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Boppudi SM, Scheil-Bertram S, Faust E, Annamneedi A, Fisseler-Eckhoff A. Assessing and Evaluating the Scope and Constraints of Idylla Molecular Assays by Using Different Source Materials in Routine Diagnostic Settings. Int J Mol Sci 2022; 23:ijms232012515. [PMID: 36293374 PMCID: PMC9604085 DOI: 10.3390/ijms232012515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
For cancer treatment, diagnostics concerning tumor type and determination of molecular markers in short TAT is critical. The fully automated, real-time PCR-based molecular diagnostic Idylla assays are well established in many laboratories for qualitative detection, short TAT and routine screening of clinically relevant oncogenic mutations. According to the manufacturer, all IVD assays are recommended for use only with FFPE tissue samples of 5–10 µM dissections with at least 10% tumor content. In this study, we tested the performance and accuracy of the IVD assays along with the gene fusion assay (RUO) with different tissue/source materials like isolated DNA/RNA, cryomaterial, etc. The study also included testing archival FFPE tissue sections dating back from 20 years and a performance check for different pan-cancer samples individually. All the assays tested with FFPE sections and gDNA/RNA input showed above 96% accuracy and sensitivity, individually with 100% specificity. The Idylla assays also performed exceptionally well on the archival FFPE tissues, and the use of assays for other solid tumors was also remarkable. The performance test and accuracy of Idylla assays showed high efficiency with certain limitations. For the use of Idylla assays, both qualitative and quantitative applicability of different tumor source materials could produce efficient results in different diagnostic settings within a short TAT.
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Affiliation(s)
- Sanga Mitra Boppudi
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
- Gemeinschaftspraxis für Pathologie, 65199 Wiesbaden, Germany
- Correspondence: (S.M.B.); (A.F.-E.)
| | - Stefanie Scheil-Bertram
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
| | - Elisabeth Faust
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
| | - Anil Annamneedi
- Team Biology of GPCR Signaling Systems (BIOS), CNRS, IFCE, INRAE, Université de Tours, Physiologie de la Reproduction et des Comportements (PRC), 37380 Nouzilly, France
- LE STUDIUM Loire Valley Institute for Advanced Studies, 45000 Orléans, France
| | - Annette Fisseler-Eckhoff
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
- Gemeinschaftspraxis für Pathologie, 65199 Wiesbaden, Germany
- Correspondence: (S.M.B.); (A.F.-E.)
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Nkosi D, Casler VL, Syposs CR, Oltvai ZN. Utility of Select Gene Mutation Detection in Tumors by the Idylla Rapid Multiplex PCR Platform in Comparison to Next-Generation Sequencing. Genes (Basel) 2022; 13:genes13050799. [PMID: 35627184 PMCID: PMC9141835 DOI: 10.3390/genes13050799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
Testing of tumors by next generation sequencing (NGS) is impacted by relatively long turnaround times and a need for highly trained personnel. Recently, Idylla oncology assays were introduced to test for BRAF, EGFR, KRAS, and NRAS common hotspot mutations that do not require specialized trained personnel. Moreover, the interpretation of results is fully automated, with rapid turnaround time. Though Idylla testing and NGS have been shown to have high concordance in identifying EGFR, BRAF, KRAS, and NRAS hotspot mutations, there is limited experience on optimal ways the Idylla system can be used in routine practice. We retrospectively evaluated all cases with EGFR, BRAF, KRAS, or NRAS mutations identified in clinical specimens sequenced on two different NGS panels at the University of Rochester Medical Center (URMC) molecular diagnostics laboratory between July 2020 and July 2021 and assessed if these mutations would be detected by the Idylla cartridges if used. We found that the Idylla system could accurately identify Tier 1 or 2 actionable genomic alterations in select associated disease pathologies if used. Yet, in a minority of cases, we would have been unable to detect NGS-identified pathogenic mutations due to their absence on the Idylla panels. We derived algorithmic practice guidelines for the use of the Idylla cartridges. Overall, Idylla molecular testing could be implemented either as a first-line standalone diagnostic tool in select indications or for orthogonal confirmation of uncertain results.
