Epidermal Growth Factor Receptor Mutation Testing Research Articles

The association of EGFR amplification with aberrant exon 20 insertion report using the cobas EGFR Mutation Test v2.

Determining the exact type of epidermal growth factor receptor (EGFR) exon 20 insertion (ex20ins) mutation in lung cancer has become important. We found that not all ex20ins mutations reported by cobas EGFR test v2 could be validated by Sanger sequencing even using surgical specimens with high tumor contents. This study aimed to validate the ex20ins results reported by the cobas test and to determine whether there were clinicopathological factors associated with aberrant cobas ex20ins report. In total, 123 cobas-reported cases with ex20ins were retrospectively collected and validated by Sanger sequencing and Idylla assay. Clinicopathological features between ex20ins cobas+/Sanger+ group (n = 71) and cobas+/Sanger- group (n = 52) were compared. The Idylla assay detected ex20ins in 82.6% of cobas+/Sanger+ cases but only in 4.9% of cobas+/Sanger- cases. The cobas+/Sanger- group was significantly associated with higher tumor contents, poorly differentiated patterns, tumor necrosis, and a lower internal control cycle threshold value reported by the Idylla which suggesting the presence of increased EGFR gene copy numbers. EGFR fluorescence in situ hybridization (FISH) revealed the majority of cobas+/Sanger- group had EGFR high copy number gain (16%) or amplification (76%) according to the Colorado criteria. Among cases reported to have concomitant classic EGFR and ex20ins mutations by the cobas, the classic EGFR mutations were all detected by Sanger sequencing and Idylla, while the ex20ins mutations were undetected by Sanger sequencing (0%) or rarely reported by Idylla assay (3%). FISH revealed high EGFR copy number gain (17.9%) and amplification (79.5%) in cases reported having concomitant classic EGFR and ex20ins mutations by the cobas. This study demonstrated an unusually high frequency of EGFR amplification in cases with aberrant cobas ex20ins report which could not be validated by Sanger sequencing or Idylla assay. Ex20ins reported by the cobas test should be validated using other methods especially those reported having concomitant ex20ins and classic EGFR mutations.

Predicting epidermal growth factor receptor mutations in non-small cell lung cancer through dual-layer spectral CT: a prospective study

ObjectiveTo determine whether quantitative parameters of detector-derived dual-layer spectral computed tomography (DLCT) can reliably identify epidermal growth factor receptor (EGFR) mutation status in patients with non-small cell lung cancer (NSCLC).MethodsPatients with NSCLC who underwent arterial phase (AP) and venous phase (VP) DLCT between December 2021 and November 2022 were subdivided into the mutated and wild-type EGFR groups following EGFR mutation testing. Their baseline clinical data, conventional CT images, and spectral images were obtained. Iodine concentration (IC), iodine no water (INW), effective atomic number (Zeff), virtual monoenergetic images, the slope of the spectral attenuation curve (λHU), enhancement degree (ED), arterial enhancement fraction (AEF), and normalized AEF (NAEF) were measured for each lesion.ResultsNinety-two patients (median age, 61 years, interquartile range [51, 67]; 33 men) were evaluated. The univariate analysis indicated that IC, normalized IC (NIC), INW and ED for the AP and VP, as well as Zeff and λHU for the VP were significantly associated with EGFR mutation status (all p < 0.05). INW(VP) showed the best diagnostic performance (AUC, 0.892 [95% confidence interval {CI}: 0.823, 0.960]). However, neither AEF (p = 0.156) nor NAEF (p = 0.567) showed significant differences between the two groups. The multivariate analysis showed that INW(AP) and NIC(VP) were significant predictors of EGFR mutation status, with the latter showing better performance (p = 0.029; AUC, 0.897 [95% CI: 0.816, 0.951] vs. 0.774 [95% CI: 0.675, 0.855]).ConclusionQuantitative parameters of DLCT can help predict EGFR mutation status in patients with NSCLC.Critical relevance statementQuantitative parameters of DLCT, especially NIC(VP), can help predict EGFR mutation status in patients with NSCLC, facilitating appropriate and individualized treatment for them.Key PointsDetermining EGFR mutation status in patients with NSCLC before starting therapy is essential.Quantitative parameters of DLCT can predict EGFR mutation status in NSCLC patients.NIC in venous phase is an important parameter to guide individualized treatment selection for NSCLC patients.Graphical

Performance characteristics of a polymerase chain reaction-based assay for the detection of EGFR mutations in plasma cell-free DNA from patients with non-small cell lung cancer using cell-free DNA collection tubes.

