1
|
Beg S, Xu K, Solomon JP, Alperstein SA, Siddiqui MT. Impact of serous fluid volume on next-generation sequencing: a significant step forward for optimization of serous fluid sample collection. J Am Soc Cytopathol 2024:S2213-2945(24)00059-0. [PMID: 39068145 DOI: 10.1016/j.jasc.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024]
Abstract
Current literature lacks data regarding the influence of serous fluid volume (SFV) on next-generation sequencing (NGS) performed on malignant cases. In this study, we highlight the impact of SFV and other parameters influencing the outcome of NGS analysis. We evaluated 827 samples of serous fluids from 607 patients. Of these, 72 samples underwent NGS analysis. Effusion volume, tumor cellularity, DNA, and RNA quality metrics, as well as clinicopathologic and molecular data were evaluated. Pleural fluid accounted for 56.3% of the fluid samples collected. The most common primary tumor site was gastrointestinal/pancreatobiliary, adenocarcinoma was the most common histologic type. Overall mean volume was 293 mL. The mean Qubit DNA of the 72 effusion samples that underwent NGS analysis was 14.3 ng/μL and mean Qubit RNA was 28.2 ng/μL. The mean Qubit DNA concentration increases in SFV up to 100 mL only. No correlation exists between SFV and mean tumor cellularity. In addition, 74.6% (50 of 67) of sequenced samples showed oncogenic drivers; KRAS was the most common driver followed by EGFR. Three cases displayed ALK fusions, and 1 case displayed NTRK1 fusion. The DNA yield is higher in SFV of 100 mL as a cutoff. Beyond 100 mL, there is no impact of SFV on DNA yield. SFV does not impact RNA yield and mean tumor cellularity. Effusion samples should be submitted for molecular testing despite low tumor cellularity. Our results as a pilot study are important in optimization of SFV for both diagnosis as well as NGS analysis for improving management.
Collapse
Affiliation(s)
- Shaham Beg
- Department of Pathology and Laboratory Medicine, New York Presbyterian-Weill Cornell Medicine, New York, New York
| | - Kemin Xu
- Department of Pathology and Laboratory Medicine, New York Presbyterian-Weill Cornell Medicine, New York, New York
| | - James P Solomon
- Department of Pathology and Laboratory Medicine, New York Presbyterian-Weill Cornell Medicine, New York, New York
| | - Susan A Alperstein
- Department of Pathology and Laboratory Medicine, New York Presbyterian-Weill Cornell Medicine, New York, New York
| | - Momin T Siddiqui
- Department of Pathology and Laboratory Medicine, New York Presbyterian-Weill Cornell Medicine, New York, New York.
| |
Collapse
|
2
|
Ehinger M, Béné MC. Morphology and multiparameter flow cytometry combined for integrated lymphoma diagnosis on small volume samples: possibilities and limitations. Virchows Arch 2024:10.1007/s00428-024-03819-3. [PMID: 38805049 DOI: 10.1007/s00428-024-03819-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
Abstract
The diagnosis of lymphoma relies mainly on clinical examination and laboratory explorations. Among the latter, morphological and immunohistochemical analysis of a tissue biopsy are the cornerstones for proper identification and classification of the disease. In lymphoma with blood and/or bone marrow involvement, multiparameter flow cytometry is useful. This technique can also be applied to fresh cells released from a biopsy sample. For full comprehension of lymphomas, surgical biopsies are best and indeed recommended by the hematopathological community. Currently, however, there is a global trend towards less invasive procedures, resulting in smaller samples such as core needle biopsies or fine needle aspirations which can make the diagnosis quite challenging. In this review, the possibilities and limitations to make an accurate lymphoma diagnosis on such small volume material are presented. After recalling the major steps of lymphoma diagnosis, the respective value of histology, cytology, and flow cytometry is discussed, including handling of small specimens. The benefits of an integrated approach are then evoked, followed by discussion about which attitude to adopt in different contexts. Perhaps contrary to the prevailing view among many pathologists, a full diagnosis on small volume material, combined with relevant ancillary techniques, is often possible and indeed supported by recent literature. A glimpse at future evolutions, notably the merit of artificial intelligence tools, is finally provided. All in all, this document aims at providing pathologists with an overview of diagnostic possibilities in lymphoma patients when confronted with small volume material such as core needle biopsies or fine needle aspirations.
Collapse
Affiliation(s)
- Mats Ehinger
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden.
| | - Marie C Béné
- Faculty of Medicine, Nantes University, Nantes, France
| |
Collapse
|
3
|
Sopić M, Devaux Y, de Gonzalo-Calvo D. Navigating the path of reproducibility in microRNA-based biomarker research with ring trials. Clin Chem Lab Med 2024; 0:cclm-2024-0531. [PMID: 38747410 DOI: 10.1515/cclm-2024-0531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 05/05/2024] [Indexed: 06/06/2024]
Abstract
The development of microRNA (miRNA)-based biomarkers has gained significant attention due to their potential diagnostic, prognostic and therapeutic applications. However, the reproducibility of miRNA biomarker research faces unique challenges, primarily due to the influence of pre-analytical and analytical factors. The absence of standardized procedures contributes to inconsistencies across studies, alongside challenges in reference gene selection, data analysis methods and miRNA profiling platforms. Inter-laboratory comparison trials, or ring trials, offer a strategic approach to address technical and biological variability in miRNA biomarker studies. These trials promote standardization, identify sources of variability and strengthen the correlation between miRNAs and clinical outcomes. Despite their underutilization in miRNA biomarker research, ring trials represent a valuable tool for enhancing reproducibility and expediting the translation of miRNA-based biomarkers into clinical applications.
Collapse
Affiliation(s)
- Miron Sopić
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - David de Gonzalo-Calvo
- 219654 Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida , Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| |
Collapse
|
4
|
Nannini M, Repaci A, Nigro MC, Colapinto A, Vicennati V, Maloberti T, Gruppioni E, Altimari A, Solaroli E, Lodi Rizzini E, Monari F, De Leo A, Damiani S, Pagotto U, Pantaleo MA, de Biase D, Tallini G. Clinical relevance of gene mutations and rearrangements in advanced differentiated thyroid cancer. ESMO Open 2023; 8:102039. [PMID: 37879236 PMCID: PMC10774965 DOI: 10.1016/j.esmoop.2023.102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Tumor genotyping is becoming crucial to optimize the clinical management of patients with advanced differentiated thyroid cancer (DTC); however, its implementation in clinical practice remains undefined. We herein report our single-center experience on molecular advanced DTC testing by next-generation sequencing approach, to better define how and when tumor genotyping can assist clinical decision making. MATERIALS AND METHODS We retrospectively collected data on all adult patients with advanced DTC who received molecular profiling at the IRCSS Sant'Orsola-Malpighi Hospital from 2008 to 2022. The genetic alterations were correlated with radioactive iodide refractory (RAI-R), RAI uptake/disease status, and time to RAI resistance (TTRR) development. RESULTS A significant correlation was found between RAI-R development and genetic alterations (P = 0.0001). About 48.7% of RAI-R cases were positive for TERT/TP53 mutations (as both a single event and comutations with other driver gene alterations, such as BRAF mutations, RAS mutations, or gene fusions), while the great majority of RAI-sensitive cases carried gene fusions (41.9%) or were wild type (WT; 41.9%). RAI uptake/disease status and time to TTRR were significantly associated with genetic alterations (P = 0.0001). In particular, DTC with TERT/TP53 mutations as a single event or as comutations displayed a shorter median TTRR of 35.4 months (range 15.0-55.8 months), in comparison to the other molecular subgroups. TERT/TP53 mutations as a single event or as comutations remained independently associated with RAI-R after Cox multivariate analysis (hazard ratio 4.14, 95% CI 1.51-11.32; P = 0.006). CONCLUSIONS Routine testing for genetic alterations should be included as part of the clinical workup, for identifying both the subset of more aggressive tumors and the subset of tumors harboring actionable gene fusions, thus ensuring the appropriate management for all patients with advanced DTC.
