TEST:

cobas® EGFR Mutation Test v2

Our study highlights that NGS is able to identify a much higher number of actionable EGFR mutations than RT-qPCR approaches, thereby providing many more patients the opportunity to receive targeted EGFR treatments.

P3; Recruiting --> Active, not recruiting

P=N/A; N=118; Recruiting; Sponsor:Istituto Oncologico Veneto IRCCS

P=N/A; N=300; Recruiting; Sponsor:LifeOS Genomics Corporation

SQI values strongly (r: 0.910, 95% 0.821-0.956) correlated to mutant allele concentrations with SQI of 5 and 10 corresponding to 6-9 (0.2-0.3%) and 64-105 (1.1-1.6%) mutant allele copies/mL (VAF) respectively. Our dual-threshold classifier of SQI 0/5/10 yielded informative results in 88% of blood draws with high NPV and good overall clinical utility for patient-centric surveillance of metastatic NSCLC.

Additionally, we observed TP53 to be a frequently co-mutated gene in EGFR-positive NSCLC patients. In conclusion, targeted NGS showed a number of superior features over qPCR in EGFR variant detection (exact identification of variants, calculation of allelic frequency, high analytical sensitivity), which might enhance the basic diagnostic report.

In this study, quantitative agreement was found in the measurements made in plasma samples with the fully automated Cobas 6800 CMV Rt-qPCR and NeuMoDx CMV Rt-qPCR tests calibrated with the CMV IQS. To the best of our knowledge, a study comparing viral load measurements made with Cobas 6800 and NeuMoDx fully automated systems in the detection of CMV DNA has not yet been conducted, and this is the first study on this subject.

In tissue EGFR mutated lung cancer patients, the patients who have ctDNA in plasma tested before surgery has shorter DFS compared with patients who without ctDNA in plasma. Conclusions : In EGFR- mutated NSCLC, ctDNA positivity measured within a week before surgery correlated with shorter DFS and OS suggesting a good indication of adjuvant Osimertinib in this population.

However, NGS had a 12-day longer TAT compared to EGFR PCR. Gene fusion-panel PCR and NGS identified an additional 11.6% of patients harboring actionable alterations who may benefit from FDA-approved targeted therapies.

NGS showed a number of superior features over qPCR in EGFR variant detection (exact identification of variants, calculation of allelic frequency, high analytical sensitivity) which might enhance the basic diagnostic report.

P2; Trial completion date: Sep 2024 --> Dec 2025 | Trial primary completion date: Sep 2024 --> Dec 2025

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.

The developed test system accurately identifies essential mutations in colorectal cancer, including rare and potentially clinically significant variants. The required DNA amount ranged from 10 to 30 ng in 5 μl, nearly ten times less than well-known commercial PCR test systems like COBAS (Roche) and therascreen (QIAGEN). The cost of the study is comparable to PCR with a minimum study duration of 4 days.

Additionally, three of the patients, who had measurable tumors, showed partial responses to afatinib and osimertinib. The L858R mutation associated with L858R-K860I and L858R-L861F doublet mutations could be detected using Idylla but not cobas EGFR tests. Using next-generation sequencing analysis should be considered after initial negative reports from the cobas test, because patients with L858R doublet mutations may benefit from EGFR-TKIs.

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.

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 2017, the Roche Cobas® EGFR Mutation Test v2 for the detection of the EGFR c.2369C>T p.(T790M) mutation in plasma-derived ctDNA was FDA-approved to identify patients eligible for osimertinib treatment...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.

It has been observed that new mutations can be detected not only at the time of diagnosis, but also in LB samples taken during the follow-up period, leading to the determination of targeted therapy. The results showed that "liquid biopsy" is a successful and alternative non-invasive method for detecting cancer-causing executive mutations, given the limitations of conventional biopsies.

The liquid-first approach enhances the yield of rare mutations by tissue NGS which is resource-dependent. It benefits regions where tissue biopsy is a rate limiting factor and EGFR mutations are prevalent.