Survival rates in non-small cell lung cancer (NSCLC) are low. Detection of circulating tumor DNA in liquid biopsy (plasma) is increasingly used to identify targeted therapies for clinically actionable mutations, including EGFR mutations in NSCLC. The cobas® EGFR Mutation Test v2 (cobas EGFR test) is FDA-approved for EGFR mutation detection in tissue or liquid biopsy from NSCLC. Standard K2EDTA tubes require plasma separation from blood within 4 to 8 hours; however, Roche Cell-Free DNA (cfDNA) Collection Tubes (Roche cfDNA tube) enable whole blood stability for up to 7 days prior to plasma separation. This analysis assessed performance of Roche cfDNA tubes with the cobas EGFR test for the detection of EGFR mutations in plasma from healthy donors or patients with NSCLC. Overall, test performance was equally robust with either blood collection tube, eg, regarding limit of detection, linearity, and reproducibility, making Roche cfDNA tubes suitable for routine clinical laboratory use in this setting. Importantly, the Roche cfDNA tubes provided more flexibility for specimen handling versus K2EDTA tubes, eg, in terms of tube mixing, plasma separation, and sample stability, and do not require processing of blood within 8 hours thereby increasing the reach of plasma biopsies in NSCLC.

Abstract 3711: Procedure establishment of EGFR mutation test with circulating tumor cells of lung cancer by in vitro assay

Abstract Introduction: Non-small cell lung cancer (NSCLC) is the most common subtype, accounting for approximately 80% of lung cancer. The treatment for NSCLC has significantly improved since the introduction of targeted therapies. Epidermal growth factor receptor (EGFR) mutations are the most frequently found genetic alterations in NSCLC, and deletion of exon 19 is a representative example. Searching for this mutation may provide important clues to the use of EGFR tyrosine kinase inhibitors in NSCLC. So, the detection of EGFR mutation is important step in cancer diagnosis and determining the drug treatment strategy, but the detection of mutation with tissues has limitations such as clinical challenge to poorly accessible tumor tissues before and after treatment. The aim of this study was to explore the feasibility and utility of implementation of EGFR molecular testing from circulating tumor cells (CTC) in NSCLC. Here, we developed and optimized the procedure of mutated EGFR detection in CTC after isolation with CytoGen’s Smart BiopsyTM CTC isolator by cobas® EGFR Mutation Test. This EGFR mutation test in CTC showed the potential to overcome the limitations of tissue biopsy with high sensitivity and specificity in an in vitro assay. Method: PC-9 cells were used the positive control of EGFR mutation (EGFR exon 19 deletion). Limit of detection (LOD) was performed with PC-9 cells (200 cells to 5 cells, 6 points) spiked into blood sample (5mL, healthy donor) to mimic CTC in the blood of lung cancer patient. CTC were isolated from spiked samples using CytoGen’s Smart BiopsyTM CTC isolator, subsequently cobas® EGFR Mutation Test was carried out to detect of EGFR mutation. Results: In in vitro experiments of recovery test using cell lines spiked into blood from healthy donor, the recovery rate of CytoGen’s Smart Biopsy TM CTC isolator showed over 80%. As a result of LOD test, EGFR exon19 deletion mutation of PC-9 cells was clearly detected even in the smallest number of cells were spiked into blood (5 cells in 5mL blood) and was not detected at all in the negative controls. The result suggested that CytoGen’s Smart Biopsy TM CTC isolator can isolate CTC with high recovery rate and apply the test of oncogenic mutations including EGFR mutation in CTC. Conclusions: Confirmation of EGFR mutation is important step in the diagnosis and selection of optimal drug for cancer patients. However, tissue biopsy has several limitations such as difficulties to get tissue samples and inaccurate information due to invasive method and tumor heterogeneity. Detection of EGFR mutation in CTC might overcome and make up for limitations of tissue biopsy. In this study, we optimized the EGFR mutation detection procedure of intact live CTC isolated by CytoGen’s Smart BiopsyTM CTC isolator. Citation Format: Jihyun Lee, Hoin Kang, Min Hyung Kim, Jubi Lee, Hyoyong Kim, Soee Kim, Hae Ung Lee, Hai-Chon Lee, Jung Won Kim. Procedure establishment of EGFR mutation test with circulating tumor cells of lung cancer by in vitro assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3711.

