{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T02:07:44Z","timestamp":1762049264770,"version":"build-2065373602"},"reference-count":49,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2022,4,29]],"date-time":"2022-04-29T00:00:00Z","timestamp":1651190400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/genes13050799","type":"journal-article","created":{"date-parts":[[2022,4,29]],"date-time":"2022-04-29T16:49:57Z","timestamp":1651250997000},"page":"799","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Utility of Select Gene Mutation Detection in Tumors by the Idylla Rapid Multiplex PCR Platform in Comparison to Next-Generation Sequencing"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3946-3016","authenticated-orcid":false,"given":"Dingani","family":"Nkosi","sequence":"first","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vektra L.","family":"Casler","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chauncey R.","family":"Syposs","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7997-397X","authenticated-orcid":false,"given":"Zolt\u00e1n N.","family":"Oltvai","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,4,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"148","DOI":"10.3816\/CLC.2009.n.020","article-title":"Individualizing therapy for non-small-cell lung cancer: A paradigm shift from empiric to integrated decision-making","volume":"10","author":"Gandara","year":"2009","journal-title":"Clin. Lung Cancer"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"370","DOI":"10.6004\/jnccn.2017.0036","article-title":"Colon Cancer, Version 1.2017, NCCN Clinical Practice Guidelines in Oncology","volume":"15","author":"Benson","year":"2017","journal-title":"J. Natl. Compr. Cancer Netw."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"945","DOI":"10.6004\/jnccn.2016.0101","article-title":"NCCN Guidelines Insights: Melanoma, Version 3.2016","volume":"14","author":"Coit","year":"2016","journal-title":"J. Natl. Compr. Cancer Netw."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"321","DOI":"10.5858\/arpa.2017-0388-CP","article-title":"Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment with Targeted Tyrosine Kinase Inhibitors: Guideline from the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology","volume":"142","author":"Lindeman","year":"2018","journal-title":"Arch. Pathol. Lab. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/path.4365","article-title":"Next-generation sequencing: A change of paradigm in molecular diagnostic validation","volume":"234","year":"2014","journal-title":"J. Pathol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1136\/jclinpath-2017-204356","article-title":"Validating a fully automated real-time PCR-based system for use in the molecular diagnostic analysis of colorectal carcinoma: A comparison with NGS and IHC","volume":"70","author":"Colling","year":"2017","journal-title":"J. Clin. Pathol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1136\/jclinpath-2017-204629","article-title":"Clinical performance evaluation of the Idylla NRAS-BRAF mutation test on retrospectively collected formalin-fixed paraffin-embedded colorectal cancer tissue","volume":"71","author":"Johnston","year":"2018","journal-title":"J. Clin. Pathol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/j.yexmp.2015.09.004","article-title":"Multi-center evaluation of the novel fully-automated PCR-based Idylla\u2122 BRAF Mutation Test on formalin-fixed paraffin-embedded tissue of malignant melanoma","volume":"99","author":"Melchior","year":"2015","journal-title":"Exp. Mol. Pathol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1136\/jclinpath-2018-205189","article-title":"A review on the Idylla platform: Towards the assessment of actionable genomic alterations in one day","volume":"71","author":"Uguen","year":"2018","journal-title":"J. Clin. Pathol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1136\/jclinpath-2019-205970","article-title":"Rapid clinical mutational testing of KRAS, BRAF and EGFR: A prospective comparative analysis of the Idylla technique with high-throughput next-generation sequencing","volume":"73","author":"Ceulemans","year":"2020","journal-title":"J. Clin. Pathol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1136\/jclinpath-2016-204025","article-title":"The usefulness of a novel fully automated PCR-based Idylla test for detection of the BRAF V600E mutation in thyroid tissue: Comparison with PNA-clamping PCR, real-time PCR and pyrosequencing","volume":"70","author":"Yeo","year":"2017","journal-title":"J. Clin. Pathol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1016\/j.jmoldx.2020.11.009","article-title":"Rapid EGFR Mutation Detection Using the Idylla Platform: Single-Institution Experience of 1200 Cases Analyzed by an In-House Developed Pipeline and Comparison with Concurrent Next-Generation Sequencing Results","volume":"23","author":"Salazar","year":"2021","journal-title":"J. Mol. Diagn."