Test V2 Research Articles

P3.02-052 Stability of EGFR Mutations in Whole Blood and Plasma in Patients with NSCLC

The cobas® EGFR Mutation Test v2 (Roche Molecular Systems Inc.) has recently been IVD approved in the US for detection of epidermal growth factor receptor (EGFR) mutations in blood samples. Knowledge of the EGFR mutation status in non-small cell lung cancer (NSCLC) patients is essential to designing optimal, individualized treatment. However, implementing blood-based analyzes to detect cancer-specific mutations demands standardized pre analytical conditions, but research in this field is rare and inadequate.

P3.02-044 Diagnosis and Monitoring of EGFR Mutation Status with cfDNA in Advanced NSCLC: A Prospective Single Institution Study in Asia

NSCLC patients in advanced stage with tumors that harbor EGFR sensitizing mutations are eligible for treatment with tyrosine kinase inhibitors (TKI) due to a high likelihood of response. The challenge with NSCLC is that often only small biopsy samples are available and when they are insufficient for molecular diagnostics, a repeat biopsy is not always possible and this results in delays in starting treatment. Molecular testing on circulating cell free DNA (cfDNA) from plasma is an alternative methodology that is readily applicable. We used the Roche cobas® EGFR Mutation Test V2 to diagnose (on tissue) and follow patients with EGFR sensitizing mutations to evaluate longitudinal changes in EGFR mutation status and SQI (Semi-quantitative Index) in plasma relative to standard of care for patients during TKI treatment. The sequential EGFR SQI values will be used to evaluate the relationship between molecular and clinical responses. We included 60 patients (36 F/24 M) who had at least three follow up blood samples drawn post TKI treatment start. Ten ml of blood was collected in EDTA tubes from each subject at every visit. All patients had both tissues as well as baseline plasma EGFR results available. Serial follow up plasma samples were available on all patients. All subjects were treatment naïve, 80% (48/60) had no history of smoking and majority (45/60, 75%) presented with extra thoracic disease with clinical stages ranging between III-IV at diagnosis. The L858R mutation was the most common EGFR mutation detected (58.3%) on the tissue followed by exon 19 deletion (35.0%). Two patients had dual mutations detected on tissue as well as in the baseline plasma. Plasma cfDNA analysis detected EGFR mutations in 78% of the baseline samples. Analysis of the serial plasma collected from patients who progressed while on 1st line TKI showed reappearance of the original EGFR sensitizing mutations with increasing SQI levels before emergence of a T790M mutation. T790M mutation was detected in 20.0% (12/60) of the patients on TKI treatment. This study clearly demonstrates that EGFR mutations can be reliably detected in plasma of NSCLC patients to confidently diagnose the presence of TKI resistance mutations using the Roche cobas® EGFR Mutation Test V2. Additionally, plasma SQI measurement can be used to monitor patients to detect the development of molecular TKI resistance. We will also show that serial measurement in the EGFR SQI can predict the relationship between molecular and clinical responses as well as tumor progression.

EGFR status evaluation by liquid biopsy during first-line therapy in advanced NSCLC patients

Background: Over the past decade, personalized management based on the molecular features of tumours in patients with advanced non small-cell lung cancer (NSCLC) has entered routine clinical practice. The poor performance of many advanced NSCLC patients may limit invasive biopsies. The liquid biopsy is a diagnostic procedure performed on cancer-derived material obtained in blood samples. In this abstract, we will describe our experience with liquid biopsies. Methods: In the Reggio Emilia Clinical Cancer Centre from March 2016 to December 2016, 42 patients with advanced NSCLC were analyzed that had had or had already started first line therapy. The liquid biopsy was repeated at each imaging response evaluation by thoracic-abdominal compound tomography (CT) scan performed every 3 months. In the liquid biopsy, the mutational status of EGFR was analyzed with real time PCR (KIT cobas EGFR mutation test v2 CE-IVD Roche); in tissue, it was evaluated by pyrosequencing. Results: 21/42 liquid biopsies were EGFR-mutated (12/21 eson 19 and 9/21 eson 21). In 3/21 (14.3%) cases, the tissue biopsies showed wild type (WT) EGFR. 6 liquid biopsies were also performed at time 0 (diagnosis). All liquid biopsies of EGFR WT remained WT during treatment and imaging evaluation. The median number of liquid biopsy tests for patients was 2 (range 1-3). In 4/21 cases, T790M was performed: 3 cases in both liquid biopsies and tissue, and 1 case in tissue but not in liquid biopsy. TKi therapy was ineffective in this patient with T790M mutation detected in tissue, but not in liquid biopsy. In all patients, the disappearance of the T790M mutation during TKi therapy was related to disease progression. In 11 cases, modification of EGFR mutation status during treatment anticipated CT scan evidence of disease progression (median = three months). Conclusion: The liquid biopsy is an excellent resource. In our experience the liquid biopsy is the sensitive method of choice during treatment of advanced NSCLC patients. EGFR modification status during TKi therapy showed advanced disease progression.