Abstract 1299: Cost-effectiveness analysis of circulating tumor DNA-based molecular profiling platforms for the detection of EGFR mutations in lung cancer

Abstract Background The detection of mutations in circulating tumor DNA (ctDNA) in blood plasma of lung cancer patients can be used to monitor the tumor-response to therapy and for the early detection of resistance mechanisms. In 2017, the Roche Cobas® EGFR Mutation Test v2 for the detection of the EGFR c.2369C&amp;gt;T p.(T790M) mutation in plasma-derived ctDNA was FDA-approved to identify patients eligible for osimertinib treatment. Today, different platforms are available for EGFR mutation testing in plasma-derived cell-free DNA (cfDNA). In this study we compared the clinical utility of five platforms for the detection of EGFR mutations in cfDNA offering insights into their operational costs, target coverage, hands-on-time and turn-around-time. Methods Four PCR-based platforms and one NGS-based approach for the detection of EGFR mutations were compared. Operational, maintenance, material and personnel costs were calculated for each platform and used as input variables for our recently developed ctDNA micro-costing framework (doi.org/10.1016/j.jmoldx.2022.10.004). This was compared to target coverage and turn-around-time of each platform in the context of therapy resistance. Results Per sample costs decreased for all platforms at maximal weekly throughput. The BioCartis Idylla™ demonstrated the shortest turn-around-time while the Roche Cobas® was the least expensive. Despite being the most expensive and time-consuming, the AVENIO ctDNA Expanded kit covered the most known resistance mechanisms to EGFR inhibitors, many of which are targetable with other TKIs. Conclusion EGFR ctDNA mutation analysis is only cost-effective when the throughput is high. This implies that centralization of cfDNA-testing is necessary to optimize cost-efficiency. With the advent of ctDNA analysis beyond EGFR in the context of targeted therapies for lung cancer, multigene detection assays will become more cost-effective with high throughput. Overview of results Platform Turn-around time at maximal weekly throughput Per sample cost at maximal weekly throughput Coverage of resistance mutations in EGFR 1Additional testing necessary Coverage of genome-wide resistance mutations to EGFR-TKI 1Additional testing necessary BioCartis Idylla™ ctEGFR Mutation Assay 2,5 hours €571 33% 12%1 Roche Cobas® EGFR Mutation Test v2 4 hours €497 33% 6% Bio-Rad QX200 droplet digital PCR (ddPCR) 7,5 hours €766 100%1 24%1 Agena MassARRAY® UltraSEEK® Lung Panel 2 days €613 53% 12% Roche AVENIO ctDNA Expanded kit 1 week €1551 100% 65% Citation Format: Pim Rozendal, Paul van der Leest, Elise M. van der Logt, Naomi Rifaela, Inge Platteel, Frank J. Scherpen, Harry J. Groen, Léon C. van Kempen, Ed M. Schuuring. Cost-effectiveness analysis of circulating tumor DNA-based molecular profiling platforms for the detection of EGFR mutations in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1299.

High-efficiency EGFR genotyping using cell-free DNA in bronchial washing fluid.

EGFR mutation testing is required for treatment of lung adenocarcinoma using epidermal growth factor receptor-tyrosine kinase inhibitor. However, the amounts of tumor tissue or tumor cells obtained by bronchoscopy are often insufficient. Bronchial washing fluid, obtained by lavage with saline after tumor biopsy or brushing, and the supernatant of bronchial washing fluid are thought to contain cell-free DNA that would be potentially applicable for EGFR testing. From among patients with suspected adenocarcinoma or non-small cell lung carcinoma diagnosed from biopsy or surgical specimens at the University of Tsukuba Hospital between 2015 and 2019, cell-free DNAs from 80 specimens of supernatant of bronchial washing fluid (50 with EGFR mutation and 30 with wild type EGFR) and 8 blood serum samples were examined for EGFR mutation using droplet digital PCR. Among the 50 patients harboring EGFR mutation, the rate of positivity for cell-free DNA extracted from supernatant of bronchial washing fluid was 80% (40/50). In nine of the EGFR mutation-positive cases, tumor cells were not detected by either biopsy or cytology, but the mutation was detected in four cases (4/9, 44%). Comparison of the cell-free DNA mutation detection rate between supernatant of bronchial washing fluid and blood serum in six cases showed that mutations were detected from the former in all cases (6/6, 100%), but from the latter in only one case (1/6, 17%). Using supernatant of bronchial washing fluid samples, the detection rate of EGFR mutation was high, and EGFR mutations were detectable even when no tumor cells had been detectable by biopsy or cytology. Supernatant of bronchial washing fluid might be an effective sample source for EGFR mutation testing.