P3; Trial completion date: Mar 2029 --> Jul 2029 | Trial primary completion date: Mar 2024 --> Jun 2024

In our pilot study, tumor microenvironment can be analyzed by multiplex IHC staining. TLS can be identified and calculated by our working definition. TLS-High predicts longer DFS regardless EGFR mutation types, stages, gender and PD-L1 TPS.

ctDNA monitoring during Osimertinib treatment helps identify a subgroup of patients with poor prognosis. A lack of cfDNA negativization could identify a subgroup of patients requiring adaptive therapy

The patient initially received 1st line Erlotinib with remission maintained more than 4 years, despite an early dose reduction due to skin toxicity. Despite loss of the original compound EGFR mutation, the rebiopsy revealed a new pathogenic and druggable driver (BRAF p.V600E), which gave the patient a new possibility of further treatment. Yet, replacing Osimertinib with a BRAF/MEK-Is combination resulted only in mixed response, suggesting that some lesions might have remained, at least in part, dependent on the original EGFR mutations. Indeed, re-challenge with Osimertinib in reduced dose together with continuation of Dabrafenib and Trametinib resulted in SD and reflected spatial and temporal heterogeneity of NSCLC.

This study investigated the distribution of EGFR E20ins in the Asian population, with p.A767_V769dup and p.S768_D770dup being the most frequently observed mutations. Since some studies have reported single EGFR E20ins sequences using different names, it is important to be cautious when describing EGFR E20ins. To ensure comprehensive coverage in real-world settings, each method used for the detection of EGFR E20ins must be annotated according to the HGVS nomenclature.

CTC were isolated by our unique blood-filtration device. And it could be useful to investigate EGFR status. However, more experiments are required to clarify the performance.

Further study is suggested to review other parameters in characterizing the insufficient sample.

P3; Trial primary completion date: Jun 2023 --> Nov 2023

Results Guide sheath flush-based genotyping yielded a mutation detection rate of 61.8% (17/24 EGFR, 1/2 ERBB2, 1/1 KRAS, 1/1 MAP2K, 1/4 MET, and 0/1 STK11), compared to 33% in plasma-based genotyping (p = 0.0151). Conclusion The detection of tumor DNA in the supernatant of guide sheath flush fluid collected during bronchoscopy represents a feasible and more sensitive alternative to circulating tumor DNA genotyping in non-small cell lung cancer.

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.

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.

The Idylla EGFR testing is an accurate and simple tool useful for the early screening of EGFR mutations. The Idylla GeneFusion is a potential screening panel with short turnaround time using a minimal amount of tissue and might be considered as a relevant complementary testing to IHC in diagnostic molecular laboratories.

ctDNA analysis is a critical challenge that often leads to false negative results due to biological variables such as stage of the disease, tumor volume, low DNA-shedding, and preanalytical variables. The current study demonstrates the utility of ctDNA as a non-invasive promising tool to detect targetable alterations in situations where tissue biopsy is inaccessible or tumor tissue is depleted. Real-time PCR- based platform is the most preferred option for molecular analysis of ctDNA in clinical settings over NGS, considering factors like cost, turnaround time, and availability of resources.

"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."

False positives for exon 20 insertion may occur when using cobas EGFR, and false negatives for exon 19 deletion and L858R mutations may occur when using ODxTT.

We demonstrated the accuracy and potential clinical utility of the Idylla EGFR Mutation Test as a molecular screening platform in terms of turnaround time and molecular testing cost if applied to a cohort with a high EGFR mutation incidence (>17.9%).

P2; Trial completion date: Mar 2024 --> Sep 2024 | Trial primary completion date: Mar 2024 --> Sep 2024

The cobas EGFR Mutation Test, ddPCR, and NGS appear to be feasible methods for analyzing CSF ctDNA in patients with NSCLC and LM. In addition, NGS may provide comprehensive information regarding the mechanisms underlying osimertinib resistance.

NGS ctDNA analysis provided a more comprehensive genetic testing than conventional single gene testing kits. The lower stage which could imply lower or lack of ctDNA shedding into the blood was associated with a discordant result of the blood-based NGS ctDNA assay. Co-occurring mutations might have an impact on the treatment duration of EGFR-TKI.

P2; Trial completion date: Mar 2023 --> Mar 2024 | Trial primary completion date: Mar 2023 --> Mar 2024

The serial monitoring of ct-DNA T790M-status in advanced EGFR-mutant NSCLC during treatment with first-generation EGFR inhibitors was feasible, and a molecular progression before RECIST PD led to an earlier switch to osimertinib in 17% of patients with satisfactory PFS and OS outcomes.

P2; Recruiting --> Active, not recruiting | N=80 --> 116

P2; N=36 --> 0 | Trial completion date: Dec 2024 --> Feb 2023 | Not yet recruiting --> Withdrawn | Trial primary completion date: Dec 2024 --> Feb 2023