A novel quantitative PCR mediated by high-fidelity DNA polymerase

The biggest challenge for accurate diagnosis of viral infectious disease is the high genetic variability of involved viruses, which affects amplification efficiency and results in low sensitivity and narrow spectrum. Here, we developed a new simple qPCR mediated by high-fidelity (HF) DNA polymerase. The new method utilizes an HFman probe and one primer. Fluorescent signal was generated from the 3′–5′ hydrolysis of HFman probe by HF DNA polymerase before elongation initiation. Mismatches between probe/primer and template have less influence on the amplification efficiency of the new method. The new qPCR exhibited higher sensitivity and better adaptability to sequence variable templates than the conventional TaqMan probe based-qPCR in quantification of HIV-1 viral load. Further comparison with COBAS TaqMan HIV-1 Test (v2.0) showed a good correlation coefficient (R2 = 0.79) between both methods in quantification of HIV-1 viral load among 21 clinical samples. The characteristics of tolerance to variable templates and one probe-one primer system imply that the probe/primer design for the new method will be easier and more flexible than the conventional method for highly heterogeneous viruses. Therefore, the HF DNA polymerase-mediated qPCR method is a simple, sensitive and promising approach for the development of diagnostics for viral infectious diseases.

Analytical and clinical performance of the Hologic Aptima HCV Quant Dx Assay for the quantification of HCV RNA in plasma samples

BackgroundChronic hepatitis C virus (HCV) infection can be effectively treated with directly acting antiviral (DAA) therapy. Measurement of HCV RNA is used to evaluate patient compliance and virological response during and after treatment. ObjectivesTo compare the analytical performance of the Aptima HCV Quant Dx Assay (Aptima) and the COBAS Ampliprep/COBAS TaqMan HCV Test v2.0 (CAPCTMv2) for the quantification of HCV RNA in plasma samples, and compare the clinical utility of the two tests in patients undergoing treatment with DAA therapy. Study designAnalytical performance was evaluated on two sets of plasma samples: 125 genotyped samples and 172 samples referred for quantification of HCV RNA. Furthermore, performance was evaluated using dilutions series of four samples containing HCV genotype 1a, 2b, 3a, and 4a, respectively. Clinical utility was evaluated on 118 plasma samples obtained from 13 patients undergoing treatment with DAAs. ResultsDeming regression of results from 187 plasma samples with HCV RNA >2 Log IU/mL indicated that the Aptima assay quantified higher than the CAPCTMv2 test for HCV RNA >4.9 Log IU/mL. The linearity of the Aptima assay was excellent across dilution series of four HCV genotypes (slope of the regression line: 1.00-1.02). The Aptima assay detected significantly more replicates below targeted 2 Log IU/mL than the CAPCTMv2 test, and yielded clearly interpretable results when used to analyze samples from patients treated with DAAs. ConclusionsThe analytical performance of the Aptima assay makes it well suited for monitoring patients with chronic HCV infection undergoing antiviral treatment.