Deep learning–radiomics integrated noninvasive detection of epidermal growth factor receptor mutations in non-small cell lung cancer patients

This study focused on a novel strategy that combines deep learning and radiomics to predict epidermal growth factor receptor (EGFR) mutations in patients with non-small cell lung cancer (NSCLC) using computed tomography (CT). A total of 1280 patients with NSCLC who underwent contrast-enhanced CT scans and EGFR mutation testing before treatment were selected for the final study. Regions of interest were segmented from the CT images to extract radiomics features and obtain tumor images. These tumor images were input into a convolutional neural network model to extract 512 image features, which were combined with radiographic features and clinical data to predict the EGFR mutation. The generalization performance of the model was evaluated using external institutional data. The internal and external datasets contained 324 and 130 EGFR mutants, respectively. Sex, height, weight, smoking history, and clinical stage were significantly different between the EGFR-mutant patient groups. The EGFR mutations were predicted by combining the radiomics and clinical features, and an external validation dataset yielded an area under the curve (AUC) value of 0.7038. The model utilized 1280 tumor images, radiomics features, and clinical characteristics as input data and exhibited an AUC of approximately 0.81 and 0.78 during the primary cohort and external validation, respectively. These results indicate the feasibility of integrating radiomics analysis with deep learning for predicting EGFR mutations. CT-image-based genetic testing is a simple EGFR mutation prediction method, which can improve the prognosis of NSCLC patients and help establish personalized treatment strategies.

Subregion-specific 18F-FDG PET-CT radiomics for the pre-treatment prediction of EGFR mutation status in solid lung adenocarcinoma.

This study aimed to assess the efficacy of fluor-18 fluorodeoxyglucose (18F-FDG) PET/CT using sub-regional-based radiomics in predicting epidermal growth factor receptor (EGFR) mutation status in pretreatment patients with solid lung adenocarcinoma. A retrospective analysis included 269 patients (134 EGFR+ and 135 EGFR-) who underwent pretreatment 18F-FDG PET/CT scans and EGFR mutation testing. The most metabolically active intratumoral sub-region was identified, and radiomics features from whole tumors or sub-regional regions were used to build classification models. The dataset was split into a 7:3 ratio for training and independent testing. Feature subsets were determined by Pearson correlation and the Kruskal Wallis test and radiomics classifiers were built with support vector machines or logistic regressions. Evaluation metrics, including accuracy, area under the curve (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were employed for different classifiers. Results indicated that the sub-region-based classifier outperformed the whole-tumor classifier in terms of accuracy (73.8% vs. 66.2%), AUC (0.768 vs. 0.632), specificity (65.0% vs. 50.0%), PPV (70.2% vs. 62.2%), and NPV (78.8% vs. 74.0%). The clinical classifier exhibited an accuracy of 75.0%, AUC of 0.768, sensitivity of 72.5%, specificity of 77.5%, PPV of 76.3%, and NPV of 73.8%. The combined classifier, incorporating sub-region analysis and clinical parameters, demonstrated further improvement with an accuracy of 77.5%, AUC of 0.807, sensitivity of 77.5%, specificity of 77.5%, and NPV of 77.5%. The study suggests that sub-region-based 18F-FDG PET/CT radiomics enhances EGFR mutation prediction in solid lung adenocarcinoma, providing a practical and cost-efficient alternative to invasive EGFR testing.

Evaluation of the Idylla™ EGFR Mutation Test on formalin-fixed, paraffin-embedded tissue of human lung cancer.

Epidermal growth factor receptor (EGFR) mutation detection is essential for the therapy of lung cancer. A sensitive, specific, and cost-effective standardized method to quickly and accurately detect EGFR mutations is urgently needed. We evaluated the Idylla™ EGFR Mutation Assay for EGFR mutations in formalin-fixed, paraffin-embedded (FFPE) tumor samples from 232 lung cancer patients, and compared the results with amplification refractory mutation system (ARMS) (n=146) and next-generation sequencing (NGS) (n=86). The surgical tumor sections and cell blocks derived from the same FFPE section were compared. Overall concordance, specificity, sensitivity, cost-effectiveness and turnaround time were compared among the three methods. The overall concordance between Idylla and ARMS was 89.51% [95% confidence interval (CI): 83.31% to 93.64%] and the specificity of Idylla was 88.68% (95% CI: 80.69% to 93.76%). A concordance of 97.67% (95% CI: 91.41% to 99.86%) was obtained between Idylla and NGS, the specificity of Idylla was 96.30% (95% CI: 86.16% to 99.36%). Compared to the ARMS and NGS, the Idylla™ system significantly reduces the turnaround time. Combining labor, equipment, reagents and time costs, Idylla is more affordable. Clinically urgent cases with adequate cellularity, can first perform Idylla to detect critical markers, then perform NGS for a comprehensive mutation analysis. Besides, with limited molecular expertise or infrastructure, the Idylla has the potential to extend EGFR testing to more pathology laboratories in primary hospitals.