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Makutani Y, Sakai K, Yamada M, Wada T, Chikugo T, Satou T, Iwasa Y, Yamamoto H, de Velasco MA, Nishio K, Kawamura J. Performance of Idylla ™ RAS-BRAF mutation test for formalin-fixed paraffin-embedded tissues of colorectal cancer. Int J Clin Oncol 2022; 27:1180-1187. [PMID: 35474548 PMCID: PMC9209352 DOI: 10.1007/s10147-022-02167-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/03/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND The Biocartis Idylla™ platform is a fully automated, real-time PCR-based diagnostic system. The Idylla™ KRAS and NRAS-BRAF Mutation Tests have been developed for the qualitative detection of mutations in KRAS, NRAS and BRAF genes, facilitating the genomic profiling of patients with colorectal cancer. The aim of the present study was to evaluate clinical performances of these tests in Japan. METHODS The RAS and BRAF mutation statuses of 253 formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissues were analyzed using the Investigational Use Only Idylla™ KRAS Mutation Test and the Idylla™ NRAS-BRAF Mutation Test and an in vitro diagnostics (IVD) kit (MEBGEN RASKET™-B kit). RESULTS The success rate for obtaining a valid mutational data without retest of the Idylla tests was 97.6% (247/253): 111 KRAS mutations (43.8%), 9 NRAS mutations (3.6%), and 36 BRAF V600E mutations (14.2%) were detected using the Idylla tests. Compared with the MEBGEN RASKET-B results, the positive concordance rate was 97.4%, the negative concordance rate was 95.7%, and the overall concordance rate was 95.3% (κ = 0.919, 95% CI 0.871-0.967). The average turnaround time to Idylla™ KRAS and NRAS-BRAF Mutation Test was 5.6 working days (range: 3-11 days). CONCLUSION This result demonstrates a high concordance between the Idylla™ KRAS and NRAS-BRAF Mutation Tests and an existing IVD kit. In this manner, the Idylla™ mutation tests were validated for the detection of clinically significant KRAS, NRAS, and BRAF mutations in FFPE samples from colorectal cancer patients.
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Affiliation(s)
- Yusuke Makutani
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka-sayama, Osaka, 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Masahiro Yamada
- Department of Surgery, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
| | - Toshiaki Wada
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka-sayama, Osaka, 589-8511, Japan
| | - Takaaki Chikugo
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takao Satou
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Yoko Iwasa
- Department of Diagnostic Pathology, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
| | - Hidekazu Yamamoto
- Department of Surgery, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
- Department of Diagnostic Pathology, Shiga General Hospital, Moriyama, Shiga, 524-8524, Japan
| | - Marco A de Velasco
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, Osaka, 589-8511, Japan.
| | - Junichiro Kawamura
- Department of Surgery, Faculty of Medicine, Kindai University, Osaka-sayama, Osaka, 589-8511, Japan
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Bourhis A, Remoué A, Samaison L, Uguen A. Diagnostic mutationnel rapide Idylla™ : applications théranostiques actuelles et futures. Ann Pathol 2022; 42:329-343. [DOI: 10.1016/j.annpat.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 12/07/2021] [Accepted: 12/12/2021] [Indexed: 10/19/2022]
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Offerman S, Prinsen CF, Knol A, Methorst N, Kamphorst J, Niemantsverdriet M. Short report: Performance evaluation of the Idylla™ KRAS and EGFR mutation tests on paraffin-embedded cytological NSCLC samples. Diagn Pathol 2021; 16:70. [PMID: 34344387 PMCID: PMC8330063 DOI: 10.1186/s13000-021-01121-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Quick and reliable testing of EGFR and KRAS is needed in non-small cell lung cancer (NSCLC) to ensure optimal decision-making for targeted therapy. The Idylla™ platform was designed for Formalin-Fixed Paraffin-Embedded (FFPE) tissue sections but recently several studies were published that evaluated its potential for cytological specimens. This study aimed to validate the Idylla™ platform for the detection of EGFR/KRAS mutations in cytological NSCLC samples prepared as cytoblocks using AGAR and paraffin embedding. MATERIAL AND METHODS The KRAS Idylla™ test were performed on 11 specimens with a known KRAS mutation. The EGFR Idylla™ test was performed on 18 specimens with a known primary EGFR mutation and 7 specimens with a primary EGFR-EGFR T790M resistance mutation combination. RESULTS Concordant KRAS and primary EGFR mutations were detected for both KRAS and primary EGFR mutations. Samples with a total CQ value of < 26 could be considered negative. Samples with a total CQ value of > 26 could not be assessed (probability of false-negative). In specimens with a primary EGFR-EGFR T790M resistance mutation combination, 5/7 cases were not concordant. CONCLUSION Our results confirm the conclusion of recent reports that the Idylla™EGFR assay is not suitable in a resistance to EGFR TKI setting, also not in our cytological NSCLC samples prepared as cytoblocks using AGAR and paraffin embedding. KRAS and primary EGFR mutations were detected using the Idylla™ assays in virtually all cytological NSCLC samples. This analysis was rapid and time-saving compared to other mutation detection assays and may be useful if the amount of material is insufficient to perform a full set of molecular tests.