Evaluation of the COBAS® AmpliPrep/COBAS® TaqMan® HCV Test v2.0 for HCV viral load monitoring using dried blood spot specimens

This study evaluated the use of dried blood spot (DBS) for HCV viral load quantification using the COBAS® AmpliPrep/COBAS® Taqman® HCV Quantitative Test v2.0 (CAP/CTM HCV v2), and compared two different procedures for preparation of DBS samples with a Specimen Pre-Extraction (SPEX) reagent (either heated [SPEX with SH] for 10min at 56°C on a thermomixer, or incubated for 1h at room temperature [SPEX at RT]) against the standard plasma input. Whole blood specimens from 48 patients with chronic HCV infection and Whatman® 903 Protein Saver Cards were used to prepare 35μL DBS. An aliquot of plasma was spun and frozen from each draw. Mean DBS viral load results were compared to the corresponding results from plasma. Correlation between DBS to plasma was linear for both SPEX with SH (R2=0.96) and SPEX at RT (R2=0.97) procedures, with a constant negative offset of approximately 2.0log10IU/mL between whole blood DBS without any adjustments and plasma results. After volume corrections, the mean offset to plasma decreased to −0.39 and −0.36 for the two procedures, respectively. The study demonstrated the use of DBS for HCV viral load correlates well with plasma with a constant offset.

EGFR status evaluation by liquid biopsy during first-line therapy in patients with advanced NSCLC.

e20524 Background: over the past decade, personalized management based on the molecular features of tumours in patients with advanced non small-cell lung cancer (NSCLC) has entered routine clinical practice. The poor performance of many advanced NSCLC patients may limit invasive biopsies. The liquid biopsy is a diagnostic procedure performed on cancer-derived material obtained in blood samples. In this abstract, we will describe our experience with liquid biopsies. Methods: In the Reggio Emilia Clinical Cancer Centrefrom March 2016 to December 2016, 42 patients with advanced NSCLC were analyzed that had had or had already started first line therapy. The liquid biopsy was repeated at each imaging response evaluation by thoracic-abdominal compound tomography (CT) scan performed every 3 months. In the liquid biopsy, the mutational status of EGFR was analyzed with real time PCR (KIT cobas EGFR mutation test v2 CE-IVD Roche); in tissue, it was evaluated by pyrosequencing. Results: 21/42 liquid biopsies were EGFR-mutated (12/21 eson 19 and 9/21 eson 21). In 3/21 (14.3%) cases, the tissue biopsies showed wild type (WT) EGFR. 6 liquid biopsies were also performed at time 0 (diagnosis). All liquid biopsies of EGFR WT remained WT during treatment and imaging evaluation. The median number of liquid biopsy tests for patients was 2 (range 1-3). In 4/21 cases, T790M was performed: 3 cases in both liquid biopsies and tissue, and 1 case in tissue but not in liquid biopsy. TKi therapy was ineffective in this patient with T790M mutation detected in tissue, but not in liquid biopsy. In all patients, the disappearance of the T790M mutation during TKi therapy was related to disease progression. In 11 cases, modification of EGFR mutation status during treatment anticipated CT scan evidence of disease progression (median = three months). Conclusions: the liquid biopsy is an excellent resource. In our experience the liquid biopsy is the sensitive method of choice during treatment of advanced NSCLC patients. EGFR modification status during TKi therapy showed advanced disease progression.

Validation of the denaturing capillary electrophoresis (DCE) assay for non-invasive liquid biopsy in lung carcinoma: A study of concordance with the cobas EGFR mutation test v2.