EGFR-mutation testing, treatment patterns and clinical outcomes in patients with stage IB–IIIA non-small cell lung cancer in Norway–a nationwide cohort study

IntroductionTesting for mutations of epidermal growth factor receptor (EGFR) is crucial to identify non-small cell lung cancer (NSCLC) patients eligible for treatment with EGFR tyrosine kinase inhibitors (EGFR-TKIs); This study aims to describe EGFR-mutation testing, treatment patterns, and overall survival (OS) in localized NSCLC patients. Materials and MethodsPatients with localized (Stage IB–IIIA) NSCLC registered in the Norwegian Cancer Registry during 2010–2017 were followed from diagnosis until emigration, death, or end of study in 2018. The cohort was linked to data from the Norwegian Patient Registry, the Prescription Database, and the Cause of Death Registry. ResultsOf 2367 patients identified with localized NSCLC, 52 % were females and median age at diagnosis was 69 years. Most (66 %) were treated with surgery, while 16 % received curatively-intended radiotherapy (RT). EGFR-mutation testing increased significantly from 58 to 84 % during the study period. Testing frequencies varied across regions and comorbidity levels. Nine-percent of tested patients were EGFR-mutation positive (EGFRm+), of whom 27 % were treated with EGFR-TKIs. There was no correlation between initial treatment with either surgery or RT and EGFR-TKI use. The 3-year OS did not vary considerably by EGFR-mutation testing, but EGFRm+ patients had a higher 3-year OS (78.8 %) than wild-type EGFR (EGFRwt) patients (65.9 %). DiscussionAlthough EGFR-mutation testing is increasingly being implemented in the early-stage setting in line with national recommendations, some patients are still not being tested for molecular markers as part of their diagnostic workup–a prerequisite for providing equal access to effective targeted treatments, such as EGFR-TKIs, to eligible patients.

Concordance of Immunohistochemistry and Fluorescence In Situ Hybridization in the Detection of Anaplastic Lymphoma Kinase (ALK) and Ros Proto-oncogene 1 (ROS1) Gene Rearrangements in Non-Small Cell Lung Carcinoma: A 4.5-Year Experience Highlighting Challenges and Pitfalls.

ALK and ROS1 rearrangements are essential biomarkers to be tested in advanced lung adenocarcinomas. While D5F3 Ventana assay is a companion diagnostic for anaplastic lymphoma kinase-targeted therapy, immunohistochemistry is only a screening tool for detecting ROS1 rearrangement. Confirmation by cytogenetic or molecular techniques is necessary. To evaluate the utility of ALK and ROS1 fluorescence in situ hybridization as a complement to immunohistochemistry in routine predictive biomarker testing algorithms. The study was ambispective, spanning 4.5 years during which lung adenocarcinoma samples were subjected to EGFR mutation testing by real-time polymerase chain reaction, and ALK/ROS1 rearrangement testing by immunohistochemistry (Ventana D5F3 assay for anaplastic lymphoma kinase protein; manual assay with D4D6 clone for Ros proto-oncogene 1 protein). Fluorescence in situ hybridization was performed in all anaplastic lymphoma kinase equivocal and Ros proto-oncogene 1 immunopositive cases. Of 1874 samples included, EGFR mutations were detected in 27% (481 of 1796). Anaplastic lymphoma kinase immunohistochemistry was positive in 10% (174 of 1719) and equivocal in 3% (58 of 1719) of samples tested. ALK fluorescence in situ hybridization showed 81% (77 of 95) concordance with immunohistochemistry. Ros proto-oncogene 1 immunopositivity was noted in 13% (190 of 1425) of cases, with hybridization-confirmed rearrangements in 19.3% (26 of 135) of samples, all of which showed diffuse, strong- to moderate-intensity, cytoplasmic staining in tumor cells. Ros proto-oncogene 1 protein overexpression without rearrangement was significantly common in EGFR-mutant and ALK-rearranged adenocarcinomas. Immunostaining is a robust method for ALK-rearrangement testing, with fluorescence in situ hybridization adding value in the rare equivocal stained case. ROS1-rearrangement testing is more cost-effective if immunohistochemistry is followed by fluorescence in situ hybridization after excluding EGFR-mutant and ALK-rearranged adenocarcinomas.

Correlation between carcinoembryonic antigen (CEA) expression and EGFR mutations in non-small-cell lung cancer: a meta-analysis.