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Affiliation(s)
- Saskia Offerman
- Isala Pathology, Dr. Van Heesweg 2, 8025 AB Zwolle, Postbus 10400, 8000 GK, Zwolle, The Netherlands
| | - Clemens F Prinsen
- Isala Pathology, Dr. Van Heesweg 2, 8025 AB Zwolle, Postbus 10400, 8000 GK, Zwolle, The Netherlands
- Department Pathology C66, Canisius Wilhelmina Ziekenhuis, Weg door Jonkerbos 100, 6532 SZ, Nijmegen, The Netherlands
| | - Ageeth Knol
- Isala Pathology, Dr. Van Heesweg 2, 8025 AB Zwolle, Postbus 10400, 8000 GK, Zwolle, The Netherlands
| | - Natalie Methorst
- Isala Pathology, Dr. Van Heesweg 2, 8025 AB Zwolle, Postbus 10400, 8000 GK, Zwolle, The Netherlands
| | - Jeanette Kamphorst
- Isala Pathology, Dr. Van Heesweg 2, 8025 AB Zwolle, Postbus 10400, 8000 GK, Zwolle, The Netherlands
| | - Maarten Niemantsverdriet
- Isala Pathology, Dr. Van Heesweg 2, 8025 AB Zwolle, Postbus 10400, 8000 GK, Zwolle, The Netherlands.
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Drastic Reduction of Turnaround Time After Implementation of a Fully Automated Assay for RAS-BRAF Mutations in Colorectal Cancer: A Pilot Prospective Study in Real-life Conditions. Pathol Oncol Res 2020; 26:2469-2473. [PMID: 32572821 DOI: 10.1007/s12253-020-00818-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 04/23/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022]
Abstract
In some situations, there is a need for rapid mutation tests for guiding clinical decisions and starting targeted therapies with minimal delays. In this study we evaluated the turnaround time before and after the implementation of a fully automated multiplex assay for KRAS and NRAS/BRAF mutation tests (Idylla™ platform, Biocartis) in metastatic colorectal cancer. The objective of this project was to compare the turnaround times in 2017-2018 with the fully automated multiplex assay to the 2016 results with previous methods. Centers with a number of tests for metastatic colorectal cancer > 100 yearly and a usual turnaround time ≥ 3 weeks for mutation detection were selected. Results of 505 KRAS tests and 369 NRAS/BRAF tests were transmitted by 10 centers. The mean turnaround time from test prescription to reception of results was reduced from 25.8 days in 2016 to 4.5 days in 2017-2018. In conclusion, this pilot project shows that the Idylla™ platform for testing KRAS and NRAS/BRAF mutations allows an optimized turnaround time from test prescription to reception of results.
