scholarly journals Detection of EGFR Mutations in Plasma Cell-Free Tumor DNA of TKI-Treated Advanced-NSCLC Patients by Three Methodologies: Scorpion-ARMS, PNAClamp, and Digital PCR

Diagnostics ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1062
Author(s):  
Annamaria Siggillino ◽  
Paola Ulivi ◽  
Luigi Pasini ◽  
Maria Sole Reda ◽  
Elisa Chiadini ◽  
...  
Keyword(s):  
Kinase Inhibitors ◽  
Growth Factor Receptor ◽  
Digital Pcr ◽  
Egfr Mutations ◽  
Amplification Refractory Mutation System ◽  
Clinical Method ◽  
Thermo Fisher Scientific ◽  
Exon 19 Deletion ◽  
Nsclc Patients ◽  
Tumor Dna

Analysis of circulating cell-free tumor DNA (cftDNA) has emerged as a specific and sensitive blood-based approach to detect epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) patients. Still, there is some debate on what should be the preferential clinical method for plasma-derived cftDNA analysis. We tested 31 NSCLC patients treated with anti-EGFR tyrosine kinase inhibitors (TKIs), at baseline and serially during therapy, by comparing three methodologies in detecting EGFR mutations (L858R, exon 19 deletion, and T790M) from plasma: scorpions-amplification refractory mutation system (ARMS) methodology by using EGFR Plasma RGQ PCR Kit-QIAGEN, peptide nucleic acid (PNA) clamp and PANA RealTyper integration by using PNAClamp EGFR-PANAGENE, and digital real time PCR by using QuantStudio 3D Digital PCR System-Thermo Fisher Scientific. Specificity was 100% for all three mutations, independently from the platform used. The sensitivity for L858R (42.86%) and T790M (100%) did not change based on the method, while the sensitivity for Del 19 differed markedly (Scorpion-ARMS 45%, PNAClamp 75%, and Digital PCR 85%). The detection rate was also higher (94.23%) as measured by Digital PCR, and when we monitored the evolution of EGFR mutations over time, it evidenced the extreme inter-patient heterogeneity in terms of levels of circulating mutated copies. In our study, Digital PCR showed the best correlation with tissue biopsy and the highest sensitivity to attain the potential clinical utility of monitoring plasma levels of EGFR mutations.

Assessment of EGFR mutation status in matched plasma and tumor tissue of NSCLC patients.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e20032-e20032
Author(s):  
Qin Feng
Keyword(s):  
Tumor Tissue ◽  
Egfr Mutation ◽  
Circulating Tumor Dna ◽  
Egfr Mutations ◽  
Amplification Refractory Mutation System ◽  
Circulating Dna ◽  
Mutation Status ◽  
Nsclc Patients ◽  
Tumor Dna ◽  
Egfr Tkis

e20032 Background: Tumor tissue is currently used for EGFR testing non-small cell lung cancer (NSCLC) patients, but the detection of circulating tumor DNA (ctDNA) is being actively investigated as a new method for the detection and longitudinal monitoring of actionable mutations in plasma samples. Around 30% patients with EGFR mutation presented inconsistent status of EGFR mutation between in tissues and plasma. We compared EGFR mutation detection in circulating tumor DNA from blood to that in matched tissue. Methods: EGFR mutation status were assessed by the Human EGFR Gene Mutations Detection Kit (Beijing ACCB Biotech Ltd.) both in tissue and plasma. Retrospective analysis to evaluate the concordance of tissue and plasma EGFR determination for assessing eligibility for EGFR-TKIs therapy in NSCLC patients. 10 mL tubes of blood were collected from patients who never had been treated by EGFR TKI, and plasma circulating tumor DNA were extracted from plasma by Biomark Circulating DNA Kit. Qubit2.0 Fluorometer was used to make plasma circulating DNA tumor quantitation. The concentration of final DNA sample is ≦2ng/μl. Results: A total of 224 NSCLC patients were detected by Amplification Refractory Mutation System (ARMS), with 92 tissue positive and 49 blood positive. Results showed 53.3% sensitivity in overall samples, but 81.4% sensitivity in ⅢB~Ⅲ patients. The specificity is 100%. Conclusions: The high sensitivity and specificity between tissue and plasma EGFR determination supports the blood-based EGFR mutation testing to determinate the eligibility of NSCLC patients for EGFR-TKIs treatment, especialy in ⅢB~Ⅲ NSCLC patients. Blood, in particular plasma, is a good screening substitute when tumor tissue is absent or insufficient for testing EGFR mutations to guide EGFR TKIs treatment in patients with NSCLC. EGFR mutation positivity in blood could be used to recommend EGFR TKIs treatment, but the blood negativity should be confirmed with other sample, biopsy tissue, pleural effusion, etc..