Collapse
Affiliation(s)
- M Nannini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna; Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna.
| | - A Repaci
- Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - M C Nigro
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna
| | - A Colapinto
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna
| | - V Vicennati
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna; Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - T Maloberti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna
| | - E Gruppioni
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - A Altimari
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - E Solaroli
- Endocrinology Unit-Azienda USL di Bologna, Bologna
| | - E Lodi Rizzini
- Division of Radiation Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Sant'Orsola-Malpighi Hospital, Bologna
| | - F Monari
- Division of Radiation Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Sant'Orsola-Malpighi Hospital, Bologna
| | - A De Leo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna
| | - S Damiani
- Pathology Unit, Department of Pathology, Bellaria & Maggiore Hospital, AUSL di Bologna, Bologna
| | - U Pagotto
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna; Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - M A Pantaleo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna; Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| | - D de Biase
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna; Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - G Tallini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna; Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna
| |
Collapse
|
5
|
Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathol 2023; 131:289-299. [PMID: 36650408 PMCID: PMC10614161 DOI: 10.1002/cncy.22679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Rather than surgical resection, cytologic specimens are often used as first-line clinical diagnostic procedures due to higher safety, speed, and cost-effectiveness. Archival diagnostic cytology slides containing cancer can be equivalent to tissue biopsies for DNA mutation testing, but the accuracy of transcriptomic profiling by RNA sequencing (RNA-seq) is less understood. METHODS This study compares the results from whole transcriptome RNA-seq and a targeted RNA-seq assay of stained cytology smears (CS) versus matched tumor tissue samples preserved fresh-frozen (FF) and processed as formalin-fixed paraffin-embedded (FFPE) sections. Cellular cytology scrapes from all 11 breast cancers were fixed and stained using three common protocols: Carnoy's (CS_C) or 95% ethanol (CS_E) fixation and then Papanicolaou stain or air-dried then methanol fixation and DiffQuik stain (CS_DQ). Agreement between samples was assessed using Lin's concordance correlation coefficient. RESULTS Library yield for CS_DQ was too low, therefore it was not sequenced. The distributions of concordance correlation coefficient of gene expression levels in comparison to FF were comparable between CS_C and CS_E, but expression of genes enriched in stroma was lower in cytosmear samples than in FF or FFPE. Six signatures showed similar concordance to FF for all methods and two were slightly worse in CS_C and CS_E. Genomic signatures were highly concordant using targeted RNA-seq. The allele fraction of selected mutations calculated on cytosmear specimens was highly correlated with FF tissues using both RNA-seq methods. CONCLUSION RNA can be reliably extracted from cytology smears and is suitable for transcriptome profiling or mutation detection, except for signatures of tumor stroma.
Collapse
Affiliation(s)
- Michal Marczyk
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Chunxiao Fu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rosanna Lau
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lili Du
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexander J. Trevarton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bruno V. Sinn
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Rebekah E. Gould
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lajos Pusztai
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
| | - Christos Hatzis
- Yale Cancer Center Yale School of Medicine, New Haven, Connecticut, USA
| | - William Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
6
|
Bironzo P, Pepe F, Russo G, Pisapia P, Gragnano G, Aquino G, Bessi S, Buglioni S, Bartoccini F, Ferrero G, Bresciani MA, Francia di Celle P, Sibona F, Giusti A, Movilia A, Farioli RM, Santoro A, Salemi D, Scarpino S, Galafate D, Tommasi S, Lacalamita R, Seminati D, Sajjadi E, Novello S, Pagni F, Troncone G, Malapelle U. An Italian Multicenter Perspective Harmonization Trial for the Assessment of MET Exon 14 Skipping Mutations in Standard Reference Samples. Diagnostics (Basel) 2023; 13:diagnostics13040629. [PMID: 36832117 PMCID: PMC9955861 DOI: 10.3390/diagnostics13040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/24/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Lung cancer remains the leading cause of cancer deaths worldwide. International societies have promoted the molecular analysis of MET proto-oncogene, receptor tyrosine kinase (MET) exon 14 skipping for the clinical stratification of non-small cell lung cancer (NSCLC) patients. Different technical approaches are available to detect MET exon 14 skipping in routine practice. Here, the technical performance and reproducibility of testing strategies for MET exon 14 skipping carried out in various centers were evaluated. In this retrospective study, each institution received a set (n = 10) of a customized artificial formalin-fixed paraffin-embedded (FFPE) cell line (Custom METex14 skipping FFPE block) that harbored the MET exon 14 skipping mutation (Seracare Life Sciences, Milford, MA, USA), which was previously validated by the Predictive Molecular Pathology Laboratory at the University of Naples Federico II. Each participating institution managed the reference slides according to their internal routine workflow. MET exon 14 skipping was successfully detected by all participating institutions. Molecular analysis highlighted a median Cq cut off of 29.3 (ranging from 27.1 to 30.7) and 2514 (ranging from 160 to 7526) read counts for real-time polymerase chain reaction (RT-PCR) and NGS-based analyses, respectively. Artificial reference slides were a valid tool to harmonize technical workflows in the evaluation of MET exon 14 skipping molecular alterations in routine practice.
Collapse
Affiliation(s)
- Paolo Bironzo
- Department of Oncology, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Francesco Pepe
- Department of Public Health, University Federico II of Naples, 80131 Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University Federico II of Naples, 80131 Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University Federico II of Naples, 80131 Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University Federico II of Naples, 80131 Naples, Italy
| | - Gabriella Aquino
- Department of Pulmonary Oncology, AORN Dei Colli Monaldi, 80131 Naples, Italy
| | - Silvia Bessi
- Departmental Structure of Oncological Molecular Pathology, Oncological Department Azienda USL Toscana Centro, S. Stefano Hospital, 59100 Prato, Italy
| | - Simonetta Buglioni
- Pathology Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Federico Bartoccini
- Pathology Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | | | | | - Paola Francia di Celle
- Molecular Pathology, AOU Città della Salute e della Scienza di Torino-Presidio Ospedaliero Molinette, 10126 Turin, Italy
| | - Francesca Sibona
- Molecular Pathology, AOU Città della Salute e della Scienza di Torino-Presidio Ospedaliero Molinette, 10126 Turin, Italy
| | - Andrea Giusti
- ASL Toscana Nord Ovest, Pathology Unit, Centro Polispecialistico “Achille Sicari”, 54033 Carrara, Italy
| | - Alessandra Movilia
- Department of Pathology, ASST Ovest Milanese, Ospedale di Legnano, 20025 Legnano, Italy
| | | | - Alessandra Santoro
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy
| | - Domenico Salemi
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy
| | - Stefania Scarpino
- Pathology Unit, Department of Clinical and Molecular Medicine, St. Andrea University Hospital, University of Rome La Sapienza, 00189 Rome, Italy
| | - Dino Galafate
- Pathology Unit, Department of Clinical and Molecular Medicine, St. Andrea University Hospital, University of Rome La Sapienza, 00189 Rome, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy
| | - Davide Seminati
- Department of Surgery and Translational Medicine, Section of Pathology, Università degli Studi di Mila-no-Bicocca, 20126 Milan, Italy
| | - Elham Sajjadi
- Department of Oncology and Hemato-Oncology, University of Milan, 20136 Milan, Italy
| | - Silvia Novello
- Department of Oncology, S. Luigi Gonzaga Hospital, University of Turin, 10043 Orbassano, Italy
| | - Fabio Pagni
- Department of Surgery and Translational Medicine, Section of Pathology, Università degli Studi di Mila-no-Bicocca, 20126 Milan, Italy
| | - Giancarlo Troncone
- Department of Public Health, University Federico II of Naples, 80131 Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, 80131 Naples, Italy
- Correspondence:
| |
Collapse
|
7
|
Sura GH, Tran K, Fu C, Du L, Marczyk M, Martinez Y, Tinnirello AA, Gould RE, Lau R, Symmans WF. Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing. J Am Soc Cytopathol 2023; 12:10-19. [PMID: 36270909 PMCID: PMC10644714 DOI: 10.1016/j.jasc.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION RNA sequencing (RNAseq) analysis is emerging as a clinical research or diagnostic approach for cytologic samples, but there is need for formal comparison of different sample preparation methods in the cytology laboratory to identify which pre-analytic methods could provide alternatives to formalin-fixed paraffin-embedded (FFPE) sections. MATERIALS AND METHODS We prepared 13 malignant effusions (metastatic estrogen receptor-positive breast cancer) in the cytology laboratory using 6 routine cytologic methods: FFPE cell block, Carnoy's solution, 95% ethanol (EtOH), air-dried and Diff-Quik, ThinPrep, and SurePath preparations. Measurements of RNA quality, expression of 2 multigene expression signatures, molecular subtype, and 4 common activating mutation sites in each preparation were compared with fresh frozen (FF) cell pellet in RNA preservative using distribution of fragment length and concordance correlation coefficient (CCC). RESULTS The fraction of RNA fragments measuring 200 bases or more (DV200) were 24% higher from cytospins fixed in Carnoy's solution or 95% EtOH than DV200 from FFPE cell blocks. SurePath samples failed RNAseq quality control. There was high concordance of gene expression measurements with FF samples using cytospins fixed in Carnoy's solution, 95% EtOH, Diff-Quik (CCC = 0.829, 0.812, 0.760, respectively), or ThinPrep (CCC = 0.736), but lower using FFPE cell block (CCC = 0.564). The proportion of mutant transcripts was concordant between FF and any cytologic preparation methods. CONCLUSIONS Cytospin preparations fixed with Carnoy's or 95% ETOH then Papanicolaou stained produced RNAseq results that were equivalent to FF samples and superior to FFPE cell block sections.