e23040 Background: The detection of circulating tumor DNA (ctDNA), referred to as “liquid biopsy” is becoming a preferred option for some patients with lung adenocarcinomas. The key for a suitable technology is high sensitivity enabling to detect small fractions of mutated alleles, the method has to be solid against false-positives. The aim of this work was to compare our method based on capillary electrophoresis under denaturing conditions (DCE) to FDA and CE IVD approved commercial kit - cobas EGFR Mutation Test v2. Methods: A total of 44 plasma samples were acquired from patients with clinicaly confirmed stage IV lung adenocarcinoma. There were samples from patients prior to receiving therapy (with a known tissue EGFR genotype) as well as several ones showing progression on a previously administered antiEGFR-therapy (with no tissue info available at the time of plasma sampling). DNA was isolated from multiple 2 mL aliquots of each plasma. The first aliquot was run on cobas z480 real-time instrument using unmodified manufacturer's protocol. Another 2ml aliquot was run by DCE assay (accredited method under ISO 15189:2012), which is based on a PCR followed by a fragment analysis on an ABI capillary analyzer (Sanger sequencer). Results: The mutual concordance was 84.1% (37/44). cobas assay identified 11 EGFR-positive plasma samples (6 x Ex19del, 3 x L858R, 1x T790M combined with Ex19del and 1x T790M combined with L858R). DCE identified 8 EGFR-positive samples (6 x Ex19del, 1 x L858R, 1xT790M combined with L858R). DCE missed 5 of cobas-positive samples (2x Ex19del, 2x L858R and 1x T790M) while in turn identifying 2x Ex19del plasma samples that were concordant with tissue, but missed by cobas. Overall concordance with tissue was 73.3% (22/30) for cobas, 70.0% (21/30) for DCE assay and 80.0% (24/30) for both combined. Conclusions: DCE approach is reliable for low levels of mutations in plasma of lung cancer patients and comparable (and complementary) to cobas. Its advantage is simplicity, low cost and a universal, straighforward adaptability to virtually any mutation at any site allowing to detect oncogenic as well as tumor supressor mutations in ctDNA. Supported by grant 17-30748A.

Comparison of the Hologic Aptima HIV-1 Quant Dx Assay to the Roche COBAS Ampliprep/COBAS TaqMan HIV-1 Test v2.0 for the quantification of HIV-1 RNA in plasma samples.

BackgroundHIV-RNA is the most important parameter for monitoring antiviral treatment in individuals infected with HIV-1. Knowledge of the performance of different tests for the quantification of HIV-1 RNA is therefore important for clinical care. ObjectivesTo compare the analytical performance of the Aptima HIV-1 Quant Dx Assay (Aptima) and the COBAS Ampliprep/COBAS TaqMan HIV-1 Test v2.0 (CAPCTMv2) for the quantification of HIV-1 RNA in plasma samples. Study designThe performance of the two tests was compared on 216 clinical plasma samples, on dilutions series in seven replicates of five clinical samples of known subtype and on ten replicates of the Acrometrix High and Low Positive Control. ResultsBland-Altman analysis of 130 samples that quantified in both tests did not show indications of gross mis-quantification of either test. A tendency of the Aptima assay to quantify higher at high viral load compared to the CAPCTMv2 was observed in Bland-Altman analysis, by Deming regression (Slope 1.13) and in dilution series of clinical samples. Precision evaluated using the Acrometrix Positive Controls was similar for the High Control (CV: 1.2% vs. 1.3%; Aptima assay vs. CAPCTMv2 test, respectively), but differed for the Low control (CV: 17.9% vs. 7.1%; Aptima assay vs. CAPCTMv2 test, respectively). However, this did not impact clinical categorization of clinical samples at neither the 50 cp/mL nor 200 cp/mL level. ConclusionThe Aptima assay and the CAPCTMv2 test are highly correlated and are useful for monitoring HIV-infected individuals.

Plasma ctDNA Analysis for Detection of the EGFR T790M Mutation in Patients with Advanced Non–Small Cell Lung Cancer

IntroductionTumor biopsies for detecting EGFR mutations in advanced NSCLC are invasive, costly, and not always feasible for patients with late-stage disease. The clinical utility of the cobas EGFR Mutation Test v2 (Roche Molecular Systems, Inc., Pleasanton, CA) with plasma samples from patients with NSCLC at disease progression after previous EGFR tyrosine kinase inhibitor therapy was investigated to determine eligibility for osimertinib treatment. MethodsMatched tumor tissue and plasma samples from patients screened for the AURA extension and AURA2 phase II studies were tested for EGFR mutations by using tissue- and plasma-based cobas EGFR mutation tests. Plasma test performance was assessed by using the cobas tissue test and a next-generation sequencing method (MiSeq [Illumina Inc., San Diego, CA]) as references. The objective response rate, measured by blinded independent central review, was assessed in patients receiving osimertinib with a plasma T790M mutation–positive status. ResultsDuring screening, 551 patients provided matched tumor tissue and plasma samples. Pooled analysis of the positive and negative percent agreements between the cobas plasma and tissue tests for detection of T790M mutation were 61% and 79%, respectively. Comparing cobas plasma test with next-generation sequencing demonstrated positive and negative percent agreements of 90% or higher. The objective response rate was 64% (95% confidence interval: 57–70) in T790M mutation–positive patients by both cobas tissue and plasma tests (evaluable for response). ConclusionsThe cobas plasma test detected the T790M mutation in 61% of tumor tissue T790M mutation–positive patients. To mitigate the risk of false-negative plasma results, patients with a negative plasma result should undergo a tissue test where feasible.

