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Performance of Idylla KRAS assay on extracted DNA and de-stained cytology smears: Can we rescue small sample? Ann Diagn Pathol 2022; 60:152023. [DOI: 10.1016/j.anndiagpath.2022.152023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022]
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Malapelle U, De Luca C, Iaccarino A, Pepe F, Pisapia P, Russo M, Sgariglia R, Nacchio M, Vigliar E, Bellevicine C, Schmitt FC, Troncone G. Predictive molecular pathology in the time of COVID-19. J Clin Pathol 2021; 74:234-237. [PMID: 32434770 PMCID: PMC7242869 DOI: 10.1136/jclinpath-2020-206711] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 12/22/2022]
Abstract
AIMS In the time of COVID-19, predictive molecular pathology laboratories must still timely select oncological patients for targeted treatments. However, the need to respect social distancing measures may delay results generated by laboratory-developed tests based on sequential steps a long hands-on time. Laboratory workflows should now be simplified. METHODS The organisation of the University of Naples Federico II predictive pathology laboratory was assessed before (March-April 2019) and during (March-April 2020) the Italian lockdown. RESULTS The number of patients undergoing single or multiple biomarker testing was similar in 2019 (n=43) and in 2020 (n=45). Considering adequate samples for molecular testing, before the outbreak, next-generation sequencing was mostly used (35/42, 83.3%). Testing six genes had a reagent cost of €98/patient. Conversely, in 2020, almost all cases (38/41, 92.7%) were analysed by automated testing. This latter had for any single assay/gene a significant reagent cost (€95-€136) and a faster mean turnaround time (5.3 vs 7.9 working days). CONCLUSION In the times of coronavirus, laboratory fully automated platforms simplify predictive molecular testing. Laboratory staff may be more safely and cost-effectively managed.
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Affiliation(s)
| | | | | | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | - Maria Russo
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | - Elena Vigliar
- Public Health, University of Naples Federico II, Naples, Italy
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Tsongalis GJ, Al Turkmani MR, Suriawinata M, Babcock MJ, Mitchell K, Ding Y, Scicchitano L, Tira A, Buckingham L, Atkinson S, Lax A, Aisner DL, Davies KD, Wood HN, O’Neill SS, Levine EA, Sequeira J, Harada S, DeFrank G, Paluri R, Tan BA, Colabella H, Snead C, Cruz-Correa M, Ramirez V, Rojas A, Huang H, Mackinnon AC, Garcia FU, Cavone SM, Elfahal M, Abel G, Vasef MA, Judd A, Linder MW, Alkhateeb K, Skinner WL, Boccia R, Patel K. Comparison of Tissue Molecular Biomarker Testing Turnaround Times and Concordance Between Standard of Care and the Biocartis Idylla Platform in Patients With Colorectal Cancer. Am J Clin Pathol 2020; 154:266-276. [PMID: 32525522 PMCID: PMC10893851 DOI: 10.1093/ajcp/aqaa044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES Management of colorectal cancer warrants mutational analysis of KRAS/NRAS when considering anti-epidermal growth factor receptor therapy and BRAF testing for prognostic stratification. In this multicenter study, we compared a fully integrated, cartridge-based system to standard-of-care assays used by participating laboratories. METHODS Twenty laboratories enrolled 874 colorectal cancer cases between November 2017 and December 2018. Testing was performed on the Idylla automated system (Biocartis) using the KRAS and NRAS-BRAF cartridges (research use only) and results compared with in-house standard-of-care testing methods. RESULTS There were sufficient data on 780 cases to measure turnaround time compared with standard assays. In-house polymerase chain reaction (PCR) had an average testing turnaround time of 5.6 days, send-out PCR of 22.5 days, in-house Sanger sequencing of 14.7 days, send-out Sanger of 17.8 days, in-house next-generation sequencing (NGS) of 12.5 days, and send-out NGS of 20.0 days. Standard testing had an average turnaround time of 11 days. Idylla average time to results was 4.9 days with a range of 0.4 to 13.5 days. CONCLUSIONS The described cartridge-based system offers rapid and reliable testing of clinically actionable mutation in colorectal cancer specimens directly from formalin-fixed, paraffin-embedded tissue sections. Its simplicity and ease of use compared with other molecular techniques make it suitable for routine clinical laboratory testing.