Molecular characteristics of EGFR exon 19 deletion subtypes in NSCLC patients.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 8530-8530
Author(s):  
Weiquan Gu ◽  
Zhongyu Lu ◽  
Shulin Shi ◽  
Juan Ma ◽  
Guanghua Lu ◽  
...  
Keyword(s):  
Kinase Inhibitors ◽  
Egfr Mutations ◽  
Molecular Characteristics ◽  
Three Samples ◽  
Egfr Tyrosine Kinase Inhibitors ◽  
Exon 19 Deletion ◽  
Clinical Responses ◽  
Tki Treatment ◽  
Nsclc Patients ◽  
Exon 19

8530 Background: EGFR exon 19 deletion mutations are well characterized, known to be activating, and are associated with responses to EGFR tyrosine kinase inhibitors (TKIs). A variety of methods have been developed to identify EGFR mutations. Deletions of EGFR exon 19 are more complex compare to the other because they consist of different subtypes. Methods: In this study, we retrospectively analyzed the different subtypes of EGFR exon 19 deletions using next-generation sequencing(NGS). From May 2019 to December 2020, 3275 patients who were diagnosed with Non-small cell lung cancer (NSCLC)were detected. Results: In this analyzed cohort, the average age of patients was 62 years (range, 24-92 years). Most of the patients were female (61.07%) and were diagnosed with lung adenocarcinoma (82.60%). It is worth noting that the deletions in exon 19 of EGFR were also detected in 35 patients (1.07%) with squamous cell carcinoma and 1 patient (0.03%) with sarcomatoid. The most frequent EGFR exon 19 deletions were delE746-A750 (63.4%), followed by delL747-P753insS (9.7%) and L747-T751 (6.9%). The characteristics of the patients in this study are presented. Significantly, three samples with compound EGFR exon 19 deletions were detected: 1) S1:E746_A750delinsFP+E746_A750del; 2) S2: E746_S752delinsV+L747_P753delinsS; 3) S3:E746_P753delinsVS + L747_P753delinsS. Conclusions: EGFR exon 19 starting at codon 729 to 761, our data showed the deletions occur throughout almost the entire exon 19 amino acid. As our integrated data results, EGFR exon 19 has many different deletions and insertion subtypes could be defined as 79 subtypes. Among those subtypes,70 were complex with an accompanying insertion. The most frequent deletions were starting at E746 and L747. Based on several clinical researches, different deletion subtypes may have significantly different clinical responses after TKI treatment. However, more clinical research is needed to support this finding.

scholarly journals Neoadjuvant EGFR-TKI Therapy for EGFR-Mutant NSCLC in Traditionally Unresectable Patients

2021 ◽  
Author(s):  
Ke-Cheng Chen ◽  
Shuenn-Wen Kuo ◽  
Chen-Hao Hsiao ◽  
Jing-Shing Chen
Keyword(s):  
Thoracic Surgery ◽  
Lung Adenocarcinoma ◽  
Surgical Resection ◽  
Kinase Inhibitors ◽  
Growth Factor Receptor ◽  
Progression Free Survival ◽  
Egfr Mutations ◽  
Multidisciplinary Management ◽  
Advanced Stage ◽  
Nsclc Patients