Quantification of intrahepatic total HBV DNA in liver biopsies of HBV-infected patients by a modified version of COBAS® Ampliprep/COBAS®TaqMan HBV test v2.0

Intrahepatic total HBV DNA (it-HBV DNA) level might reflect the size of virus reservoir and correlate with the histological status of the liver. To quantitate it-HBV DNA in a series of 70 liver biopsies obtained from hepatitis B chronic patients, a modified version of the COBAS®Ampliprep/COBAS®TaqMan HBV test v2.0 was used for this purpose. The linearity and reproducibility of the modified protocol was tested by quantifying serial dilutions of a full-length HBV containing plasmid and it-HBV DNA from a reference patient. A good linear trend between the expected values and those generated by the assay was observed at different concentrations of both plasmid and reference patient (R 2=0.994 and 0.962, respectively). Differences between the values obtained in two independent runs were ≤0.3 log IU for the plasmid and ≤0.6 log IU/mg for the reference patient, showing a high inter-run reproducibility. In the 70 liver biopsies, it-HBV DNA level ranged from 1.4 to 5.4log IU/mg, with a good linearity and reproducibility between the values obtained in two runs [R 2=0.981; median (IQR) difference of it-HBV DNA 0.05 (0.02-0.09) IU/mg]. The modified COBAS®Ampliprep/COBAS®TaqMan HBV test v2.0 allows an accurate quantitation of it-HBV DNA. Its determination may have prognostic value and may be a useful tool for the new therapeutic strategies aimed at eradicating the HBV infection.

Analytical characteristics and comparative evaluation of Aptima HCV quant Dx assay with the Abbott RealTime HCV assay and Roche COBAS AmpliPrep/COBAS TaqMan HCV quantitative test v2.0

BackgroundThe Aptima HCV Quant Dx assay (Aptima assay) is a fully automated quantitative assay on the Panther® system. This assay is intended for confirmation of diagnosis and monitoring of HCV RNA in plasma and serum specimens. The purpose of the testing described in this paper was to evaluate the performance of the Aptima assay.MethodsThe analytical sensitivity, analytical specificity, precision, and linearity of the Aptima assay were assessed. The performance of the Aptima assay was compared to two commercially available HCV assays; the Abbott RealTime HCV assay (Abbott assay, Abbott Labs Illinois, USA) and the Roche COBAS Ampliprep/COBAS Taqman HCV Quantitative Test v2.0 (Roche Assay, Roche Molecular Systems, Pleasanton CA, USA). The 95% Lower Limit of Detection (LoD) of the assay was determined from dilutions of the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) and HCV positive clinical specimens in HCV negative human plasma and serum. Probit analysis was performed to generate the 95% predicted detection limits. The Lower Limit of Quantitation (LLoQ) was established for each genotype by diluting clinical specimens and the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) in HCV negative human plasma and serum. Specificity was determined using 200 fresh and 536 frozen HCV RNA negative clinical specimens including 370 plasma specimens and 366 serum specimens. Linearity for genotypes 1 to 6 was established by diluting armored RNA or HCV positive clinical specimens in HCV negative serum or plasma from 8.08 log IU/mL to below 1 log IU/mL. Precision was tested using a 10 member panel made by diluting HCV positive clinical specimens or spiking armored RNA into HCV negative plasma and serum. A method comparison was conducted against the Abbott assay using 1058 clinical specimens and against the Roche assay using 608 clinical specimens from HCV infected patients. In addition, agreement between the Roche assay and the Aptima assay using specimens with low HCV concentrations (</= 25 IU/mL by Roche) was tested using 107 clinical specimens.ResultsThe 95% LoD was 5.1 IU/mL or lower for serum and 4.8 IU/mL or lower for plasma depending on the HCV genotype. The LLoQ for the assay was 10 IU/mL. Specificity was 100% with 95% confidence intervals of 99.6 to 100% for serum and plasma data combined. The assay demonstrated good linearity across the range for all genotypes. The Precision as estimated by the standard deviation (sd) was 0.17 log or lower across the range of the assay for both serum and plasma. HCV viral load results were compared using the Aptima assay and the Abbott assay giving a slope of 1.06, an intercept of 0.08 and an R2 of 0.98. HCV viral load results were compared for the Aptima and Roche assays giving a slope of 1.05, an intercept of −0.12 and an R2 of 0.96. Positive and negative agreement for the Aptima assay vs the Roche assay was 89% for low level specimens.ConclusionThe Aptima assay is a highly sensitive and specific assay. The assay gave comparable HCV viral load results when compared to the Abbott and Roche assays. The performance of the Aptima assay makes it an excellent candidate for the detection and monitoring of HCV.