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Affiliation(s)
- Gregory J Tsongalis
- Clinical Genomics and Advanced Technology (CGAT) Laboratory, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Health System, Lebanon, NH
- Geisel School of Medicine at Dartmouth, Hanover, NH
| | - M Rabie Al Turkmani
- Clinical Genomics and Advanced Technology (CGAT) Laboratory, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Health System, Lebanon, NH
- Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Michael Suriawinata
- Clinical Genomics and Advanced Technology (CGAT) Laboratory, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Health System, Lebanon, NH
- Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Michael J Babcock
- Bioinformatics & Molecular Pathology, Dahl-Chase Diagnostic Services & Pathology Associates, Bangor, ME
| | - Kristi Mitchell
- Bioinformatics & Molecular Pathology, Dahl-Chase Diagnostic Services & Pathology Associates, Bangor, ME
| | - Yi Ding
- Diagnostic Medicine Institute, Geisinger Medical Center, Danville, PA
| | - Lisa Scicchitano
- Diagnostic Medicine Institute, Geisinger Medical Center, Danville, PA
| | - Adrian Tira
- Department of Pathology, Rush University Medical Center, Chicago, IL
| | - Lela Buckingham
- Department of Pathology, Rush University Medical Center, Chicago, IL
| | - Sara Atkinson
- Department of Cytology, Cone Health Moses Cone Hospital, Greensboro, NC
| | - Amy Lax
- Department of Cytology, Cone Health Moses Cone Hospital, Greensboro, NC
| | - Dara L Aisner
- Colorado Molecular Correlates Laboratory (CMOCO), Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora
| | - Kurtis D Davies
- Colorado Molecular Correlates Laboratory (CMOCO), Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora
| | - Holly N Wood
- Colorado Molecular Correlates Laboratory (CMOCO), Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora
| | - Stacey S O’Neill
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Edward A Levine
- Division of Surgical Oncology, Department of Surgery, Wake Forest School of Medicine, Winston-Salem, NC
| | - Judy Sequeira
- Department of Pathology and Laboratory Medicine, Comprehensive Care and Research Center, Cancer Treatment Centers of America Atlanta, Newnan, GA
| | - Shuko Harada
- Molecular Diagnostics Laboratory, Department of Pathology, University of Alabama Birmingham School of Medicine, Birmingham
| | - Gina DeFrank
- Molecular Diagnostics Laboratory, Department of Pathology, University of Alabama Birmingham School of Medicine, Birmingham
| | - Ravikumar Paluri
- Department of Medicine, Division of Hematology/Oncology, University of Alabama Birmingham School of Medicine, Birmingham
| | - Bradford A Tan
- Department of Pathology and Laboratory Medicine, Comprehensive Care and Research Center, Cancer Treatment Centers of America Chicago, Zion, IL
| | - Heather Colabella
- Department of Pathology and Laboratory Medicine, Comprehensive Care and Research Center, Cancer Treatment Centers of America Chicago, Zion, IL
| | | | - Marcia Cruz-Correa
- Pan American Center for Oncology Trials, Oncologic Hospital, Puerto Rico Medical Center, Rio Piedras, Puerto Rico
| | - Virginia Ramirez
- Pan American Center for Oncology Trials, Oncologic Hospital, Puerto Rico Medical Center, Rio Piedras, Puerto Rico
| | - Arnaldo Rojas
- Pan American Center for Oncology Trials, Oncologic Hospital, Puerto Rico Medical Center, Rio Piedras, Puerto Rico
| | - Huiya Huang
- Department of Pathology, Medical College of Wisconsin, Milwaukee
| | | | - Fernando U Garcia
- Department of Pathology and Laboratory Medicine, Comprehensive Care and Research Center, Cancer Treatment Centers of America Philadelphia, Philadelphia, PA
| | - Sharon M Cavone
- Department of Pathology and Laboratory Medicine, Comprehensive Care and Research Center, Cancer Treatment Centers of America Philadelphia, Philadelphia, PA
| | - Mutasim Elfahal
- Department of Pathology and Laboratory Medicine, Lahey Hospital and Medical Center, Beth Israel Lahey Health, Burlington, MA
| | - Gyorgy Abel
- Department of Pathology and Laboratory Medicine, Lahey Hospital and Medical Center, Beth Israel Lahey Health, Burlington, MA
| | - Mohammad A Vasef
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque
| | - Andrew Judd
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville Hospital, Louisville, KY
| | - Khaled Alkhateeb
- Department of Pathology and Laboratory Medicine, University of Louisville Hospital, Louisville, KY
| | | | - Ralph Boccia
- The Center for Cancer and Blood Disorders, Bethesda, MD
| | - Kashyap Patel
- Carolina Blood and Cancer Care Associates, PA, Rock Hill, SC
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De Luca C, Sgariglia R, Nacchio M, Pisapia P, Migliatico I, Clery E, Gragnano G, Campione S, Vigliar E, Malapelle U, De Dominicis G, Bellevicine C, Troncone G. Rapid On-site Molecular Evaluation in thyroid cytopathology: A same-day cytological and molecular diagnosis. Diagn Cytopathol 2020; 48:300-307. [PMID: 31904908 DOI: 10.1002/dc.24378] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/27/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Thyroid fine-needle aspirates (FNAs) with undetermined morphology can be outsourced to centralized laboratories for comprehensive molecular profiling. When a local, rapid screening rules out easily detectable BRAF and NRAS mutations outsourcing is minimized, leading to cost savings. The fully automated Idylla technology, that does not require trained staff, is an emerging option. However, Idylla platform has only been validated to process formalin fixed paraffin embedded (FFPE) sections. Here we investigate whether also the FNA needle rinse could be genotyped by the same cytopathologist who performs the FNA, a procedure that can be termed rapid on site molecular evaluation (ROME). METHODS To validate this approach, the Idylla BRAF and NRAS Test was performed on the rinses from 25 simulated (bench-top) FNAs, in a first part of the study. Genotyping data were compared with those obtained on matched histological FFPE blocks. The second part of the study was carried out on 25 prospectively collected routine FNAs to assess the performance of the Idylla BRAF and NRAS assay against a gold standard real time polymerase chain reaction method. RESULTS Idylla NRAS-BRAF Mutation Test was performed on needle rinse as well as histological FFPE blocks. A sensitivity of 88.9%, a specificity of 100.0% were obtained comparing the Idylla NRAS-BRAF Mutation Test on needle rinse to the reference method. CONCLUSIONS The FNA needle rinse can be directly genotyped. This obviates the need of cell block preparation, making possible a rapid combined morphological and molecular evaluation. Since DNA extraction is no longer necessary, the cytopathologist can perform ROME him/herself.