Abstract IntroductionAdvanced stage non-small cell lung cancer (NSCLC) patients harboring epidermal growth factor receptor (EGFR) mutations may have benefit from tyrosine kinase inhibitors (TKI). However, the role of multidisciplinary management including neoadjuvant TKI therapy and thoracic surgery is uncertain. This study assessed the possible impact of neoadjuvant TKI therapy and thoracic surgery in selected advanced stage patients.MethodsAdvanced stage of IIIB and IVA NSCLC patients were retrospectively reviewed from 2010 to 2013. Patients with EGFR mutations who received neoadjuvant TKI followed by surgical resection were included. All patients were followed up for 5 years or until death.ResultsThere were total 15 advanced stage lung adenocarcinoma patients in the study. 8 patients were stage IIIB and 7 were stage IVA. All tumor sizes significantly decreased after neoadjuvant TKI therapy (p value = 0.0002). 11 patients received adjuvant TKI therapy after surgical resection and others received adjuvant cisplatin-based chemotherapy. Progression-free survival was superior in the group of adjuvant TKI therapy than in the group of adjuvant chemotherapy (median 14 months versus 5.9 months, p value = 0.016). Overall survival (OS) was not different between two groups (p value = 0.755). In the group of adjuvant TKI therapy, median OS in patients harboring exon 19 deletion and exon 21 L858R was 60 months and 44.9 months, respectively (p value = 0.078). ConclusionTKI may decrease the size of EGFR mutation lung adenocarcinoma. A multidisciplinary management including neoadjuvant TKI therapy and thoracic surgery may be discussed in selected advanced stage lung adenocarcinoma.

Routine detection of EGFR mutations in patients with NSCLC: A comparative study of three alternative methods in 105 patients

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 7184-7184
Author(s):  
G. Zalcman ◽  
N. Richard ◽  
A. Hardouin ◽  
R. Gervais ◽  
M. Antoine ◽  
...  
Keyword(s):  
High Performance ◽  
Kinase Inhibitors ◽  
Direct Sequencing ◽  
Tumor Resection ◽  
Growth Factor Receptor ◽  
Alternative Methods ◽  
Egfr Mutations ◽  
Genomic Sequencing ◽  
Surgical Biopsy ◽  
Nsclc Patients

7184 Background: The efficacy of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) has been reported in lung adenocarcinoma patients with tumoral EGFR mutations. Those mutations were found mainly by direct genomic sequencing on snap-frozen surgical specimens. Conversely, TKIs are used in metastatic patients who do not undergo tumor resection. In these patients, there is a need for routine sensitive molecular procedures, to overcome the small size of non-surgical bronchoscopy paraffin-embedded biopsy samples. Methods: Patients were selected on clinical and pathological characteristics: never (n = 43) or former smokers, patients with non-squamous NSCLC (n = 105) or patients with bronchioloalveolar adenocarcinoma (n = 34). Direct genomic sequencing assay was performed as reported elsewhere. Denaturing, high-performance, liquid chromatography (DHPLC) assay was performed with EGFR-specific primers that amplify exons 18, 19, and 21. A multiplex, allele-specific, oligonucleotide PCR (MASO-PCR) assay was carried out with a set of primers that identify the 14 most frequent molecular events described for the EGFR gene, which covers 90% of EGFR gain-of-function mutations described to date. Results: 123 samples were screened from 105 non-squamous NSCLC patients (female/male ratio = 0.84). Non-surgical biopsy specimens were available in 38 patients. EGFR mutations were detected by at least two of three procedures in 18/105 patients (17%). In paraffin-embedded specimens with low tumor content, EGFR heterozygous mutations were found either by MASO-PCR alone (n = 2, confirmed in the matched surgical sample by another procedure), or both by MASO-PCR and DHPLC (n = 16); they were missed by nucleotidic sequencing in 6 samples. 18 patients received TKI. 6 dramatic responses were achieved in patients with EGFR mutation, while no mutation could be found in non-responsive patients. Overall disease control was obtained in 8/18 patients (44%). Conclusions: MASO-PCR and DHPLC appear more sensitive than direct sequencing in non-surgical paraffin-embedded biopsies, which represent the bulk of samples in lung cancer patients. We propose that the cost-effective MASO-PCR be used for routine screening of EGFR mutations in NSCLC patients. No significant financial relationships to disclose.