Profile of the Roche cobas® EGFR mutation test v2 for non-small cell lung cancer

ABSTRACTIntroduction: The discovery of driver mutations in non-small cell lung cancer (NSCLC) has led to the development of genome-based personalized medicine. Fifteen to 20% of adenocarcinomas harbor an epidermal growth factor receptor (EGFR) activating mutation associated with responses to EGFR tyrosine kinase inhibitors (TKIs). Individual laboratories’ expertise and the availability of appropriate equipment are valuable assets in predictive molecular pathology, although the choice of methods should be determined by the nature of the samples to be tested and whether the detection of only well-characterized EGFR mutations or rather, of all detectable mutations, is required.Areas covered: The EGFR mutation testing landscape is manifold and includes both screening and targeted methods, each with their own pros and cons. Here we review one of these companion tests, the Roche cobas® EGFR mutation test v2, from a methodological point of view, also exploring its liquid-biopsy applications.Expert commentary: The Roche cobas® EGFR mutation test v2, based on real time RT-PCR, is a reliable option for testing EGFR mutations in clinical practice, either using tissue-derived DNA or plasma-derived cfDNA. This application will be valuable for laboratories with whose purpose is purely diagnostic and lacking high-throughput technologies.

A CROSS-SECTIONAL STUDY OF HEPATITIS B VIRUS INFECTION IN HIV-INFECTED CHILDREN IN WINDHOEK, NAMIBIA

BackgroundHepatitis B virus (HBV) remains endemic in Africa and an important co-morbidity in the HIV epidemic. The HIV treatment guidelines of the World Health Organisation (WHO) recommend tenofovir−lamivudine (or emtricitabine)...

Semi-quantitative real-time PCR: A useful approach to identify persons with low replicative chronic hepatitis B

Antiviral therapy can be avoided during the low replicative phase of chronic Hepatitis B virus (HBV) infection which is characterized notably by HBV DNA concentration below 2000IU/ml. Simplified diagnostic tests can improve access to HBV DNA monitoring in resource-limited settings. The capacity of a new semi-quantitative real-time PCR approach based on sample-to-standard relative detection of the target to discriminate samples with HBV DNA levels above or below the clinical threshold of 2000IU/ml was compared to a quantitative assay (Roche CobasAmpliPrep/CobasTaqMan HBV Test v2.0). The semi-quantitative assay correctly identified 40/40 (100%) low replicative HBV DNA patients and 58/61 (95%) samples from HBV-infected subjects with moderate/high levels of viral DNA. Our results suggested that this alternative PCR test is efficient to guide therapeutic decision based on identification of low replicative HBV infection from all of the chronic hepatitis B carriers requiring treatment, and may be useful in resource-limited settings where the vast majority of cases live.