The purpose of this meta-analysis was to investigate the relationship between serum carcinoembryonic antigen (CEA) expression and epidermal growth factor receptor (EGFR) mutation status in non-small cell lung cancer (NSCLC). Databases such as PubMed, Cochrane, EMBASE and Google Scholar were systematically searched to identify studies assessing the association of serum CEA expression with EGFR mutations. Across 19 studies, 4168 patients were included between CEA expression and EGFR mutations odds ratio (OR) conjoint analysis of correlations. Compared with CEA-negative NSCLC, CEA-positive tumors had an increased EGFR mutation rate (OR = 1.85, 95% confidence interval: 1.48-2.32, P < 0.00001). This association was observed in both stage IIIB/IV patients (OR = 1.60, 95% CI: 1.18-2.15, P = 0.002) and stage I-IIIA (OR = 1.67, 95% CI: 1.01-2.77, P = 0.05) patients. In addition, CEA expression was associated with exon 19 (OR = 1.97, 95% CI: 1.25-3.11, P = 0.003) and exon 21 (OR = 1.51, 95% CI: 1.07-2.12, P = 0.02) EGFR mutations. In ADC pathological type had also showed the correlation (OR = 1.84, 95% CI: 1.31-2.57, P = 0.0004). This meta-analysis indicated that serum CEA expression was associated with EGFR mutations in NSCLC patients. The results of this study suggest that CEA level may play a predictive role in the EGFR mutation status of NSCLC patients. Detecting serum CEA expression levels can give a good suggestion to those patients who are confused about whether to undergo EGFR mutation tests. Moreover, it may help better plan of the follow-up treatment.

EP06.03-09 Characteristics of Insufficient Samples for EGFR Mutation Testing at the Lung Center of the Philippines

EP06.03-09 Characteristics of Insufficient Samples for EGFR Mutation Testing at the Lung Center of the Philippines

Adequacy of cytology and small biopsy samples obtained with rapid onsite evaluation (ROSE) for predictive biomarker testing in non-small cell lung cancer

Complete biomarker workup of non-small cell lung cancer (NSCLC) specimens is essential for appropriate and timely clinical management decisions. This can be challenging to achieve from small cytology and histology specimens, with increasing numbers of molecular and immunohistochemical biomarkers required. We conducted a 5 year retrospective audit of cases at our institution to assess the diagnostic and biomarker testing adequacy rates, particularly those specimens obtained with rapid onsite evaluation (ROSE), performed by a cytopathologist and a cytology scientist or pathology trainee, including all endobronchial ultrasound guided transbronchial needle aspirations (EBUS-TBNA), CT guided lung fine needle aspirations (FNA) and CT guided lung core biopsies. A total of 5,354 cases were identified, of which 92.2% had sufficient material for diagnosis. Of the 1506 cases identified with a recorded diagnosis of lung adenocarcinoma or NSCLC, not otherwise specified, 1001 (66.5%) had biomarker testing requested. Sufficient material was available in 89.5% of cases for a complete biomarker workup which included EGFR and KRAS mutational testing (all cases), ALK, ROS1 and PD-L1 immunohistochemistry (all cases), and ALK and ROS1 FISH (as required). For EGFR and KRAS mutational testing across both cytology and histology specimens, 99% of cases were sufficient. Of the samples in which a complete biomarker workup was unable to be performed, approximately half were only insufficient due to inadequate numbers of tumour cells for PD-L1 immunohistochemistry. Excluding PD-L1 IHC, 952 (95.1%) of samples obtained with ROSE were sufficient for the remainder of the testing requirements. Next generation sequencing using a 33 gene custom AmpliSeq panel was achieved in up to 72% of cases. In conclusion, small cytology and histology specimens obtained with ROSE are suitable for predictive biomarker testing in NSCLC, although attention needs to be paid to obtaining sufficient cells (>100) for PD-L1 immunohistochemistry.

EGFR mutation testing from pleural effusions of non-small cell lung cancer patients at the institute for oncology and radiology of Serbia

BackgroundThe use tumor-derived cell-free DNA extracted from body fluids is being evaluated for genetic testing in lung cancer. The aim of this study was to explore the feasibility and utility of implementation of EGFR molecular testing from pleural effusions in non-small cell lung cancer in the clinical diagnostics workflow. Patients and methodsThis study included patients diagnosed with primary lung adenocarcinoma in the period July 2016 to June 2023. EGFR mutation testing was performed by qPCR (Cobas®) and dPCR. Testing was performed from 211 plasma samples when tissue was unavailable at diagnosis, and from 301 plasma samples and 18 pleural effusions at progression on first/second generation of EGFR TKIs. Descriptive methods of statistical analysis were used to summarize the sample data. Fisher's exact test, McNemar's test, Cohen's kappa tests were used for statistical analyses. Two-sided p-values <0.05 were considered statistically significant. ResultsA significantly higher detection rate of the T790M mutation in pleural effusion was obtained compared to blood (50% and 20%, p=0.047). When comparing the detection success rate of the resistant T790M mutation in pleural effusion and blood, a statistically significant difference was obtained in favor of pleural effusion (50% vs. 21.87%, p=0.01). ConclusionsSuperior performance of pleural effusions compared to blood plasma was shown both in the analysis of success rate and in the detection of the resistant T790M mutation, at progression on EGFR TKIs. Pleural effusion should be considered in this setting whenever available, especially in countries with limited health resources.