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Bourhis A, De Luca C, Cariou M, Vigliar E, Barel F, Conticelli F, Marcorelles P, Nousbaum JB, Robaszkiewicz M, Samaison L, Badic B, Doucet L, Troncone G, Uguen A. Evaluation of KRAS, NRAS and BRAF mutational status and microsatellite instability in early colorectal carcinomas invading the submucosa (pT1): towards an in-house molecular prognostication for pathologists? J Clin Pathol 2020; 73:741-747. [PMID: 32273401 DOI: 10.1136/jclinpath-2020-206496] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
Abstract
AIM We aimed to study the prognostic value of KRAS, NRAS, BRAF mutations and microsatellite stable (MSS)/instable (MSI) in the field of colorectal cancer invading the submucosa (ie, pT1 colorectal cancer (CRC)). METHODS We led a case-control study in tumour samples from 60 patients with pT1 CRC with (20 cases) and without (40 cases) metastatic evolution (5 years of follow-up) which were analysed for KRAS, NRAS, BRAF mutations (Idylla testing and next generation sequencing, NGS) and MSS/MSI status (Idylla testing and expression of mismatch repair (MMR) proteins using immunohistochemistry). RESULTS KRAS mutations were encountered in 11/20 (55%) cases and 21/40 (52.5%) controls (OR=1.11 (0.38 to 3.25), p=0.8548), NRAS mutations in 1/20 (5%) cases and 3/40 (7.5%) controls (OR=3.08 (0.62 to 15.39), p=0.1698) and BRAF mutations in 3/20 (15%) cases and 6/40 (15%) controls (OR=1.00 (0.22 to 4.5), p=1.00). A MSI status was diagnosed in 3/20 (15%) cases and 5/40 (12.5%) controls (OR=1.2353 (0.26 to 5.79), p=0.7885). Beyond the absence of significant association between the metastatic evolution and any of the studied molecular parameters, we observed a very good agreement between methods analysing KRAS, NRAS and BRAF mutations (Kappa value of 0.849 (0.748 to 0.95) between Idylla and NGS) and MSS/MSI (Idylla)-proficient MMR/deficient MMR (immunohistochemistry) status (Kappa value of 1.00). CONCLUSION Although being feasible using the fully automated Idylla method as well as NGS, the molecular testing of KRAS, NRAS, BRAF and MSS/MSI status does not seem useful for prognostic purpose in the field of pT1 CRC.
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Affiliation(s)
| | - Caterina De Luca
- Public Health, University of Naples "Federico II", Naples, Italy
| | - Mélanie Cariou
- Registre des cancers digestifs du Finistère, Brest, France
| | - Elena Vigliar
- Public Health, University of Naples "Federico II", Naples, Italy
| | | | | | | | | | | | | | | | | | | | - Arnaud Uguen
- Pathology, CHRU de Brest, Brest, France .,Univ Brest, Inserm, CHU de Brest, LBAI, UMR1227, Brest, France, Univ Brest, Brest, France
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Franczak C, Witz A, Geoffroy K, Demange J, Rouyer M, Husson M, Massard V, Gavoille C, Lambert A, Gilson P, Gambier N, Scala-Bertola J, Merlin JL, Harlé A. Evaluation of KRAS, NRAS and BRAF mutations detection in plasma using an automated system for patients with metastatic colorectal cancer. PLoS One 2020; 15:e0227294. [PMID: 31940389 PMCID: PMC6961936 DOI: 10.1371/journal.pone.0227294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
Background Cell-free DNA detection is becoming a surrogate assay for tumor genotyping. Biological fluids often content a very low amount of cell-free tumor DNA and assays able to detect very low allele frequency mutant with a few quantities of DNA are required. We evaluated the ability of the fully-automated molecular diagnostics platform Idylla for the detection of KRAS, NRAS and BRAF hotspot mutations in plasma from patients with metastatic colorectal cancer (mCRC). Materials and methods First, we evaluated the limit of detection of the system using two set of laboratory made samples that mimic mCRC patient plasma, then plasma samples from patients with mCRC were assessed using Idylla system and BEAMing digital PCR technology. Results Limits of detection of 0.1%, 0.4% and 0.01% for KRAS, NRAS and BRAF respectively have been reached. With our laboratory made samples, sensitivity up to 0.008% has been reached. Among 15 patients’ samples tested for KRAS mutation, 2 discrepant results were found between Idylla and BEAMing dPCR. A 100% concordance between the two assays has been found for the detection of NRAS and BRAF mutations in plasma samples. Conclusions The Idylla system does not reach as high sensitivity as assays like ddPCR but has an equivalent sensitivity to modified NGS technics with a lower cost and a lower time to results. These data allowed to consider the Idylla system in a routine laboratory workflow for KRAS, NRAS and BRAF mutations detection in plasma.