MA08.09 Monitoring Plasma EGFR Mutations during First Line Treatment with EGFR TKIs in NSCLC Patients

Genotyping cell free circulating DNA (cfDNA) is a non-invasive method of detecting EGFR mutations (EGFRmu) in plasma and may provide an option to identify patients who progress while treated with EGFR TKIs. The aim of our study was to monitor plasma EGFRmu and identify dynamic case specific changes in plasma EGFRmu during routine treatment of advanced EGFRmu NSCLC patients. Plasma was collected from patients with advanced EGFRmu NSCLC treated with first- or second-generation EGFR TKIs. Plasma EGFRmu were dynamically monitored consecutively at every scheduled visit. Cobas EGFR Mutation Test v1 and v2 (Roche, USA) was used to detect 42 mutations at EGFR gene in exons 18 to 21. Liquid biopsy progression (LBP) was determined as reappearance of EGFRmu in plasma after negativization during treatment or increase of EGFRmu levels expressed by semi-quantitative index (SQI). Radiologic progression was determined in accordance with RECIST1.1 criteria. From May 2014, 23 patients were treated with EGFR TKIs for advanced EGFRmu NSCLC; 20/23 had detectable activating mutations in plasma before any treatment and were therefore included in our analysis. Dynamic changes of plasma EGFRmu during 1st line EGFR TKI treatment are shown in Figure 1. Eight patients (40%) experienced RECIST 1.1 progression while on treatment, whereas one patient was inevaluable. In 4/8 patients (50%) LBP appeared at the same time as radiologic progression, in 3/8 patients (37%) LBP appeared before radiologic progression (8w, 14w, 20w before, respectively) and in 1 patient (12%) radiologic progression appeared 6w before LBP. Among patients who did not experience radiologic progression yet, some dynamic changes in cfDNA were also observed, but alterations in the SQI values were much smaller. Monitoring EGFR mutations in plasma is a feasible and less invasive method in routine clinical practice and could be used as a predictive marker of progression on treatment with EGFR TKIs.

MA05.10 Cell-Free DNA Testing for EGFR Mutations in Clinical Practice - Facts and Figures from an Austrian Lung Cancer Center

Detection of EGFR mutations using cell-free DNA in plasma has recently emerged as a novel diagnostic approach to lung carcinoma. This “liquid biopsy” (LB) may also be useful for monitoring disease activity in EGFR-mutated tumors as well as in the management of EGFR-tyrosine kinase inhibitor (TKI) therapy. We present data collected in one year of use and report on applicability and diagnostic value in daily clinical practice. EGFR Mutations were analyzed using the semi-quantitative Roche cobas® EGFR Mutation Test v2, comprising 42 mutations. Cell free DNA was extracted from EDTA-Blood with the Qiagen QIAsymphony circulating DNA Kit. LB was initially used for follow-up of known EGFR-mutated tumors and/or in patients under TKI-therapy. Subsequently, we introduced routine LB testing in the primary diagnostic workup of lung cancer patients. From July 2015 to June 2016 we performed a total of 92 liquid biopsies in 77 patients (60% male, mean age 65y) in whom EGFR mutations could be detected in 10 cases (13%). EGFR status from histological samples was available in 40 patients, in 14 (18%) of them mutations were reported. Compared to histological EGFR status, LB reached a sensitivity and specificity of 0.57 and 0.96, respectively. A total of 9 patients had multiple LB testing during follow-up. Three of them initially had detectable mutations by LB, which turned undetectable upon tumor-specific treatment. Two patients remained EGFR-positive during follow-up despite of therapy, whereas four patients remained negative throughout follow-up and therapy. Resistance mutations under TKI-therapy were not observed. Primary LB (before initiation of any tumor-specific therapy) was obtained from 47 patients (72% male, mean age 66y). EGFR mutations by LB were detected in 2 patients (4%; 1 Ins. Exon-20, 1 L858R), while histology revealed EGFR mutations in 2 out of 22 patients (9%; both L858R). Comparison yielded a sensitivity of 0.5 and a specificity of 0.95 for LB. Testing for EGFR mutations using cell-free DNA has been established as a new powerful tool in the field of pulmonary oncology. Apart from sole detection of EGFR mutations, especially the application of LB in following patients over time will provide valuable new opportunities in clinical routine and decision making.