Epidermal Growth Factor Receptor T790M Mutation Testing in Non-Small Cell Lung Cancer: An International Collaborative Study to Assess Molecular EGFR T790M Testing in Liquid Biopsy.

The detection of the EGFR T790M (T790M) mutation in non-small cell lung cancer (NSCLC) patients who progressed under treatment with first- or second-generation EGFR-tyrosine kinase inhibitors (TKIs) is important to offer a subsequent therapy with a third-generation EGFR-TKI. Liquid biopsy is a powerful tool to determine the T790M mutation status. Several liquid biopsy platforms with varying degrees of accuracy are available to test for T790M mutations, and sensitivities may differ among these methods. As no standard exists for the testing of T790M mutation in liquid biopsy, we performed a collaborative study to describe and compare the sensitivity of different in-house liquid biopsy platforms for the detection of the T790M mutation, EGFR exon 19 deletion (del19) and EGFR L858R mutation (L858R) across multiple participating laboratories in seven Central and Eastern European countries. Of the 25 invited laboratories across Central and Eastern Europe, 21 centers participated and received 10 plasma samples spiked with cell-line DNA containing the T790M, del19, or L858R mutation in different concentrations. In-house PCR-based and NGS-based methods were used accordingly, and results were reported as in routine clinical practice. Two laboratories, which used the AmoyDx® EGFR 29 Mutations Detection Kit (AmoyDx) with Cobas® cfDNA Sample Preparation Kit and QX200 Droplet Digital PCR (ddPCR) with the QIAamp Circulating Nucleic Acid Kit identified all ten samples correctly. Cobas® EGFR Mutation Test v2 (Cobas), the NGS methods, and the IdyllaTM detection method used in this study performed within the known sensitivity range of each detection method. If a negative result was obtained from methods with lower sensitivity (e.g., Cobas), repeated liquid biopsy testing and/or tissue biopsy analysis should be performed whenever possible, to identify T790M-positive patients to allow them to receive the optimal second-line treatment with a third-generation EGFR TKI.

Clinical Validation of the Unparalleled Sensitivity of the Novel Allele-Discriminating Priming System Technology-Based EGFR Mutation Assay in Patients with Operable Non-Small Cell Lung Cancer.

Recently, we developed allele-discriminating priming system (ADPS) technology. This method increases the sensitivity of conventional quantitative polymerase chain reaction up to 100 folds, with limit of detection, 0.01%, with reinforced specificity. This prospective study aimed to develop and validate the accuracy of ADPS epidermal growth factor receptor (EGFR) Mutation Test Kit using clinical specimens. In total 189 formalin-fixed paraffin-embedded tumor tissues resected from patients with non-small cell lung cancer were used to perform a comparative evaluation of the ADPS EGFR Mutation Test Kit versus the cobas EGFR Mutation Test v2, which is the current gold standard. When the two methods had inconsistent results, next-generation sequencing-based CancerSCAN was utilized as a referee. The overall agreement of the two methods was 97.4% (93.9%-99.1%); the positive percent agreement, 95.0% (88.7%-98.4%); and the negative percent agreement, 100.0% (95.9%-100.0%). EGFR mutations were detected at a frequency of 50.3% using the ADPS EGFR Mutation Test Kit and 52.9% using the cobas EGFR Mutation Test v2. There were 10 discrepant mutation calls between the two methods. CancerSCAN reproduced eight ADPS results. In two cases, mutant allele fraction was ultra-low at 0.02% and 0.06%, which are significantly below the limit of detection of the cobas assay and CancerSCAN. Based on the EGFR genotyping by ADPS, the treatment options could be switched in five patients. The highly sensitive and specific ADPS EGFR Mutation Test Kit would be useful in detecting the patients who have lung cancer with EGFR mutation, and can benefit from the EGFR targeted therapy.

Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma EGFR Mutations.