Collapse
Affiliation(s)
- Gloria H Sura
- Department of Pathology and Genomic Medicine, Houston Methodist, Houston, Texas
| | - Kevin Tran
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunxiao Fu
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lili Du
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michał Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland; Yale Cancer Center, Yale University, New Haven, Connecticut
| | - Yadira Martinez
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Agata A Tinnirello
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rebekah E Gould
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rosanna Lau
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - W Fraser Symmans
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| |
Collapse
|
8
|
Lozano MD, Benito A, Labiano T, Pijuan L, Tejerina E, Torres H, Gómez-Román J. Recommendations for optimizing the use of cytology in the diagnosis and management of patients with lung cancer. REVISTA ESPANOLA DE PATOLOGIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ANATOMIA PATOLOGICA Y DE LA SOCIEDAD ESPANOLA DE CITOLOGIA 2023; 56:58-68. [PMID: 36599601 DOI: 10.1016/j.patol.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/01/2022] [Indexed: 01/31/2023]
Abstract
Non-small cell lung cancer (NSCLC) is one of the oncological entities with the greatest evolution in molecular diagnosis due to the large number of diagnostic biomarkers and new treatments approved by international regulatory agencies. An accurate, early diagnosis using the least amount of tissue is the goal for the establishing and developing precision medicine for these patients. Rapid on-site evaluation (ROSE) provides cytological samples of optimal quantity and quality for a complete diagnosis of NSCLC. The usefulness of cytological samples has been demonstrated, not only for massive parallel sequencing but also for the quantification of the expression of programmed death-ligand 1 (PD-L1) and tumour mutational burden (TMB). Pre-analytical, analytical, and post-analytical recommendations are made for the management and appropriate use of cytological samples in order to obtain all the information necessary for the diagnosis and treatment of patients with NSCLC according to current quality parameters.
Collapse
Affiliation(s)
| | | | | | - Lara Pijuan
- Hospital Universitari Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Eva Tejerina
- Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Héctor Torres
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Javier Gómez-Román
- Hospital Universitario Marqués de Valdecilla, Universidad de Cantabria, IDIVAL, Santander, Spain
| |
Collapse
|
9
|
Malapelle U, Pepe F, Pisapia P, Altimari A, Bellevicine C, Brunnström H, Bruno R, Büttner R, Cirnes L, De Andrea CE, de Biase D, Dumur CI, Ericson Lindquist K, Fontanini G, Gautiero E, Gentien D, Hofman P, Hofman V, Iaccarino A, Lozano MD, Mayo-de-Las-Casas C, Merkelbach-Bruse S, Pagni F, Roman R, Schmitt FC, Siemanowski J, Roy-Chowdhuri S, Tallini G, Tresserra F, Vander Borght S, Vielh P, Vigliar E, Vita GAC, Weynand B, Rosell R, Molina Vila MA, Troncone G. Reference standards for gene fusion molecular assays on cytological samples: an international validation study. J Clin Pathol 2023; 76:47-52. [PMID: 34429353 DOI: 10.1136/jclinpath-2021-207825] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/06/2021] [Indexed: 02/05/2023]
Abstract
AIMS Gene fusions assays are key for personalised treatments of advanced human cancers. Their implementation on cytological material requires a preliminary validation that may make use of cell line slides mimicking cytological samples. In this international multi-institutional study, gene fusion reference standards were developed and validated. METHODS Cell lines harbouring EML4(13)-ALK(20) and SLC34A2(4)-ROS1(32) gene fusions were adopted to prepare reference standards. Eight laboratories (five adopting amplicon-based and three hybridisation-based platforms) received, at different dilution points two sets of slides (slide A 50.0%, slide B 25.0%, slide C 12.5% and slide D wild type) stained by Papanicolaou (Pap) and May Grunwald Giemsa (MGG). Analysis was carried out on a total of 64 slides. RESULTS Four (50.0%) out of eight laboratories reported results on all slides and dilution points. While 12 (37.5%) out of 32 MGG slides were inadequate, 27 (84.4%) out of 32 Pap slides produced libraries adequate for variant calling. The laboratories using hybridisation-based platforms showed the highest rate of inadequate results (13/24 slides, 54.2%). Conversely, only 10.0% (4/40 slides) of inadequate results were reported by laboratories adopting amplicon-based platforms. CONCLUSIONS Reference standards in cytological format yield better results when Pap staining and processed by amplicon-based assays. Further investigation is required to optimise these standards for MGG stained cells and for hybridisation-based approaches.
Collapse
Affiliation(s)
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Annalisa Altimari
- Molecular Pathology, University of Bologna Hospital of Bologna Sant'Orsola-Malpighi Polyclinic, Bologna, Italy
| | | | - Hans Brunnström
- Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden
| | - Rossella Bruno
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | | | | | | | - Dario de Biase
- Pharmacy and Biotechnology (FaBiT), Molecular Pathology Laboratory, University of Bologna, Bologna, Italy
| | | | | | - Gabriella Fontanini
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | | | - David Gentien
- Translational Research Department, Genomics Platform, Curie Institute Hospital Group, Paris, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Centre Nice Pasteur Hospital, Nice, France
| | - Veronique Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Centre Nice Pasteur Hospital, Nice, France
| | | | | | | | | | - Fabio Pagni
- Medicine and Surgery, San Gerardo Hospital, Monza, Italy
| | - Ruth Roman
- Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | | | - Sinchita Roy-Chowdhuri
- Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Giovanni Tallini
- Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Sara Vander Borght
- Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Philippe Vielh
- Pathology, Medipath and American Hospital of Paris, Paris, France
| | - Elena Vigliar
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Birgit Weynand
- Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Rafael Rosell
- Oncology, Hospital Municipal de Badalona, Barcelona, Spain
| | | | | |
Collapse
|
10
|
Tischler V. [Molecular cytology: Opportunities and challenges]. PATHOLOGIE (HEIDELBERG, GERMANY) 2022; 43:130-133. [PMID: 36469117 DOI: 10.1007/s00292-022-01155-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Predictive marker (re-)analysis of tumor material can be a real obstacle in several tumor entities, like non-small cell lung cancer (NSCLC), due to difficult anatomic conditions and small biopsy samples. As reported in the literature, cytological samples comprise excellent starting material for predictive marker analysis like fluorescence in situ hybridization and next generation sequencing. As for formalin-fixed paraffin-embedded tissue samples, rigorous quality control and standardized laboratory operating procedures are mandatory. Further advantages of cytological specimens are the rapid and straightforward inspection of representativeness, for example by rapid on-site evaluation (ROSE). Another striking advantage is that the fresh cellular material from smears and serous cavity fluids can be used for the generation of two- and three-dimensional cell culture models. Hereby, in addition to the conventional biomarker testing, complex complementary functional genomic assays can also be applied, for example, to assess the effects of multiple variants in one sample and unknown variants of tumor driver genes and tumor suppressor genes. This information may provide additional vulnerabilities of the tumor to be considered for the therapy decision, for example in the molecular tumor board.