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Affiliation(s)
- Claire Franczak
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Andréa Witz
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Karen Geoffroy
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Jessica Demange
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Marie Rouyer
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Marie Husson
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre les Nancy, France
| | - Vincent Massard
- Institut de Cancérologie de Lorraine, Département d'oncologie médicale, Vandoeuvre les Nancy, France
| | - Céline Gavoille
- Institut de Cancérologie de Lorraine, Département d'oncologie médicale, Vandoeuvre les Nancy, France
| | - Aurélien Lambert
- Institut de Cancérologie de Lorraine, Département d'oncologie médicale, Vandoeuvre les Nancy, France
| | - Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Nicolas Gambier
- CHRU Nancy, Department of Clinical Pharmacology and Toxicology, Nancy, France.,Université de Lorraine, UMR 7365 CNRS-UL, IMoPA, Vandœuvre-lès-Nancy, France
| | - Julien Scala-Bertola
- CHRU Nancy, Department of Clinical Pharmacology and Toxicology, Nancy, France.,Université de Lorraine, UMR 7365 CNRS-UL, IMoPA, Vandœuvre-lès-Nancy, France
| | - Jean-Louis Merlin
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Alexandre Harlé
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
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Pang SW, Awi NJ, Armon S, Lim WWD, Low JSH, Peh KB, Peh SC, Teow SY. Current Update of Laboratory Molecular Diagnostics Advancement in Management of Colorectal Cancer (CRC). Diagnostics (Basel) 2019; 10:E9. [PMID: 31877940 PMCID: PMC7168209 DOI: 10.3390/diagnostics10010009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/11/2019] [Accepted: 11/23/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) continues to be one of the most common cancers globally. The incidence has increased in developing countries in the past few decades, this could be partly attributed to aging populations and unhealthy lifestyles. While the treatment of CRC has seen significant improvement since the advent of target-specific therapies and personalized medicine, CRC is oftentimes detected at late or advanced stages, thereby reducing the efficacy of treatment. Hence, screening for early detection is still the key to combat CRC and to increase overall survival (OS). Considering that the field of medical diagnostics is moving towards molecular diagnostics, CRC can now be effectively screened and diagnosed with high accuracy and sensitivity. Depending on the tumor genotype and genetic profile of the individual, personalized treatments including tyrosine kinase inhibitor therapy and immunotherapy can be administered. Notably, there can be no one single treatment that is effective for all CRC patients due to the variation in tumor genetics, which highlights the importance of molecular diagnostics. This review provides insights on therapeutic modalities, molecular biomarkers, advancement of diagnostic technologies, and current challenges in managing CRC.
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Affiliation(s)
- Siew-Wai Pang
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Noel Jacques Awi
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Subasri Armon
- Pathology Department, Hospital Kuala Lumpur, Jalan Pahang, Kuala Lumpur 50588, Malaysia
| | - Wendy Wan-Dee Lim
- Sunway Medical Centre, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - John Seng-Hooi Low
- Sunway Medical Centre, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Kaik-Boo Peh
- Mahkota Medical Centre, Mahkota Melaka, Jalan Merdeka, Melaka 75000, Malaysia
| | - Suat-Cheng Peh
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
- Sunway Medical Centre, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Sin-Yeang Teow
- Department of Medical Sciences, School of Healthcare and Medical Sciences, Sunway University, Jalan Universiti, Bandar Sunway, Subang Jaya 47500, Malaysia
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Al-Turkmani MR, Godwin KN, Peterson JD, Tsongalis GJ. Rapid Somatic Mutation Testing in Colorectal Cancer by Use of a Fully Automated System and Single-Use Cartridge: A Comparison with Next-Generation Sequencing. J Appl Lab Med 2019; 3:178-184. [DOI: 10.1373/jalm.2018.026278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/26/2018] [Indexed: 12/12/2022]
Abstract