The clinical utility of circulating tumor DNA (ctDNA) in the early detection of tumor mutations for targeted therapy and the monitoring of tumor recurrence has been reported. However, the analytical validation of ctDNA assays is required for clinical application. This study evaluated the analytical performance of the Oncomine Lung cfDNA Assay compared with the cobas®EGFR Mutation Test v2. The analytical specificity and sensitivity were estimated using commercially pre-certified reference materials. The comparative evaluation of the two assays was carried out using reference materials and plasma derived from patients diagnosed with lung cancer. Using 20 ng of input cell-free DNA (cfDNA), the analytical sensitivities for EGFR mutations with variant allele frequencies (VAFs) of 1% and 0.1% were 100% and 100%, respectively. With VAFs of 1.2% and 0.1% using 20 ng of input cfDNA, seven out of nine different mutations in six driver genes were identified in the Oncomine Lung cfDNA Assay. The two assays showed 100% concordance in 16 plasma samples clinically. Furthermore, various PIK3CA and/or TP53 mutations were identified only in the Oncomine Lung cfDNA Assay. The Oncomine Lung cfDNA Assay can be used to identify plasma EGFR mutations in patients with lung cancer, although further large-scale studies are required to evaluate the analytical validity for other types of aberrations and genes using clinical samples.

Real world EGFR testing practices for non-small cell lung cancer by thoracic pathology laboratories across Europe.

e21064 Background: Testing for EGFR mutations is an essential recommendation in both the ESMO and ASCO guidelines for metastatic non-squamous NSCLC, and is considered mandatory in European countries. However, in practice, considerable challenges are often faced when performing routine biomarker testing, including access to testing, inadequate tissue samples, and long turnaround times (TATs). Methods: In order to evaluate the real-world EGFR testing practices of thoracic pathology laboratories across Europe, an online survey was set up and validated by The Pulmonary Pathology Working Group of the European Society of Pathology and distributed to 64 expert testing laboratories across Europe. The retrospective survey focused on the laboratory organisation and daily practice of pathologists and molecular biologists between 2018 and 2021, and covered the clinical circumstances in which EGFR testing was performed, sample types used, molecular biology techniques performed, average TATs for determining EGFR status, annual EGFR testing rates, laboratory accreditation, and external quality assessment. Results: TATs varied greatly depending on different parameters (notably relating to testing practices and methods used) both between and within countries. TATs were slightly (but non-significantly) faster for liquid biopsy samples (Mean: 7 days, IQR 4.5-12.5) when compared to tissue samples (mean 7 days, IQR 5-15) but were reported to take as long as 20 or 30 days, respectively. Discrepancies in TATs may be due in part to reflex testing practices, as 20% (11/54) of laboratories performed EGFR testing only at the request of the clinician. Many laboratories across Europe still favour targeted sequencing as a primary method of EGFR mutation identification; 32.7% indicated that they only used targeted techniques, and 45.1% indicated they used targeted sequencing followed by NGS, depending on the case. Reported testing volumes were consistent over time with no significant decrease in the number of EGFR tests performed observed in 2020, despite the increased pressure and difficulties faced by testing facilities during the COVID-19 pandemic. ISO 15189 accreditation was reported by 42% of molecular biology laboratories for targeted sequencing, and by 42.3% for NGS. 92% (49/53) of laboratories indicated they regularly participate in an EQA scheme. Conclusions: The results of the survey highlight the strong heterogeneity of EGFR testing that still occurs within thoracic pathology and molecular biology laboratories across Europe. Even among expert testing facilities there remains large variability in testing capabilities, reflex testing practice and laboratory accreditation, which stresses the urgent need to harmonize budgets and reimbursement in Europe, in addition to harmonization of the technologies and decision-making algorithms.

L858R-K860I Doublet Mutation of EGFR gene in Non-Small Cell Lung Carcinoma: Cause of a False Negative Call for L858R on Initial Companion Diagnostic Test

With the advent of targeted therapy in non-small cell lung carcinoma (NSCLC), biomarker detection has become standard practice. US Food and Drug Administration (FDA) has approved a few companion diagnostics as single gene assays to find these driver mutations. We report a case of NSCLC where initial molecular tests to detect epidermal growth factor receptor ( EGFR)- sensitizing mutations by an FDA-approved assay (Cobas® EGFR Mutation Test v2) failed to identify the common EGFR mutation L858R. However, the latter was picked up on subsequent next-generation sequencing (NGS). Interestingly an additional single nucleotide variant K860I was also observed in the cis configuration. The false-negative result for L858R was assumed to be caused by the abrogation of complementarity for the probe binding site on the amplicon generated. The concurrent occurrence of L858R and K860I will not be detectable by Cobas® EGFR Mutation Test v2 (FDA-approved companion diagnostic) despite its real-world intra and inter-laboratory studies demonstrating high accuracy.