Collapse
Affiliation(s)
- Verena Tischler
- Institut für Pathologie, Universitätsklinikum Bonn, Venusberg-Campus 1, 53127, Bonn, Deutschland.
| |
Collapse
|
11
|
Malapelle U, Pepe F, Pisapia P, Sgariglia R, Nacchio M, Barberis M, Bilh M, Bubendorf L, Büttner R, Cabibi D, Castiglia M, De Andrea CE, de Biase D, Dumur CI, Fontanini G, Freire J, Gristina V, Hofman P, Ilie M, Lozano MD, Merkelbach-Bruse S, Pappesch R, Pelusi N, Roma G, Russo A, Savic S, Siemanowski J, Tallini G, Tischler V, Vander Borght S, Weynand B, Xu T, Troncone G. TargetPlex FFPE-Direct DNA Library Preparation Kit for SiRe NGS panel: an international performance evaluation study. J Clin Pathol 2022; 75:416-421. [PMID: 33766954 DOI: 10.1136/jclinpath-2021-207450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 02/05/2023]
Abstract
AIM Next generation sequencing (NGS) represents a key diagnostic tool to identify clinically relevant gene alterations for treatment-decision making in cancer care. However, the complex manual workflow required for NGS has limited its implementation in routine clinical practice. In this worldwide study, we validated the clinical performance of the TargetPlex FFPE-Direct DNA Library Preparation Kit for NGS analysis. Impressively, this new assay obviates the need for separate, labour intensive and time-consuming pre-analytical steps of DNA extraction, purification and isolation from formalin-fixed paraffin embedded (FFPE) specimens in the NGS workflow. METHODS The TargetPlex FFPE-Direct DNA Library Preparation Kit, which enables NGS analysis directly from FFPE, was specifically developed for this study by TargetPlex Genomics Pleasanton, California. Eleven institutions agreed to take part in the study coordinated by the Molecular Cytopathology Meeting Group (University of Naples Federico II, Naples, Italy). All participating institutions received a specific Library Preparation Kit to test eight FFPE samples previously assessed with standard protocols. The analytical parameters and mutations detected in each sample were then compared with those previously obtained with standard protocols. RESULTS Overall, 92.8% of the samples were successfully analysed with the TargetPlex FFPE-Direct DNA Library Preparation Kit on Thermo Fisher Scientific and Illumina platforms. Altogether, in comparison with the standard workflow, the TargetPlex FFPE-Direct DNA Library Preparation Kit was able to detect 90.5% of the variants. CONCLUSION The TargetPlex FFPE-Direct DNA Library Preparation Kit combined with the SiRe panel constitutes a convenient, practical and robust cost-saving solution for FFPE NGS analysis in routine practice.
Collapse
Affiliation(s)
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | | | - Massimo Barberis
- Clinic Unit of Histopathology and Molecular Diagnostics, Istituto Europeo di Oncologia, Milano, Italy
| | - Michel Bilh
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Reinhard Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Daniela Cabibi
- Health Promotion Sciences, Maternal and Infantile Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Marta Castiglia
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Dario de Biase
- Medicine (DIMES)a Hospital, Anatomic Pathology Unit, University of Bologna, Bologna, Italy
| | - Catherine I Dumur
- Molecular Diagnostic Department, Aurora Diagnostics, Jacksonville, Florida, USA
| | - Gabriella Fontanini
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Javier Freire
- Pathology, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Valerio Gristina
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Marius Ilie
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Nice, France
| | - Maria Dolores Lozano
- Pathology, Universidad de Navarra-Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Roberto Pappesch
- Department of Pathology, University of Cologne, Cologne, Germany
| | | | - Gianluca Roma
- R&D Department, TargetPlex Genomics, Belmont, California, USA
| | - Antonio Russo
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Spasenija Savic
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | | | | | | | - Sara Vander Borght
- Department of Pathology, Katholieke Universiteit Leuven UZ Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Pathology, Katholieke Universiteit Leuven UZ Leuven, Leuven, Belgium
| | - Tom Xu
- R&D Department, SenseCare Medicals, Inc, Pleasanton, California, USA
| | | |
Collapse
|
12
|
Abstract
For molecular diagnostics of lung cancer samples, often only a small amount of material is available. The ever-increasing number of biomarker testing is in contrast to the amount of material obtained. In that case, cytological specimens, such as serous effusion samples, are one possible option. Effusion samples were prepared as sediment smears or cytospins or as a cell block if needed. Suitable tumor cells areas were marked by a cytopathologist and used for molecular diagnostics, including fast track analysis, parallel sequencing, and/or fluorescence in situ hybridization. In 62 cases of malignant effusion with cells of pulmonary adenocarcinoma, molecular diagnostics were carried out. A fast-track result with the high-resolution melting method for hotspot mutation of KRAS Exon 2 and EGFR exon 21 and fragment length analysis of EGFR exon 19 was available for 43 out of 47 samples (92%). Parallel sequencing was successful for 56 out of 60 samples (93.3%). In the same period, 108 FISH analyses were performed for MET amplification, followed by ROS1, RET, and ALK translocation analysis. If only a limited amount of tissue/biopsy is available, a malignant effusion is advisable to perform on the molecular diagnostics with a high success rate.
Collapse
|
13
|
Dolinar A, Grubelnik G, Srebotnik-Kirbiš I, Strojan Fležar M, Žlajpah M. Optimization of pre-analytical and analytical steps for DNA and RNA analysis of fresh cytology samples. Cancer Med 2022; 11:4021-4032. [PMID: 35403378 DOI: 10.1002/cam4.4728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/16/2022] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Different cytology preparations can be used for molecular diagnostics, however the influence of pre-analytical and analytical steps on the results are not yet well defined. We aimed to determine optimal steps for efficient extraction of DNA and RNA from fresh cells for molecular diagnostics. METHODS MCF7 and FaDu human cell lines, were used as a model to determine fresh cells storage conditions (temperature: 25°C, 4°C, -20°C, -80°C; duration: 0 h, 4 h, 12 h, 24 h, 48 h) and optimal nucleic acids extraction method. Besides, the minimal number of total cells and minimal percentage of mutated cells needed for successful extraction of nucleic acids and subsequent determination of present mutation were evaluated. RESULTS Extraction of nucleic acids using spin columns yielded the highest quantity and quality of nucleic acids. Isolation of nucleic acids was feasible in all storage conditions, however higher temperature and longer duration of fresh cells storage were associated with lower quality of isolated nucleic acids and similar quantification cycle of housekeeping genes. Successful molecular testing was feasible with least 104 cells, while specific mutation was detected in as low as 5% of mutated cells. CONCLUSIONS Our cell line model, mimicking fresh cytology samples, showed that quantity of extracted either DNA or RNA declined with higher temperatures and longer duration of storage but regardless of the storage conditions, we successfully detected both housekeeping genes and mutated gene using qPCR.