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Affiliation(s)
- Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Migliatico
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Eduardo Clery
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Severo Campione
- Department of Pathology, A.O.R.N. A. Cardarelli, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Huang H, Springborn S, Haug K, Bartow K, Samra H, Menon S, Mackinnon AC. Evaluation, Validation, and Implementation of the Idylla System as Rapid Molecular Testing for Precision Medicine. J Mol Diagn 2019; 21:862-872. [DOI: 10.1016/j.jmoldx.2019.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/30/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022] Open
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Van Haele M, Vander Borght S, Ceulemans A, Wieërs M, Metsu S, Sagaert X, Weynand B. Rapid clinical mutational testing of KRAS, BRAF and EGFR: a prospective comparative analysis of the Idylla technique with high-throughput next-generation sequencing. J Clin Pathol 2019; 73:35-41. [PMID: 31296605 DOI: 10.1136/jclinpath-2019-205970] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022]
Abstract
AIMS Precision medicine therapy is remodelling the diagnostic landscape of cancer. The success of these new therapies is often based on the presence or absence of a specific mutation in a tumour. The Idylla platform is designed to determine the mutational status of a tumour as quickly and accurately as possible, as a rapid, accurate diagnosis is of the utmost importance for the treatment of patients. This is the first complete prospective study to investigate the robustness of the Idylla platform for EGFR, KRAS and BRAF mutations in non-small cell lung cancer, metastatic colorectal cancer and metastatic melanoma, respectively. METHODS We compared prospectively the Idylla platform with the results we obtained from parallel high-throughput next-generation sequencing, which is the current gold standard for mutational testing. Furthermore, we evaluated the benefits and disadvantages of the Idylla platform in clinical practice. Additionally, we reviewed all the published Idylla performance articles. RESULTS There was an overall agreement of 100%, 94% and 94% between the next-generation panel and the Idylla BRAF, KRAS and EGFR mutation test. Two interesting discordant findings among 48 cases were observed and will be discussed together with the advantages and shortcoming of both techniques. CONCLUSION Our observations demonstrate that the Idylla cartridge for the EGFR, KRAS and BRAF mutations is highly accurate, rapid and has a limited hands-on time compared with next-generation sequencing.
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Affiliation(s)
- Matthias Van Haele
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium .,Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - An Ceulemans
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Michiel Wieërs
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | - Xavier Sagaert
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.,Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.,Pathology, University Hospitals Leuven, Leuven, Belgium
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Uguen A, Troncone G. A review on the Idylla platform: towards the assessment of actionable genomic alterations in one day. J Clin Pathol 2018; 71:757-762. [DOI: 10.1136/jclinpath-2018-205189] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
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Sadlecki P, Antosik P, Grzanka D, Grabiec M, Walentowicz-Sadlecka M. KRAS mutation testing in borderline ovarian tumors and low-grade ovarian carcinomas with a rapid, fully integrated molecular diagnostic system. Tumour Biol 2017; 39:1010428317733984. [DOI: 10.1177/1010428317733984] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Pawel Sadlecki
- Department of Obstetrics and Gynecology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Paulina Antosik
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Dariusz Grzanka
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Marek Grabiec
- Department of Obstetrics and Gynecology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Malgorzata Walentowicz-Sadlecka
- Department of Obstetrics and Gynecology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
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Bellevicine C, Malapelle U, Vigliar E, Pisapia P, Vita G, Troncone G. How to prepare cytological samples for molecular testing. J Clin Pathol 2017; 70:819-826. [DOI: 10.1136/jclinpath-2017-204561] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 12/21/2022]
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