatrics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge, Bethesda, MD 20814, USA; (A.P.); (K.J.); (M.C.M.-T.); (J.C.)
- Correspondence: ; Tel.: +1-(240)-423-1051
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30
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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: 14] [Impact Index Per Article: 2.8] [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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31
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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: 4] [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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32
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Nishino M. Sustainable cytopathology in the precision medicine era: Exploring new sources for molecular testing in thyroid cytology specimens. Cancer Cytopathol 2019; 127:143-145. [PMID: 30707506 DOI: 10.1002/cncy.22107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Michiya Nishino
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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