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/nm.4333","article-title":"Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients","volume":"23","author":"Zehir","year":"2017","journal-title":"Nat. Med."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Yao, Y., Xu, Y., Li, L., Gong, Y., Zhang, K., Zhang, M., Guan, Y., Chang, L., and Xia, X. (2021). Pan-cancer circulating tumor DNA detection in over 10,000 Chinese patients. Nat. Commun., 12.","DOI":"10.1038\/s41467-020-20162-8"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1038\/s41588-020-00710-0","article-title":"Cancer therapy shapes the fitness landscape of clonal hematopoiesis","volume":"52","author":"Bolton","year":"2020","journal-title":"Nat. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Pereira, B., Chin, S.-F., Rueda, O.M., Vollan, H.-K.M., Provenzano, E., Bardwell, H.A., Pugh, M., Jones, L., Russell, R., and Sammut, S.-J. (2016). The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes. Nat. Commun., 7.","DOI":"10.1038\/ncomms11908"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1158\/1078-0432.CCR-21-2577","article-title":"Differences in prostate cancer genomes by self-reported race: Contributions of genetic ancestry, modifiable cancer risk factors, and clinical factors","volume":"28","author":"Stopsack","year":"2022","journal-title":"Clin. Cancer Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.ccell.2018.08.008","article-title":"The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers","volume":"34","author":"Razavi","year":"2018","journal-title":"Cancer Cell"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1038\/s41588-018-0312-8","article-title":"Tumor mutational load predicts survival after immunotherapy across multiple cancer types","volume":"51","author":"Samstein","year":"2019","journal-title":"Nat. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.eururo.2020.03.024","article-title":"Pan-cancer Analysis of CDK12 Alterations Identifies a Subset of Prostate Cancers with Distinct Genomic and Clinical Characteristics","volume":"78","author":"Nguyen","year":"2020","journal-title":"Eur. Urol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1158\/2159-8290.CD-20-1726","article-title":"INK4 tumor suppressor proteins mediate resistance to CDK4\/6 kinase inhibitors","volume":"12","author":"Li","year":"2022","journal-title":"Cancer Discov."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/ng.3564","article-title":"Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas","volume":"48","author":"Campbell","year":"2016","journal-title":"Nat. Genet."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.ccell.2017.12.004","article-title":"Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer","volume":"33","author":"Yaeger","year":"2018","journal-title":"Cancer Cell"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4276","DOI":"10.1172\/JCI128227","article-title":"Genetic hallmarks of recurrent\/metastatic adenoid cystic carcinoma","volume":"129","author":"Ho","year":"2019","journal-title":"J. Clin. Investig."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/s41588-018-0078-z","article-title":"The long tail of oncogenic drivers in prostate cancer","volume":"50","author":"Armenia","year":"2018","journal-title":"Nat. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"5537","DOI":"10.1158\/1078-0432.CCR-19-0032","article-title":"Genomic Correlates of Disease Progression and Treatment Response in Prospectively Characterized Gliomas","volume":"25","author":"Jonsson","year":"2019","journal-title":"Clin. Cancer Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.cell.2017.09.027","article-title":"Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma","volume":"171","author":"Reddy","year":"2017","journal-title":"Cell"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1158\/2159-8290.CD-16-1337","article-title":"Prospective Comprehensive Molecular Characterization of Lung Adenocarcinomas for Efficient Patient Matching to Approved and Emerging Therapies","volume":"7","author":"Jordan","year":"2017","journal-title":"Cancer Discov."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/nature25480","article-title":"The landscape of genomic alterations across childhood cancers","volume":"555","author":"Worst","year":"2018","journal-title":"Nature"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/j.cell.2015.09.033","article-title":"Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer","volume":"163","author":"Ciriello","year":"2015","journal-title":"Cell"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.cell.2015.12.028","article-title":"Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma","volume":"164","author":"Ceccarelli","year":"2016","journal-title":"Cell"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1038\/s41586-018-0623-z","article-title":"Functional genomic landscape of acute myeloid