Collapse
Affiliation(s)
- Ana Dolinar
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Gašper Grubelnik
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Srebotnik-Kirbiš
- Department of cytopathology, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Margareta Strojan Fležar
- Department of cytopathology, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Margareta Žlajpah
- Department of molecular genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
14
|
Sorber L, Claes B, Zwaenepoel K, Van Dorst B, De Winne K, Fransen E, Wener R, Lapperre T, Lardon F, Pauwels P. Evaluation of Cytologic Sample Preparations for Compatibility With Nucleic Acid Analysis. Am J Clin Pathol 2022; 157:293-304. [PMID: 34542583 PMCID: PMC8824667 DOI: 10.1093/ajcp/aqab121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022] Open
Abstract
Objectives In this study, the influence of several key elements of the cytologic sample workflow on DNA and RNA content was evaluated. Methods The A549 cell line, patient-derived organoids, and pleural effusions were used to investigate the effect of (1) several collection media and delayed time to processing; (2) cytology specimens; (3) cytologic staining; and (4) formalin-fixed, paraffin-embedded (FFPE) cell block processing on nucleic acid quality and quantity as determined by fragment analyzer, Qubit analysis (Thermo Fisher Scientific), and quantitative polymerase chain reaction–based analysis on the Idylla platform (Biocartis). Results Alcohol-based collection media (CytoRich Red [Thermo Fisher Scientific] and EtOH95%) displayed high DNA and RNA preservation capacity, while phosphate-buffered saline and, to a lesser extent, formalin were associated with high RNA quality. Cytospin and smear cytology specimens were subject to DNA and RNA loss. Cytologic staining had no further impact on sample quality, hence destaining is not necessary. Both H&E-stained and unstained FFPE sections are compatible with nucleic acid analysis, despite a strong decrease in DNA and RNA quality. Conclusions Although several key elements of the cytologic sample workflow have an influence on DNA and RNA quality and quantity, the selection of these elements is also dependent on the downstream (ancillary) testing methods.
Collapse
Affiliation(s)
- Laure Sorber
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), Wilrijk, Belgium
| | - Bart Claes
- Biocartis NV, Mechelen, Belgium
- miDIAGNOSTICS, Heverlee,Belgium
| | - Karen Zwaenepoel
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), Wilrijk, Belgium
- Department of Pathology, University Hospital Antwerp (UZA), Edegem, Belgium
| | | | | | | | - Reinier Wener
- Department of Pulmonology, University Hospital Antwerp (UZA), Edegem, Belgium
| | - Therese Lapperre
- Department of Pulmonology, University Hospital Antwerp (UZA), Edegem, Belgium
- Laboratory of Experimental Medicine and Paediatrics, University of Antwerp, Wilrijk, Belgium
| | - Filip Lardon
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), Wilrijk, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), Wilrijk, Belgium
- miDIAGNOSTICS, Heverlee,Belgium
| |
Collapse
|
15
|
The 2021 WHO Classification of Lung Tumors: Impact of advances since 2015. J Thorac Oncol 2021; 17:362-387. [PMID: 34808341 DOI: 10.1016/j.jtho.2021.11.003] [Citation(s) in RCA: 461] [Impact Index Per Article: 153.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022]
Abstract
The 2021 World Health Organisation (WHO) Classification of Thoracic Tumours was published earlier this year, with classification of lung tumors being one of the chapters. The principles remain those of using morphology first, supported by immunohistochemistry and then molecular techniques. In 2015, there was particular emphasis on using immunohistochemistry to make classification more accurate. In 2021, there is greater emphasis throughout the book on advances in molecular pathology across all tumor types. Major features within this edition are 1) broader emphasis on genetic testing than in the 2015 WHO Classification, 2) a chapter entirely dedicated to the classification of small diagnostic samples, 3) continued recommendation to document percentages of histological patterns in invasive non-mucinous adenocarcinomas, with utilization of these features to apply a formal grading system, as well as using only invasive size for T-factor size determination in part lepidic non-mucinous lung adenocarcinomas as recommended by the 8th Edition TNM Classification, 4) recognition of spread through airspaces (STAS) as a histological feature with prognostic significance, 5) moving lymphoepithelial carcinoma to squamous cell carcinomas, 6) update on evolving concepts in lung neuroendocrine neoplasm classification, 7) recognition of bronchiolar adenoma/ciliated muconodular papillary tumor (BA/CMPT) as a new entity within the adenoma subgroup, 8) recognition of thoracic SMARCA4-deficient undifferentiated tumor, and 9) inclusion of essential and desirable diagnostic criteria for each tumor.
Collapse
|
16
|
Pisapia P, Pepe F, Sgariglia R, Nacchio M, Russo G, Gragnano G, Conticelli F, Salatiello M, De Luca C, Girolami I, Eccher A, Iaccarino A, Bellevicine C, Vigliar E, Malapelle U, Troncone G. Methods for actionable gene fusion detection in lung cancer: now and in the future. Pharmacogenomics 2021; 22:833-847. [PMID: 34525844 DOI: 10.2217/pgs-2021-0048] [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] [Indexed: 12/28/2022] Open
Abstract
Although gene fusions occur rarely in non-small-cell lung cancer (NSCLC) patients, they represent a relevant target in treatment decision algorithms. To date, immunohistochemistry and fluorescence in situ hybridization are the two principal methods used in clinical trials. However, using these methods in routine clinical practice is often impractical and time consuming because they can only analyze single genes and the quantity of tissue material is often insufficient. Thus, novel technologies, able to test multiple genes in a single run with minimal sample input, are being under investigation. Here, we discuss the utility of next-generation sequencing and nCounter technologies in detecting simultaneous gene fusions in NSCLC patients.
Collapse
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
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Caterina De Luca
- 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 & Diagnostics, University & Hospital Trust of Verona, Verona, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, 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
| |
Collapse
|
17
|
What Is New in Biomarker Testing at Diagnosis of Advanced Non-Squamous Non-Small Cell Lung Carcinoma? Implications for Cytology and Liquid Biopsy. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The discovery and clinical validation of biomarkers predictive of the response of non-squamous non-small-cell lung carcinomas (NS-NSCLC) to therapeutic strategies continue to provide new data. The evaluation of novel treatments is based on molecular analyses aimed at determining their efficacy. These tests are increasing in number, but the tissue specimens are smaller and smaller and/or can have few tumor cells. Indeed, in addition to tissue samples, complementary cytological and/or blood samples can also give access to these biomarkers. To date, it is recommended and necessary to look for the status of five genomic molecular biomarkers (EGFR, ALK, ROS1, BRAFV600, NTRK) and of a protein biomarker (PD-L1). However, the short- and more or less long-term emergence of new targeted treatments of genomic alterations on RET and MET, but also on others’ genomic alteration, notably on KRAS, HER2, NRG1, SMARCA4, and NUT, have made cellular and blood samples essential for molecular testing. The aim of this review is to present the interest in using cytological and/or liquid biopsies as complementary biological material, or as an alternative to tissue specimens, for detection at diagnosis of new predictive biomarkers of NS-NSCLC.
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Siemanowski J, Heydt C, Merkelbach-Bruse S. Predictive molecular pathology of lung cancer in Germany with focus on gene fusion testing: Methods and quality assurance. Cancer Cytopathol 2021; 128:611-621. [PMID: 32885916 DOI: 10.1002/cncy.22293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022]
Abstract
Predictive molecular testing has become an important part of the diagnosis of any patient with lung cancer. Using reliable methods to ensure timely and accurate results is inevitable for guiding treatment decisions. In the past few years, parallel sequencing has been established for mutation testing, and its use is currently broadened for the detection of other genetic alterations, such as gene fusion and copy number variations. In addition, conventional methods such as immunohistochemistry and in situ hybridization are still being used, either for formalin-fixed, paraffin-embedded tissue or for cytological specimens. For the development and broad implementation of such complex technologies, interdisciplinary and regional networks are needed. The Network Genomic Medicine (NGM) has served as a model of centralized testing and decentralized treatment of patients and incorporates all German comprehensive cancer centers. Internal quality control, laboratory accreditation, and participation in external quality assessment is mandatory for the delivery of reliable results. Here, we provide a summary of current technologies used to identify patients who have lung cancer with gene fusions, briefly describe the structures of NGM and the national NGM (nNGM), and provide recommendations for quality assurance.