AbstractBackgroundMolecular tests have been increasingly used in the management of various cancers as more targeted therapies are becoming available as treatment options. The Idylla™ system is a fully integrated, cartridge-based platform that provides automated sample processing (deparaffinization, tissue digestion, and DNA extraction) and real-time PCR-based mutation detection with all reagents included in a single-use cartridge. This retrospective study aimed at evaluating both the Idylla KRAS and NRAS-BRAF-EGFR492 Mutation Assay cartridges (research use only) against next-generation sequencing (NGS) by using colorectal cancer (CRC) tissue samples.MethodsForty-four archived formalin-fixed paraffin-embedded (FFPE) CRC tissue samples previously analyzed by targeted NGS were tested on the Idylla system. Among these samples, 17 had a mutation in KRAS proto-oncogene, GTPase (KRAS), 5 in NRAS proto-oncogene, GTPase (NRAS), and 12 in B-Raf proto-oncogene, serine/threonine kinase (BRAF) as determined using the Ion AmpliSeq 50-gene Cancer Hotspot Panel v2. The remaining 10 samples were wild-type for KRAS, NRAS, and BRAF. Two 10-μm FFPE tissue sections were used for each Idylla run, 1 for the KRAS cartridge, and 1 for the NRAS-BRAF-EGFR492 cartridge. All cases met the Idylla minimum tumor content requirement for KRAS, NRAS, and BRAF (≥10%). Assay reproducibility was evaluated by testing commercial controls derived from human cell lines, which had an allelic frequency of 50% and were run in triplicate.ResultsThe Idylla system successfully detected all mutations previously identified by NGS in KRAS (G12C, G12D, G12V, G13D, Q61K, Q61R, A146T), NRAS (G12V, G13R, Q61H), and BRAF (V600E). Compared with NGS, Idylla had a sensitivity of 100%. Analysis of the mutated commercial controls demonstrated agreement with the expected result for all samples and 100% reproducibility. The Idylla system produced results quickly with a turnaround time of approximately 2 h.ConclusionThe Idylla system offers reliable and sensitive testing of clinically actionable mutations in KRAS, NRAS, and BRAF directly from FFPE tissue sections.
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Affiliation(s)
- M Rabie Al-Turkmani
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center and Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Kelley N Godwin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center and Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Jason D Peterson
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center and Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Gregory J Tsongalis
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center and Geisel School of Medicine at Dartmouth, Hanover, NH
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Zekri J, Baghdadi MA, Alardati H, Khallaf H, Kabanja JH. Evaluation of the Idylla KRAS and NRAS mutation test in colorectal cancer tissue. Exp Mol Pathol 2019; 110:104270. [DOI: 10.1016/j.yexmp.2019.104270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/02/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023]
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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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Vallée A, Denis-Musquer M, Herbreteau G, Théoleyre S, Bossard C, Denis MG. Prospective evaluation of two screening methods for molecular testing of metastatic melanoma: Diagnostic performance of BRAF V600E immunohistochemistry and of a NRAS-BRAF fully automated real-time PCR-based assay. PLoS One 2019; 14:e0221123. [PMID: 31415669 PMCID: PMC6695223 DOI: 10.1371/journal.pone.0221123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Screening for theranostic biomarkers is mandatory for the therapeutic management of cutaneous melanoma. BRAF and NRAS genes must be tested in routine clinical practice. The methods used to identify these alterations must be sensitive to detect mutant alleles in a background of wild type alleles, and specific to identify the correct mutation. They should not require too much material, since in some cases the available samples are small biopsies. Finally, they should also be quick enough to allow a rapid therapeutic management of patients. Sixty five consecutive formalin-fixed paraffin-embedded (FFPE) melanoma samples were prospectively tested for BRAF mutations with the VE1 (anti-BRAF V600E) antibody and for both BRAF and NRAS mutations with the Idylla NRAS-BRAF-EGFR S492R Mutation Assay cartridges. Results were compared to our routine laboratory practice, allele specific amplification and/or Sanger sequencing and discordant cases confirmed by digital PCR. Excluding discordant by-design-mutations, system failures and DNA quantity or quality failures, BRAF IHC demonstrated an overall concordance of 89% for BRAF V600E mutation detection, the Idylla system gave a concordance of 100% for BRAF mutation detection and of 92.1% for NRAS mutation detection when compared to our reference. When discrepancies were observed, all routine results were confirmed by digital PCR. Finally, BRAF IHC positive predictive value (PPV) was of 82% and negative predictive value (NPV) of 92%. The Idylla cartridges showed a PPV and NPV of both 100% for BRAF mutation detection and a PPV and NPV of 100% and 87% respectively, for NRAS mutation detection. In conclusion, BRAF V600E immunohistochemistry is efficient for detecting the V600E mutation, but negative cases should be further evaluated by molecular approaches for other BRAF mutations. Since 3 NRAS mutations have not been detected by the Idylla NRAS-BRAF-EGFR S492R Mutation Assay, these cartridges should not be used as a substitute for traditional molecular methods in the conventional patient therapeutic care process without the expertise needed to have a critical view of the produced results.