Enhanced detection of EGFR mutations in plasma from non-small cell lung cancer (NSCLC) patients using Scorpion primers

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 7682-7682
Author(s):  
W. Holland ◽  
A. M. Davies ◽  
N. C. Farneth ◽  
O. Gautschi ◽  
P. N. Lara ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Kinase Inhibitors ◽  
Direct Sequencing ◽  
Nsclc Patient ◽  
Detection Methods ◽  
Egfr Mutations ◽  
Wild Type ◽  
Allele Specific ◽  
Nsclc Patients ◽  
Tumor Dna

7682 Background: Activating epidermal growth factor receptor (EGFR) mutations identified in NSCLC patient tumors are often associated with rapid and profound response to EGFR tyrosine kinase inhibitors (TKIs). Conventional detection methods are cumbersome and may underestimate mutations frequencies due to limited sensitivity. We and others have shown that tumor-specific mutations such as KRAS can be detected in tumor DNA shed into patient plasma (Kimura, Ann N Y Acad Sci, 2004). Here we describe the performance of an allele- specific real-time PCR system utilizing Scorpion primers (kindly provided by DxS, UK) to detect EGFR mutations in plasma. Methods: DNA was extracted from archival tumor blocks, slides and plasma obtained from consenting patients. In order to determine the sensitivity of this technique both in terms of the ratio of mutant-to-wild-type genomic DNA as well as the minimum amount of DNA required for detection, a dilution experiment was conducted. Genomic DNA from cell lines containing either the exon 21 L858R point mutation or the exon 21 E746–750 deletion was diluted with wild-type genomic DNA at ratios ranging from 1:2 to 1:10,000. Clinical specimens including plasma and/or tissue from 35 advanced stage NSCLC patients treated with EGFR-TKIs were examined. Results: Mutant DNA was successfully detected when it comprised as little as 0.1% of the total sample or as low as 25 pg of mutant-positive genomic DNA in a pool of 2.5 μg of total DNA. EGFR mutations were identified by this approach in both plasma and tissue of 2 patients who were complete responders to EGFR-TKI therapy, only one of which was detectable by direct sequencing. For the 7 patients where only tissue was available, two were positive both with the Scorpion primers and direct sequencing while the rest were wild-type. Of 21 patients where only plasma was available, 6 mutations were detected using the Scorpion primers. Conclusions: Allele-specific Scorpion technology is 1) highly specific and sensitive for EGFR mutation analysis, 2) able to detect mutations that were not observable by direct sequencing in plasma and tissue, 3) capable of detecting mutations in shed tumor DNA in plasma of advanced NSCLC patients and 4) may be suitable for monitoring response or detecting recurrence. No significant financial relationships to disclose.

scholarly journals FBXL2 counteracts Grp94 to destabilize EGFR and inhibit EGFR-driven NSCLC growth

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Mengmeng Niu ◽  
Jing Xu ◽  
Yang Liu ◽  
Yuhuang Li ◽  
Tao He ◽  
...  
Keyword(s):  
Kinase Inhibitors ◽  
Critical Role ◽  
Growth Factor Receptor ◽  
Egfr Mutations ◽  
Inhibitory Effects ◽  
Molecule Inhibitor ◽  
Epidermal Growth ◽  
F Box Protein ◽  
Nsclc Patients ◽  
Egfr Tki

