Rapid clinical mutational testing ofKRAS,BRAFandEGFR: a prospective comparative analysis of the Idylla technique with high-throughput next-generation sequencing

Haele, Matthias Van; Borght, Sara Vander; Ceulemans, An; Wieërs, Michiel; Metsu, Sofie; Weynand, Birgit

doi:10.1136/jclinpath-2019-205970

Cited by 32 publications

(25 citation statements)

References 43 publications

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“…The platform can be easily integrated into any clinical molecular diagnostic laboratory, enabling rapid triaging for critical molecular markers. Although several publications have already documented the use of Idylla for FFPE biopsy samples, [39][40][41][42][43][44][45] descriptions of the suitability of cytology samples for this platform have remained confined to a few small, proof-of-principle studies, 46 and the corresponding performance characteristics, clinical validation, and extended clinical experience have remained largely undefined. The application to cytologic material is ideal, however, as it can easily address the issues of TAT and also provide rapid assessment in samples that are very scant and otherwise unsuitable for any other kind of testing.…”

Section: Discussionmentioning

confidence: 99%

Ultrarapid EGFR Mutation Screening Followed by Comprehensive Next-Generation Sequencing: A Feasible, Informative Approach for Lung Carcinoma Cytology Specimens With a High Success Rate

Arcila

Yang

Momeni

et al. 2020

JTO Clinical and Research Reports

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Introduction: For patients with advanced NSCLC, cytologic samples may be the only diagnostic specimen available for molecular profiling. Although both rapid and comprehensive assessment are essential in this setting, an integrated multitest approach remains an important strategy in many laboratories, despite the risks and challenges when working with scant samples. In this study, we describe our experience and high success rate in using a multitest approach, focusing on the clinical validation and incorporation of ultrarapid EGFR testing using the Idylla system followed by comprehensive next-generation sequencing (NGS). Methods: Cytology samples received for routine molecular testing were included in this study. The performance characteristics of the EGFR Idylla assay were assessed; tissue suitability parameters and interpretation criteria to supplement automated mutation calling were established. The assay performance was monitored for 1 year, comparing the results with those of concurrent NGS testing by MSK-IMPACT (primarily) or MSK-AmpliSeq and MSK-Fusion solid panel in a subset of cases.

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Section: Discussionmentioning

confidence: 99%

Ultrarapid EGFR Mutation Screening Followed by Comprehensive Next-Generation Sequencing: A Feasible, Informative Approach for Lung Carcinoma Cytology Specimens With a High Success Rate

Arcila

Yang

Momeni

et al. 2020

JTO Clinical and Research Reports

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“…Such approaches offer shorter reporting times (<1 day), lower limits of detection (down to 1%), less-costly equipment and infrastructure, and less hands-on time, especially for recently developed platforms in which the starting material is a formalin-fixed, paraffin-embedded section. 70 However, the last option may not allow for the discrimination of specific mutations such as G12C. Pyrosequencing is an alternative method of sensitive mutation detection in short stretches of genomic DNA, but fewer laboratories have the requisite platform.…”

Section: State Of Kras-mutation Testing In Tissue Biopsies and Aspiratesmentioning

confidence: 99%

KRAS G12C–Mutant Non–Small Cell Lung Cancer

Mack

Houldsworth

Elkhouly

et al. 2021

The Journal of Molecular Diagnostics

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Mutation in the gene that encodes Kirsten rat sarcoma viral oncogene homolog (KRAS ) is the most common oncogenic driver in advanced nonesmall cell lung cancer, occurring in approximately 30% of lung adenocarcinomas. Over 80% of oncogenic KRAS mutations occur at codon 12, where the glycine residue is substituted by different amino acids, leading to genomic heterogeneity of KRas-mutant tumors. The KRAS glycine-to-cysteine mutation (G12C) composes approximately 44% of KRAS mutations in nonesmall cell lung cancer, with mutant KRas G12C present in approximately 13% of all patients with lung adenocarcinoma. Mutant KRas has been an oncogenic target for decades, but no viable therapeutic agents were developed until recently. However, advances in KRas molecular modeling have led to the development and clinical testing of agents that directly inhibit mutant KRas G12C . These agents include sotorasib (AMG-510), adagrasib (MRTX-849), and JNJ-74699157. In addition to testing for known actionable oncogenic driver alterations in EGFR, ALK, ROS1, BRAF, MET exon 14 skipping, RET, and NTRK and for the expression of programmed cell-death protein ligand 1, pathologists, medical oncologists, and community practitioners will need to incorporate routine testing for emerging biomarkers such as MET amplification, ERBB2 (alias HER2), and KRAS mutations, particularly KRAS G12C, considering the promising development of direct inhibitors of KRas G12C protein.

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“…In the previous reports, the usefulness of kits based on real-time PCR performed in FFPE samples of different tumours was confirmed 16–22. However, records concerning GIST samples analysis are scarce and do not involve mutations in KIT and PDGFRα genes.…”

Section: Discussionmentioning

confidence: 84%

“…It is well known that tissue fixation with formalin affects DNA yield and quality through induction of DNA crosslinking, reflected further in poor results of mutational analysis 15. However, with the more advanced kits and reagents adjusted to such demanding material, currently the mutational analysis on FFPE samples is easier and more commonly performed 16–22. Although KIT and PDGFRα mutations may be detected with the use of various molecular techniques, to date, no such report comparing different methods was provided for GIST samples.…”

Section: Discussionmentioning

confidence: 99%

Justification of direct Sanger sequencing application for detection ofKITandPDGFRαgene mutations in formalin-fixed, paraffin-embedded samples from gastrointestinal stromal tumours

et al. 2019

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AimsThe knowledge concerning genetic background of gastrointestinal stromal tumours (GISTs) is well recognised, and the accurate detection of KIT and PDGFRα mutations is of great importance for the process of disease diagnosis and patient’s treatment. In this study, we compare the usefulness of real-time PCR-based techniques and Sanger sequencing to detect mutations of both genes in 41 formalin-fixed, paraffin-embedded GIST samples.MethodsThe analysis encompassed most frequently mutated coding regions of KIT (exons 9, 11, 13 and 17) and PDGFRα (exons 12, 14 and 18) genes. The GIST Mutation Detection Kit (EntroGen), direct Sanger sequencing and high-resolution melting (HRM) analysis were applied to conduct the study.ResultsWith the application of EntroGen kit, we found alterations in 22/38 samples, with Sanger sequencing variants were found in 36/41 samples. The concordant results for both methods were observed in 19/38 samples. With subsequently applied HRM analysis, we have confirmed that all samples, except one, harboured alterations in the regions indicated by Sanger sequencing.ConclusionsOur results show that in GIST samples, carrying a broad spectrum of deletions, Sanger sequencing is a better, more sensitive method for mutational analysis of KIT and PDGFRα genes.

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Rapid clinical mutational testing ofKRAS,BRAFandEGFR: a prospective comparative analysis of the Idylla technique with high-throughput next-generation sequencing

Cited by 32 publications

References 43 publications

Ultrarapid EGFR Mutation Screening Followed by Comprehensive Next-Generation Sequencing: A Feasible, Informative Approach for Lung Carcinoma Cytology Specimens With a High Success Rate

Ultrarapid EGFR Mutation Screening Followed by Comprehensive Next-Generation Sequencing: A Feasible, Informative Approach for Lung Carcinoma Cytology Specimens With a High Success Rate

KRAS G12C–Mutant Non–Small Cell Lung Cancer

Justification of direct Sanger sequencing application for detection ofKITandPDGFRαgene mutations in formalin-fixed, paraffin-embedded samples from gastrointestinal stromal tumours

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