leukaemia","volume":"562","author":"Tyner","year":"2018","journal-title":"Nature"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1016\/j.celrep.2016.03.075","article-title":"Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma","volume":"15","author":"Giannakis","year":"2016","journal-title":"Cell Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nature15395","article-title":"Mutations driving CLL and their evolution in progression and relapse","volume":"526","author":"Landau","year":"2015","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/nature20805","article-title":"Integrated genomic characterization of oesophageal carcinoma","volume":"541","author":"Kim","year":"2017","journal-title":"Nature"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive molecular portraits of human breast tumours","volume":"490","author":"Koboldt","year":"2012","journal-title":"Nature"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nature14666","article-title":"Non-coding recurrent mutations in chronic lymphocytic leukaemia","volume":"526","author":"Puente","year":"2015","journal-title":"Nature"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Abida, W., Armenia, J., Gopalan, A., Brennan, R., Walsh, M., Barron, D., Danila, D., Rathkopf, D., Morris, M., and Slovin, S. (2017). Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making. JCO Precis Oncol, 2017.","DOI":"10.1200\/PO.17.00029"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1918","DOI":"10.1182\/blood-2016-07-418434","article-title":"BRAF V600E mutation in hairy cell leukemia: From bench to bedside","volume":"128","author":"Falini","year":"2016","journal-title":"Blood"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"493","DOI":"10.2353\/jmoldx.2008.080105","article-title":"KRAS mutations: An old oncogene becomes a new predictive biomarker","volume":"10","author":"Riely","year":"2008","journal-title":"J. Mol. Diagn"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1200\/JCO.2006.07.3585","article-title":"Molecular predictors of response to epidermal growth factor receptor antagonists in non-small-cell lung cancer","volume":"25","author":"Sequist","year":"2007","journal-title":"J. Clin. Oncol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/jnci\/dji055","article-title":"Clinical and biological features associated with epidermal growth factor receptor gene mutations in lung cancers","volume":"97","author":"Shigematsu","year":"2005","journal-title":"J. Natl. Cancer Inst."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Delgado-Garc\u00eda, M., Weynand, B., G\u00f3mez-Izquierdo, L., Hern\u00e1ndez, M.J., Blanco, \u00c1.M., Varela, M., Matias-Guiu, X., Nadal, E., M\u00e1rquez-Lobo, B., and Alarc\u00e3o, A. (2020). Clinical performance evaluation of the Idylla\u2122 EGFR Mutation Test on formalin-fixed paraffin-embedded tissue of non-small cell lung cancer. BMC Cancer, 20.","DOI":"10.1186\/s12885-020-6697-7"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1016\/j.jmoldx.2019.06.010","article-title":"Multicenter Evaluation of the Fully Automated PCR-Based Idylla EGFR Mutation Assay on Formalin-Fixed, Paraffin-Embedded Tissue of Human Lung Cancer","volume":"21","author":"Evrard","year":"2019","journal-title":"J. Mol. Diagn."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/ajcp\/aqaa044","article-title":"Comparison of Tissue Molecular Biomarker Testing Turnaround Times and Concordance Between Standard of Care and the Biocartis Idylla Platform in Patients with Colorectal Cancer","volume":"154","author":"Tsongalis","year":"2020","journal-title":"Am. J. Clin. Pathol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1136\/jclinpath-2017-204579","article-title":"Financial implications of Idylla testing in colorectal cancer, lung cancer and melanoma: A French laboratory point of view","volume":"70","author":"Guibourg","year":"2017","journal-title":"J. Clin. Pathol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1136\/jclinpath-2016-204202","article-title":"Evaluation of a fast and fully automated platform to diagnose EGFR and KRAS mutations in formalin-fixed and paraffin-embedded non-small cell lung cancer samples in less than one day","volume":"70","author":"Lambros","year":"2017","journal-title":"J. Clin. Pathol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1093\/ajcp\/aqab023","article-title":"IDH1 and IDH2 Mutations in Colorectal Cancers","volume":"156","author":"Huang","year":"2021","journal-title":"Am. J. Clin. Pathol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/5\/799\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:04:02Z","timestamp":1760137442000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/5\/799"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,29]]},"references-count":49,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2022,5]]}},"alternative-id":["genes13050799"],"URL":"https:\/\/doi.org\/10.3390\/genes13050799","relation":{},"ISSN":["2073-4425"],"issn-type":[{"type":"electronic","value":"2073-4425"}],"subject":[],"published":{"date-parts":[[2022,4,29]]}}}