AbstractAbnormal activation of epidermal growth factor receptor (EGFR) drives non-small cell lung cancer (NSCLC) development. EGFR mutations-mediated resistance to tyrosine-kinase inhibitors (TKIs) is a major hurdle for NSCLC treatment. Here, we show that F-box protein FBXL2 targets EGFR and EGFR TKI-resistant mutants for proteasome-mediated degradation, resulting in suppression of EGFR-driven NSCLC growth. Reduced FBXL2 expression is associated with poor clinical outcomes of NSCLC patients. Furthermore, we show that glucose-regulated protein 94 (Grp94) protects EGFR from degradation via blockage of FBXL2 binding to EGFR. Moreover, we have identified nebivolol, a clinically used small molecule inhibitor, that can upregulate FBXL2 expression to inhibit EGFR-driven NSCLC growth. Nebivolol in combination with osimertinib or Grp94-inhibitor-1 exhibits strong inhibitory effects on osimertinib-resistant NSCLC. Together, this study demonstrates that the FBXL2-Grp94-EGFR axis plays a critical role in NSCLC development and suggests that targeting FBXL2-Grp94 to destabilize EGFR may represent a putative therapeutic strategy for TKI-resistant NSCLC.

Sensitivity of TargetSelector in clinical experience in ctDNA profiling of NSCLC 2000 cases.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e23033-e23033
Author(s):  
Veena M. Singh ◽  
Anthony J. Daher ◽  
Jeffery J. Chen ◽  
Lyle Arnold ◽  
Cecile Rose T. Vibat
Keyword(s):  
Kinase Inhibitors ◽  
Acquired Resistance ◽  
Growth Factor Receptor ◽  
Egfr Mutations ◽  
Wild Type ◽  
T790m Mutation ◽  
Blood Samples ◽  
Copy Numbers ◽  
Activating Mutation ◽  
Nsclc Patients

e23033 Background: Targeted cancer therapy relies on identifying specific DNA mutations from a patient’s tumor. Tyrosine kinase inhibitors (TKIs) tend to be effective for non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) activating mutations, of which exon 19 deletions (Del19) and L858R are most common. Acquired resistance to TKI therapy is associated with a T790M mutation. Standard biomarker analyses may not reflect tumor heterogeneity; they entail tissue biopsies often with surgical complications. To address these limitations, Biocept developed a minimally invasive method to characterize cancer biomarkers in blood. Biocept's proprietary TargetSelector assays selectively amplify relevant mutations from circulating tumor DNA (ctDNA). Clinical validations demonstrated high concordances between molecular tests in blood vs tissue. As further validation, EGFR mutation detection frequencies were compared to US averages (mycancergenome.org). Here we analyze 2000 blood samples received at Biocept from 1Mar 2016 to 4Jan 2017 from late stage NSCLC patients. Methods: Blood was collected in Biocept OncoCEE BCT validated to preserve DNA ≤ 8 days. TargetSelector was used to detect ctDNA L858R, Del19 and T790M.EGFR allele copy numbers for wild type and each mutant were calculated. The prevalence of each mutation was compared to US averages. Results: Del19, L858R, and T790M mutations were detected in 12.9%, 8.5%, and 9.9% of the analyzed blood samples, respectively. This is concordant with US averages, which are 10% for each mutation. Median copy numbers/ml of blood were 30 for Del19 (range: 1 – 91974), 15 for L858R (range: 1 – 91200), and 10 for T790M (range: 1 – 137360). The median wild type EGFR copy number detected/ml blood was 2304 (range: 8 – 2498725). In ~80% of T790M cases, ≥ 1 concomitant activating mutation was detected. Conclusions: Biocept's TargetSelector detects EGFR mutations (Del19, L585R, and T790M) at a very high level of sensitivity down to 1 mutant copy/ml in advanced NSCLC patients at frequencies consistent with cited US rates. Moreover, the underlying activating mutation was detected in ~80% of T790M cases.

EGFR-mutation detection in VTX-1-enriched CTCs, ctDNA, and comparison to tumor in patients with non-small cell lung cancer (NSCLC).