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Affiliation(s)
- Audrey Vallée
- Department of Biochemistry, Nantes University Hospital, Nantes, France
| | | | | | | | - Céline Bossard
- Department of Pathology, Nantes University Hospital, Nantes, France
| | - Marc G. Denis
- Department of Biochemistry, Nantes University Hospital, Nantes, France
- * E-mail:
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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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Samaison L, Grall M, Staroz F, Uguen A. Microsatellite instability diagnosis using the fully automated Idylla platform: feasibility study of an in-house rapid molecular testing ancillary to immunohistochemistry in pathology laboratories. J Clin Pathol 2019; 72:830-835. [DOI: 10.1136/jclinpath-2019-205935] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 12/25/2022]
Abstract
AimTo study the performances of the Idylla MSI Assay in the diagnosis of microsatellite instability (MSI) or microsatellite stability (MSS).MethodsWe selected 12 tumour samples previously tested for MSI focusing on cases with discrepant results between MLH1, PMS2, MSH2 and MSH6 immunohistochemistry and microsatellite molecular analyses (five cases) or doubtful immunohistochemistry (two cases). Idylla MSI Assay was compared with retrospective immunohistochemistry and molecular results.ResultsIdylla MSI Assay showed an almost perfect concordance with microsatellite analysis results previously obtained (only one case with not fully conclusive analysis due to sample exhaustion). The full molecular analysis took less than 150 min per sample and revealed no mutation in any of the seven microsatellite sequences in five MSS samples and four to six mutated ones in seven MSI-High samples.ConclusionAt the era when the determination of MSI/MSS status is becoming important for rapid treatment choices, the Idylla MSI Assay consists of a valuable easy-to-perform diagnostic tool that allows, complementary to MLH1, PMS2, MSH2 and MSH6 immunohistochemistry, the diagnosis of MSI/MSS status in a single day.
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Fast and Easy-to-Perform BRAF Testing in Melanoma Samples: An Accessible Tool for Pathologists With no Experience in Molecular Analyses. Appl Immunohistochem Mol Morphol 2018; 27:535-536. [PMID: 30320660 DOI: 10.1097/pai.0000000000000666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BRAFV600 mutation testing is mandatory for treatment choices in patients with advanced melanomas. Besides molecular methods, VE-1 immunohistochemistry has paved the way for BRAF mutation detection by every pathologist, but it only detects BRAFV600E mutant protein, and additional DNA-based molecular analyses are often delegated to molecular genetics laboratories to detect mutations other than BRAFV600E. In this technical article, we present a new diagnostic device that is easy to implement in surgical pathology laboratories, even for pathologists lacking any experience in molecular analyses, to diagnose most of the BRAF mutations encountered in melanoma. The implementation of this fast (<2 h per analysis) and fully automated new real-time polymerase chain reaction diagnostic device, in pathology laboratories, could help to reduce the turnaround times for molecular results, to allow rapid subsequent therapeutic choices in patients with advanced melanomas and other cancers.