Collapse
Affiliation(s)
- Janna Siemanowski
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | |
Collapse
|
20
|
Rossi ED, Wiles A, Vecchione A. Lung cancer and molecular testing in small biopsies versus cytology: The Logics of Worlds. Cancer Cytopathol 2021; 128:637-641. [PMID: 32885910 DOI: 10.1002/cncy.22291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022]
Abstract
The 8th Annual National Molecular Cytopathology Meeting, held in Naples, Italy, on December 2 to 3, 2019, addressed updates in diagnostic cytopathology and molecular classifications and specifically focused on lung cancer biomarker testing in cytology samples. Lung cancer continues to be the most commonly diagnosed noncutaneous malignancy in the world. In the majority of patients, lung cancers are frequently identified when they cannot be surgically accessed, and this leads to the use of cytology for a diagnosis and theragnostic testing. The meeting was an international forum for discussing new roles and updates for cytopathology in molecular testing as the basis for provoking new trends and novel approaches. The relevant literature is referenced. The significance of these updates for the practice of pathology in general is discussed.
Collapse
Affiliation(s)
- Esther Diana Rossi
- Division of Anatomic Pathology and Histology, Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, Rome, Italy
| | - Austin Wiles
- Division of Anatomic Pathology, Department of Pathology, Virginia Commonwealth University Health System, Richmond, Virginia, USA
| | - Andrea Vecchione
- Division of Anatomic Pathology, Morphology and Molecular, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
21
|
Pisapia P, Pepe F, Iaccarino A, Sgariglia R, Nacchio M, Conticelli F, Salatiello M, Tufano R, Russo G, Gragnano G, Girolami I, Eccher A, Malapelle U, Troncone G. Next Generation Sequencing in Cytopathology: Focus on Non-Small Cell Lung Cancer. Front Med (Lausanne) 2021; 8:633923. [PMID: 33644101 PMCID: PMC7904874 DOI: 10.3389/fmed.2021.633923] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular cytopathology is a rapidly evolving field embracing both conventional microscopy and molecular pathology. Its growing popularity stems from the fact that in many types of advanced cancers, including non small cell lung cancer (NSCLC), cytological samples often constitute the only available specimens for morphomolecular analysis. Indeed, non formalin fixed and paraffin embedded (FFPE) cytological samples feature a higher quality of extracted nucleic acids than histological specimens. However, because of the growing complexity of molecular testing, several efforts should be made to validate the analytical performance of the wide array of currently available molecular technologies, including next generation sequencing (NGS). This technology has the terrific advantage of allowing simultaneous detection of scores of predictive biomarkers even in low-input DNA/RNA specimens. Here, we briefly review the role of the modern cytopathologist in the morphomolecular diagnosing of advanced stage NSCLC and the adoption of NGS in conventional cytopreparations (cell blocks, direct smears, and liquid-based cytology) and supernatants.
Collapse
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| |
Collapse
|
22
|
RNA-Based Multiplexing Assay for Routine Testing of Fusion and Splicing Variants in Cytological Samples of NSCLC Patients. Diagnostics (Basel) 2020; 11:diagnostics11010015. [PMID: 33374879 PMCID: PMC7824402 DOI: 10.3390/diagnostics11010015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
The detection of ALK receptor tyrosine kinase (ALK), ROS proto-oncogen1, receptor tyrosine kinase (ROS1), ret proto-oncogen (RET), and MET proto-oncogen exon 14 skipping (METΔex14) allows for the selection of specific kinase inhibitor treatment in patients with non-small cell lung cancer (NSCLC). Multiplex technologies are recommended in this setting. We used nCounter, a multiplexed technology based on RNA hybridization, to detect ALK, ROS1, RET, and METΔex14 in RNA purified from cytological specimens (n = 16) and biopsies (n = 132). Twelve of the 16 cytological samples (75.0%) were evaluable by nCounter compared to 120 out of 132 (90.9%) biopsies. The geometrical mean (geomean) of the housekeeping genes of the nCounter panel, but not the total amount of RNA purified, was significantly higher in biopsies vs. cytological samples. Among cytological samples, we detected ALK (n = 3), METΔex14 (n = 1) and very high MET expression (n = 1) positive cases. The patient with METΔex14 had a partial response to tepotinib, one of the patients with ALK fusions was treated with crizotinib with a complete response. Cell blocks and cytological extensions can be successfully used for the detection of fusions and splicing variants using RNA-based methods such as nCounter.
Collapse
|
23
|
Pisapia P, Pepe F, Iaccarino A, Sgariglia R, Nacchio M, Russo G, Gragnano G, Malapelle U, Troncone G. BRAF: A Two-Faced Janus. Cells 2020; 9:E2549. [PMID: 33260892 PMCID: PMC7760616 DOI: 10.3390/cells9122549] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Gain-of-function of V-Raf Murine Sarcoma Viral Oncogene Homolog B (BRAF) is one of the most frequent oncogenic mutations in numerous cancers, including thyroid papillary carcinoma, melanoma, colon, and lung carcinomas, and to a lesser extent, ovarian and glioblastoma multiforme. This mutation aberrantly activates the mitogen-activated protein (MAP) kinase extracellular signal-regulated kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathway, thereby eliciting metastatic processes. The relevance of BRAF mutations stems from its prognostic value and, equally important, from its relevant therapeutic utility as an actionable target for personalized treatment. Here, we discuss the double facets of BRAF. In particular, we argue the need to implement diagnostic molecular algorithms that are able to detect this biomarker in order to streamline and refine diagnostic and therapeutic decisions.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (P.P.); (F.P.); (A.I.); (R.S.); (M.N.); (G.R.); (G.G.); (U.M.)
| |
Collapse
|
24
|
Delcourt T, Vanneste K, Soumali MR, Coucke W, Ghislain V, Hebrant A, Van Valckenborgh E, De Keersmaecker SCJ, Roosens NH, Van De Walle P, Van Den Bulcke M, Antoniou A. NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program. Cancers (Basel) 2020; 12:E3180. [PMID: 33138022 PMCID: PMC7692129 DOI: 10.3390/cancers12113180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) is being integrated into routine clinical practice in the field of (hemato-) oncology to search for variants with diagnostic, prognostic, or therapeutic value at potentially low allelic frequencies. The complex sequencing workflows used require careful validation and continuous quality control. Participation in external quality assessments (EQA) helps laboratories evaluate their performance and guarantee the validity of tests results with the ultimate goal of ensuring high-quality patient care. Here, we describe three benchmarking trials performed during the period 2017-2018 aiming firstly at establishing the state-of-the-art and secondly setting up a NGS-specific EQA program at the national level in the field of clinical (hemato-) oncology in Belgium. DNA samples derived from cell line mixes and artificially mutated cell lines, designed to carry variants of clinical relevance occurring in solid tumors, hematological malignancies, and BRCA1/BRCA2 genes, were sent to Belgian human genetics, anatomic pathology, and clinical biology laboratories, to be processed following routine practices, together with surveys covering technical aspects of the NGS workflows. Despite the wide variety of platforms and workflows currently applied in routine clinical practice, performance was satisfactory, since participating laboratories identified the targeted variants with success rates ranging between 93.06% and 97.63% depending on the benchmark, and few false negative or repeatability issues were identified. However, variant reporting and interpretation varied, underlining the need for further standardization. Our approach showcases the feasibility of developing and implementing EQA for routine clinical practice in the field of (hemato-) oncology, while highlighting the challenges faced.