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e20525-e20525
Author(s):  
Jonathan Wade Goldman ◽  
Haiyan Liu ◽  
Meghah Vuppalapaty ◽  
Charles Wilkerson ◽  
Clementine Lemaire ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Kinase Inhibitors ◽  
Low Cost ◽  
Growth Factor Receptor ◽  
High Sensitivity ◽  
Circulating Tumor Dna ◽  
Egfr Mutations ◽  
Label Free ◽  
Enhanced Sensitivity ◽  
Nsclc Patients

e20525 Background: Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI's) have shown dramatic clinical benefits when EGFR mutations are detected. These assays are mainly performed on tumor biopsies, which carry risks, are expensive and are not always successful. Moreover, secondary mutations, causing resistance to 1st & 2nd generation TKI’s develop during treatment and therefore mutations require ongoing monitoring. Circulating tumor cells (CTCs) or circulating tumor DNA (ctDNA) are promising for monitoring the patient over time and show enhanced sensitivity when combined1. The VTX-1 Liquid Biopsy System enables label-free capture of CTCs from blood and genomic assays downstream2. In this study, we demonstrate the sensitivity of a combined EGFR assay on VTX-1-enriched CTCs and ctDNA, using blood spiked with cancer cells & DNA and then with NSCLC patients. Methods: NSCLC cells (A549: wt, H1975: L858R+ & T790M+, HCC827: 19del+) were used to validate the assay. H1975 cells and HCC827 DNA were spiked in blood. Plasma was extracted and the plasma depleted blood was processed through VTX-1. The collected plasma and enriched cells were subjected to the detection of 19del, L858R and T790M EGFR mutations using the EntroGen ctEGFR kit. Later, blood and tumor were collected from NSCLC patients and analyzed for EGFR mutations on biopsies, ctDNA and CTCs. Results: Mutant DNA was detected for an input as low as 0.5 ng (~83 cells), with a sensitivity from 0.1% to 2% for a total DNA of 25ng (~4 cancer cells & 4000 WBCs) to 1ng (~4 cancer cells & 200 WBCs). Processing of plasma-depleted-blood with Vortex showed the same efficiency compared to whole blood. Mutations were detected from enriched cells and plasma respectively for 100 H1975 cells and 0.5ng of HCC827 DNA spiked in 2mL blood. NSCLC patients are being enrolled and results will be presented at the conference. Conclusions: The ctEGFR assay performed well on VTX-1 enriched cells and ctDNA, enabling a low cost approach to analyze EGFR mutations from a single blood tube with high sensitivity, potentially being a useful tool for guiding treatment of NSCLC patients. 1.Sundaresan, et al. Clin Cancer Res 2016. 2. Kidess-Sigal, et al. Oncotarget 2016.

Multiplexed Detection of Mutant Circulating Tumor DNA Using Peptide Nucleic Acid Clamping Asymmetric Polymerase Chain Reaction and Liquidchip

2019 ◽  
Vol 15 (7) ◽  
pp. 1578-1588
Author(s):  
Xiaomin Chen ◽  
Ding Sheng-Zi Zhang ◽  
Lin Wang ◽  
Qiaomei Guo ◽  
Hong Xu ◽  
...  
Keyword(s):  
Growth Factor Receptor ◽  
High Specificity ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Genetic Alterations ◽  
High Background ◽  
Multiplexed Detection ◽  
Specificity And Sensitivity ◽  
Exon 19 Deletion ◽  
Tumor Dna

Circulating tumor DNA (ctDNA) in blood has been investigated as a feasible substitute for genetic alterations in tumor tissues to predict and assess drug responses, but current techniques of screening clinical relevant mutations still have great limitations in sensitivity, specificity, or multiplexed detection because of highly fragmented ctDNA and its low concentration in a high background of normal DNA. In this study, we developed PNA-aPCR-Liquidchip (PAPL), a novel method that aims to detect multiple mutant ctDNA. In order to demonstrate its utility, we analyzed three high frequent epidermal growth factor receptor (EGFR) mutations (exon 19 deletion, L858R, and T790M) in non-small cell lung cancer (NSCLC). Multiplexed analyses indicated that this method has high specificity and sensitivity which could detect down to 2∼5 copies of mutant EGFR in a background of 10,000 copies of wild-type genomic DNA, achieving the mutant abundance of 0.02%∼0.05%. Furthermore, PAPL had no significant differences with droplet digital PCR (ddPCR) in plasma cell-free DNA (cfDNA) detection. Thus, PAPL can be used to detect EGFR mutations in NSCLC patients' plasma, indicating that this method has great potential for application in the context of precision medicine based on mutant ctDNA detection.

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