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Lièvre A, Merlin JL, Sabourin JC, Artru P, Laurent-Puig P, Ducreux M. Towards a RAS mutation status in a single day for patients with advanced colorectal cancers. Authors' reply. Dig Liver Dis 2018; 50:974-975. [PMID: 30005959 DOI: 10.1016/j.dld.2018.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Astrid Lièvre
- Department of Gastroenterology, CHU Pontchaillou, Rennes, France; University of Rennes 1, Rennes, France; INSERM U1242, Oncogenesis, Stress & Signaling, Rennes, France.
| | - Jean-Louis Merlin
- University of Lorraine, Nancy, France; CNRS UMR7039 CRAN, Vandoeuvre-lès-Nancy, France; Biopathology Department, Cancer Institute of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Jean-Christophe Sabourin
- Pathology Department, CHU Charles Nicolle, Rouen, France; Inserm 1079, University of Normandy, Rouen, France
| | - Pascal Artru
- Department of Digestive Oncology, Jean Mermoz Hospital, Lyon, France
| | - Pierre Laurent-Puig
- UMRS-1174 Personnalized Medicine, Pharmacogenomic, Therapeutic Optimization, Paris Descartes University, Paris, France; Department of Biology, Georges Pompidou European Hospital, Paris, France
| | - Michel Ducreux
- Department of Oncology, Gustave Roussy, Paris-Saclay University, Villejuif, France
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Prieto-Potin I, Montagut C, Bellosillo B, Evans M, Smith M, Melchior L, Reiltin W, Bennett M, Pennati V, Castiglione F, Bürrig KF, Cooper U, Dockhorn-Dworniczak B, Rossenbach C, Luna-Aguirre CM, Barrera-Saldaña HA, Machado JC, Costa JL, Yacobi R, Tabibian-Keissar H, Buglioni S, Ronchetti L, Douglas-Berger L, Dubbink HJ, Alorini M, Sabourin JC, Rojo F. Multicenter Evaluation of the Idylla NRAS-BRAF Mutation Test in Metastatic Colorectal Cancer. J Mol Diagn 2018; 20:664-676. [PMID: 29959022 DOI: 10.1016/j.jmoldx.2018.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/01/2018] [Accepted: 05/15/2018] [Indexed: 12/22/2022] Open
Abstract
Treatment of colorectal cancer (CRC) with monoclonal antibodies against epidermal growth factor receptor requires the assessment of the mutational status of exons 2, 3, and 4 of the NRAS and KRAS oncogenes. Moreover, the mutational status of exon 15 of the BRAF oncogene is a marker of poor prognosis in CRC. The Idylla NRAS-BRAF Mutation Test is a reliable, simple (<2 minutes hands-on time), and quick (<2 hours turnaround time) sample-to-result solution, enabling the detection of clinically relevant mutations in NRAS (18 mutations) and BRAF (5 mutations). A multicenter study was conducted in 14 centers using the Idylla NRAS-BRAF Mutation Test to assess the NRAS and BRAF mutational status of 418 formalin-fixed, paraffin-embedded tissue samples from CRC patients. Results were compared with those obtained earlier by routine reference methods, including next-generation sequencing, pyrosequencing, mass spectrometry-based assays, PCR-based assays, and Sanger sequencing. In case of discordance, additional tests were performed by digital droplet PCR. Overall, after testing confirmation and excluding invalids/errors by design, concordances between the Idylla NRAS-BRAF Mutation Test and the reference test results were found in almost perfect agreement. In conclusion, the Idylla NRAS-BRAF Mutation Test enables the routine detection of all NRAS and BRAF mutations deemed clinically relevant according to the latest clinical guidelines, without necessitating molecular expertise or infrastructure.
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Affiliation(s)
- Iván Prieto-Potin
- Molecular Diagnostics Laboratory, Department of Pathology, CIBERONC, The Fundación Jiménez Díaz University Hospital Health Research Institute, Autonomous University of Madrid, Madrid, Spain
| | - Clara Montagut
- Oncology Department, Hospital del Mar, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Matthew Evans
- Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Matthew Smith
- Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Linea Melchior
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | | | - José C Machado
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - José L Costa
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | | | | | - Simonetta Buglioni
- Department of Pathology, Regina Elena National Cancer Institute, Rome, Italy
| | - Livia Ronchetti
- Department of Pathology, Regina Elena National Cancer Institute, Rome, Italy
| | - Lotte Douglas-Berger
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | | - Federico Rojo
- Molecular Diagnostics Laboratory, Department of Pathology, CIBERONC, The Fundación Jiménez Díaz University Hospital Health Research Institute, Autonomous University of Madrid, Madrid, Spain.
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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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