Collapse
Affiliation(s)
- Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Mohamed Rida Soumali
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Wim Coucke
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Vanessa Ghislain
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Aline Hebrant
- Cancer Centre, Sciensano, 1050 Brussels, Belgium; (A.H.); (E.V.V.); (M.V.D.B.)
| | | | - Sigrid C. J. De Keersmaecker
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Nancy H. Roosens
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Philippe Van De Walle
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Marc Van Den Bulcke
- Cancer Centre, Sciensano, 1050 Brussels, Belgium; (A.H.); (E.V.V.); (M.V.D.B.)
| | - Aline Antoniou
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| |
Collapse
|
25
|
Gentien D, Piqueret-Stephan L, Henry E, Albaud B, Rapinat A, Koscielny S, Scoazec JY, Vielh P. Digital Multiplexed Gene Expression Analysis of mRNA and miRNA from Routinely Processed and Stained Cytological Smears: A Proof-of-Principle Study. Acta Cytol 2020; 65:88-98. [PMID: 33011718 DOI: 10.1159/000510174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Although transcriptomic assessments of small samples using high-throughput techniques are usually performed on fresh or frozen tissues, there is a growing demand for those performed on stained cellular specimens already used for diagnostic purposes. STUDY DESIGN The possibility of detecting mRNAs and microRNAs (miRNAs) from routinely processed cytological samples using nCounter® technology was explored. Fresh samples from pleural and peritoneal effusions were analyzed using 2 parallel methods: samples were smeared and routinely stained using the May-Grünwald-Giemsa or Diff-Quik® method and mounted using conventional methods, and they were also studied following a snap freezing method, in which samples were maintained at -80°C until use. mRNAs and miRNAs were assessed and compared after total RNA extraction from both routinely processed samples and their matched frozen controls. RESULTS A good concordance was found between the gene expression measured in routinely processed samples and their matched frozen controls for the majority of mRNAs and miRNAs tested. However, the standard deviation of low-expressed miRNA was high. CONCLUSIONS Although nCounter® technology is a robust method to measure and characterize both mRNAs and miRNAs from routinely processed cytological samples, caution is recommended for the interpretation of low-expressed miRNA.
Collapse
Affiliation(s)
- David Gentien
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Laure Piqueret-Stephan
- INSERM UMR 981, Villejuif, France
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France
| | - Emilie Henry
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Benoît Albaud
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Audrey Rapinat
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Serge Koscielny
- Department of Biostatistics, Gustave Roussy, Villejuif, France
| | - Jean-Yves Scoazec
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France
| | - Philippe Vielh
- INSERM UMR 981, Villejuif, France,
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France,
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France,
| |
Collapse
|
26
|
How the COVID-19 Pandemic Impacted Oncological Molecular Diagnosis: A Picture from a National Reference Center for Molecular Pathology. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8397053. [PMID: 33029526 PMCID: PMC7537698 DOI: 10.1155/2020/8397053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/17/2020] [Indexed: 01/06/2023]
Abstract
Introduction The Portuguese healthcare system had to adapt at short notice to the COVID-19 pandemic. We implemented workflow changes to our molecular pathology laboratory, a national reference center, to maximize safety and productivity. We assess the impact this situation had on our caseload and what conclusions can be drawn about the wider impact of the pandemic in oncological therapy in Portugal. Material and Methods. We reviewed our database for all oncological molecular tests requested between March and April of 2019 and 2020. For each case, we recorded age, sex, region of the country, requesting institution, sample type, testing method, and turnaround time (TAT). A comparison between years was made. Results The total number of tests decreased from 421 in 2019 to 319 in 2020 (p = 0.0027). The greatest reduction was in clinical trial-related cases. Routine cases were similar between years (267 vs. 256). TAT was higher in 2019 (mean 15 days vs. 12.3 days; p = 0.0003). Medium- to large-sized public hospitals in the north of the country were mostly responsible for the reduction in cases (p = 0.0153). Conclusions Case reduction was observed at hospitals that have mostly been involved in the treatment of COVID-19 and in the north of the country, the region worst-hit by the pandemic. Similar to other studies, our TAT decreased, even with a similar number of routine cases. Thus, we conclude that it is possible to successfully adapt the workflow of a molecular pathology laboratory to new safety standards without losing efficiency.
Collapse
|
27
|
Alborelli I, Bratic Hench I, Chijioke O, Prince SS, Bubendorf L, Leuenberger LP, Tolnay M, Leonards K, Quagliata L, Jermann P, Matter MS. Robust assessment of tumor mutational burden in cytological specimens from lung cancer patients. Lung Cancer 2020; 149:84-89. [PMID: 32980613 DOI: 10.1016/j.lungcan.2020.08.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/23/2020] [Accepted: 08/31/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVES Tumor mutational burden (TMB) has emerged as a promising predictive biomarker for immune checkpoint inhibitor therapy. While the feasibility of TMB analysis on formalin-fixed paraffin-embedded (FFPE) samples has been thoroughly evaluated, only limited analyses have been performed on cytological samples, and no dedicated study has investigated concordance of TMB between different sample types. Here, we assessed TMB on matched histological and cytological samples from lung cancer patients and evaluated the accuracy of TMB estimation in these sample types. MATERIALS AND METHODS We analyzed mutations and resulting TMB in FFPE samples and matched ethanol-fixed cytological smears (n = 12 matched pairs) by using a targeted next-generation sequencing assay (Oncomine™ Tumor Mutational Load). Two different variant allele frequency (VAF) thresholds were used to estimate TMB (VAF = 5% or 10%). RESULTS At 5% VAF threshold, 73% (107/147) of mutations were concordantly detected in matched histological and cytological samples. Discordant variants were mainly unique to FFPE samples (34/40 discordant variants) and mostly C:G > T:A transitions with low allelic frequency, likely indicating formalin fixation artifacts. Increasing the VAF threshold to 10% clearly increased the number of concordantly detected mutations in matched histological and cytological samples to 96% (100/106 mutations), and drastically reduced the number of FFPE-only mutations (from 34 to 4 mutations). In contrast, cytological samples showed consistent mutation count and TMB values at both VAF thresholds. Using FFPE samples, 2 out of 12 patients were classified as TMB-high at VAF cutoff of 5% but TMB-low at 10%, whereas cytological specimens allowed consistent patient classification independently from VAF cutoff. CONCLUSION Our results show that cytological smears provide more consistent TMB values due to high DNA quality and lack of formalin-fixation induced artifacts. Therefore, cytological samples should be the preferred sample type for robust TMB estimation.
Collapse
Affiliation(s)
- Ilaria Alborelli
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland.
| | - Ivana Bratic Hench
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Obinna Chijioke
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Spasenija Savic Prince
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Lukas Bubendorf
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Laura P Leuenberger
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Markus Tolnay
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Katharina Leonards
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | | | - Philip Jermann
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Matthias S Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Switzerland
| |
Collapse
|
28
|
Xu J, Qu S, Sun N, Zhang W, Zhang J, Song Q, Lin M, Gao W, Zheng Q, Han M, Na C, Xu R, Chang X, Yang X, Huang J. Construction of a reference material panel for detecting KRAS/ NRAS/ EGFR/ BRAF/ MET mutations in plasma ctDNA. J Clin Pathol 2020; 74:314-320. [PMID: 32817175 PMCID: PMC8070650 DOI: 10.1136/jclinpath-2020-206745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/24/2022]
Abstract
Background The absence of high-quality next-generation sequencing (NGS) reference material (RM) has impeded the clinical use of liquid biopsies with plasma cell-free DNA (cfDNA) in China. Objective This study aimed to develop a national RM panel for external quality assessment and performance evaluation during kit registration of non-small-cell lung cancer (NSCLC)-related Kirsten rat sarcoma viral oncogene (KRAS)/neuroblastoma ras oncogene (NRAS)/epidermal growth factor receptor (EGFR)/B-type Raf kinase (BRAF)/mesenchymal–epithelial transition factor (MET) genetic assays using plasma circulating tumor DNA (ctDNA). Methods Mutation cell lines detected by NGS and validated by Sanger sequencing were selected to establish the RM. Cell line genomic DNA was sheared and used to spike basal plasma cfDNA at 10% concentration. Then, the calibration accuracy was determined by four sequencing platforms. Average values were adopted and diluted to 0.1%, 0.3%, 1% and 3% concentrations with basal plasma as the RM panel. Then, five manufacturers were invited to evaluate the performance of the RM panel. Results 20 cell lines with 23 clinically important mutations were selected, including six mutations in KRAS, two mutations in NRAS, three in BRAF, four in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), six in EGFR, one EGFR Gain (4-5 copy) and one MET Gain (2-5 copy). The RM panel consisted of 87 samples, including these 21 mutations at four concentrations (0.1%, 0.3%, 1% and 3%), one MET gain, one EGFR gain and one wild type. The detection rate was 100% for the 3%, 1% and 0.3% samples at all five companies. For the 0.1% concentration, 15 samples had inconsistent results, but at least three companies had correct results for each mutation. Conclusion RM for a KRAS/NRAS/EGFR/BRAF/MET mutation panel for plasma ctDNA was developed, which will be essential for quality control of the performance of independent laboratories.
Collapse
Affiliation(s)
- Jun Xu
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Shoufang Qu
- Division of Diagnostic for Non-infectious Disease, National Institutes for Food and Drug Control, Beijing, China
| | - Nan Sun
- Division of Diagnostic for Non-infectious Disease, National Institutes for Food and Drug Control, Beijing, China
| | - Wenxin Zhang
- Division of Diagnostic for Non-infectious Disease, National Institutes for Food and Drug Control, Beijing, China
| | - Juanli Zhang
- Department of Invitro Diagnostic Reagents Testing, Henan Medical Equipment Inspection Institute, Zhengzhou, China
| | - Qingtao Song
- R&D Center, Amoy Diagnostics Co., Ltd, Xiamen, China
| | - Mufei Lin
- Oncology Business Unit, BGI Geonmics Co., Ltd, Shenzhen, China
| | - Wei Gao
- R&D Center, Geneplus-Beijing Institute, Beijing, China
| | - Qiaosong Zheng
- R&D Center, Genetron Health (Beijing) Co, Beijing, China
| | - Mipeng Han
- R&D Center, Berry Genomics Co., Ltd, Beijing, China
| | - Chenglong Na
- R&D Center, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Ren Xu
- R&D Center, Shanghai Yuanqi Bio-Pharmaceutical Co. Ltd, Shanghai, China
| | - Xiaoyan Chang
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Xuexi Yang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Jie Huang
- Division of Diagnostic for Non-infectious Disease, National Institutes for Food and Drug Control, Beijing, China
| |
Collapse
|
29
|
The Birth of the Journal of Molecular Pathology. JOURNAL OF MOLECULAR PATHOLOGY 2020. [DOI: 10.3390/jmp1010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In the era of personalized/precision medicine, the relevance of molecular pathology cannot be overemphasized [...]
Collapse
|
30
|
de Biase D, Acquaviva G, Visani M, Sanza V, Argento CM, De Leo A, Maloberti T, Pession A, Tallini G. Molecular Diagnostic of Solid Tumor Using a Next Generation Sequencing Custom-Designed Multi-Gene Panel. Diagnostics (Basel) 2020; 10:diagnostics10040250. [PMID: 32340363 PMCID: PMC7236002 DOI: 10.3390/diagnostics10040250] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 02/05/2023] Open
Abstract
Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid lesions. We report a custom-designed 128 multi-gene panel engineered to cover the relevant targets in 22 oncogene/oncosuppressor genes for the analysis of the solid tumors most frequently subjected to routine genotyping. A total of 1695 solid tumors were analyzed for panel validation. The analytical sensitivity is 5%. Analytical validation: (i) Accuracy: sequencing results obtained using the multi-gene panel are concordant using two different NGS platforms and single-gene approach sequencing (100% of 83 cases); (ii) Precision: consistent results are obtained in the samples analyzed twice with the same platform (100% of 20 cases). Clinical validation: the frequency of mutations identified in different tumor types is consistent with the published literature. This custom-designed multi-gene panel allows to analyze with high sensitivity and throughput 22 oncogenes/oncosuppressor genes involved in diagnostic/prognostic/predictive characterization of central nervous system tumors, non-small-cell lung carcinomas, colorectal carcinomas, thyroid nodules, pancreatic lesions, melanoma, oral squamous carcinomas and gastrointestinal stromal tumors.
Collapse
Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
- Correspondence: ; Tel.: +39-051-2144717; Fax: +39-051-6363689
| | - Viviana Sanza
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Chiara M. Argento
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Antonio De Leo
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Thais Maloberti
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| |
Collapse
|
31
|
Malapelle U, Pepe F, Pisapia P, Sgariglia R, Nacchio M, De Luca C, Lacalamita R, Tommasi S, Pinto R, Palomba G, Palmieri G, Vacirca D, Barberis M, Bottillo I, Grammatico P, Grillo LR, Costa V, Smeraglio R, Bruzzese D, Troncone G. Harmonization of Next-Generation Sequencing Procedure in Italian Laboratories: A Multi-Institutional Evaluation of the SiRe® Panel. Front Oncol 2020; 10:236. [PMID: 32219061 PMCID: PMC7078327 DOI: 10.3389/fonc.2020.00236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/12/2020] [Indexed: 01/08/2023] Open
Abstract
Background: Next-generation sequencing (NGS) needs to be validated and standardized to ensure that cancer patients are reliably selected for target treatments. In Italy, NGS is performed in several institutions and harmonization of wet and dry procedures is needed. To this end, a consortium of five different laboratories, covering the most part of the Italian peninsula, was constituted. A narrow gene panel (SiRe®) covering 568 clinically relevant mutations in six different genes (EGFR, KRAS, NRAS, BRAF, cKIT, and PDGFRα) with a predictive role for therapy selection in non-small cell lung cancer (NSCLC), gastrointestinal stromal tumor, colorectal carcinoma (CRC), and melanoma was evaluated in each participating laboratory. Methods: To assess the NGS inter-laboratory concordance, the SiRe® panel, with a related kit and protocol for library preparation, was used in each center to analyze a common set of 20 NSCLC and CRC routine samples. Concordance rate, in terms of mutation detected and relative allelic frequencies, was assessed. Then, each institution prospectively analyzed an additional set of 40 routine samples (for a total of 160 specimens) to assess the reproducibility of the NGS run parameters in each institution. Results: An inter-laboratory agreement of 100% was reached in analyzing the data obtained from the 20 common sample sets; the concordance rate of allelic frequencies distribution was 0.989. The prospective analysis of the run metric parameters obtained by each center locally showed that the analytical performance of the SiRe® panel in the different institutions was highly reproducible. Conclusions: The SiRe® panel represents a robust diagnostic tool to harmonize the NGS procedure in different Italian laboratories.
Collapse
Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - 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
| | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Rosanna Lacalamita
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosamaria Pinto
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Grazia Palomba
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Davide Vacirca
- Pathology Unit, European Institute of Oncology, Milan, Italy
| | | | - Irene Bottillo
- Laboratory of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Paola Grammatico
- Laboratory of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Lucia Rosalba Grillo
- Department of Pathology, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics (CNR), Naples, Italy
| | - Riccardo Smeraglio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| |
Collapse
|
32
|
Chen CL, Chen CK, Ho CL, Chi WM, Yeh CH, Hu SP, Friebe P, Palmer S, Huang CS. Clinical Evaluation of IntelliPlex™ KRAS G12/13 Mutation Kit for Detection of KRAS Mutations in Codon 12 and 13: A Novel Multiplex Approach. Mol Diagn Ther 2019; 23:645-656. [DOI: 10.1007/s40291-019-00418-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|