P1.02-008 2-Year Single Institution Experience with EGFR Plasma Testing in Advanced NSCLC

Lung adenocarcinoma patients in advanced stage of disease that harbor EGFR sensitizing mutations are eligible for treatment with tyrosine kinase inhibitors (TKI) due to a high likelihood of response. Most patients will ultimately develop resistance at disease progression. The T790M mutation is a dominant resistance mechanism to TKI. EGFR plasma testing enables non-invasive monitoring and detection of T790M. We followed patients with EGFR sensitizing mutations by measuring EGFR mutations in plasma during TKI treatment. We analyzed patients who were diagnosed lung adenocarcinoma stage IV, detected EGFR sensitizing mutations in tumor tissue samples and treated with TKI at University Clinic Golnik. We collected baseline plasma samples prior to TKI treatment and consecutive plasma samples at different time intervals after initiation of therapy. At the beginning, two separate tests, cobas® EGFR Mutation Test for tissue (CE-IVD) and plasma (under development) were used, and since October 2015 one test for tissue and plasma, cobas® EGFR Mutation Test v2 (Roche, Pleasanton, CA, USA) is used. Detected EGFR mutations in plasma samples were expressed as semi-quantitative index (SQI) which reflects a proportion of mutated versus wild-type copies of the EGFR gene. During 2-year period we collected 414 peripheral blood samples from 63 patients and performed 619 EGFR plasma tests. There are 25 patients with baseline and serial follow-up EGFR plasma tests, 16 patients with only serial follow-up EGFR tests since they started with TKI treatment before EGFR plasma testing was available, 5 patients are included in adjuvant setting, and 17 patients had no monitoring due to various reasons. Maximum number of EGFR plasma tests done per patient was 27 at 20 time-points. When introducing EGFR plasma testing, we prepared two aliquots of plasma out of 10 ml blood sample in EDTA-tubes and run test for both aliquots. Results of reproducibility study showed 95% concordance rate between both aliquots and thus we modified protocol to run the second aliquot only if the first one was negative. At disease progression, reappearance of EGFR sensitizing mutations with increasing SQI levels was detected. In 14 patients who progressed we detected T790M mutation, in 10 of them during monitoring TKI treatment. We also observed daily variation in EGFR mutation levels in the plasma. These data support the value of EGFR plasma testing to monitor the patient's response to TKI and detect T790M resistance mutation prior to clinical progression in a routine clinical setting.

P3.02b-106 Local Experience of Osimertinib Use; Retrospective Review Based on Plasma EGFR Using ddPCR Technique: Topic: EGFR RES

Osimertinib was approved by FDA in Nov 2016 for treatment of patients with metastatic EGFR-T790M mutation positive NSCLC, as detected by an FDA-approved test (Cobas ® EGFR Mutation Test v2) after EGFR-TKI failure, with an ORR up to 70% and a PFS around 11 months. We report local experience on EGFR mutations detected by droplet digital polymerase chain reaction (ddPCR) technique on cell free tumor DNA from lung cancer patients, guiding osimertinib therapy after 1st or 2nd generation TKI failure. All patients with plasma EGFR testing done using ddPCR technique from Nov 2015 to Mar 2016 are retrospectively identified and analyzed. 47 patients were tested for EGFR mutations by ddPCR after EGFR TKI failure. 19 patients had detectable T790M mutant copies of 3.5 - 65887.3 mutant copies/ml plasma (median 61.5). All had previous use of TKI > 6 months (range 171 – 1592 day, median 544). Among the 14 patients who received osimertinib, the median PFS and OS were not reached over a mean follow up of 4.3 months. There was one progressive disease, five stable diseases and eight partial responses as the best treatment response. The number of T790M mutant copies number/ml plasma in the PR group was numerically higher than the SD/PD group (mean 416.5 vs 25.9) but statistically insignificant (p-value 0.15) for difference. Of the limited eight patients having simultaneous tissue biopsy and molecular testing in this cohort, six was concordant with the plasma EGFR result. The two remaining had detectable T790M in plasma EGFR but not in tissue re-biopsy, and, of note, one achieved partial response and one stable disease after osimertinib. Plasma-EGFR-directed osimertinib treatment using ddPCR technique is feasible. The technique quantifies mutant load with potential prognostic implication, and detects heterogeneous tumors who might benefit from osimertinib despite negative tissue biopsy result.

P3.02b-043 Inter-Laboratory Comparison of the Roche Cobas EGFR Mutation Test v2 in Plasma: Topic: EGFR Biomarkers

Molecular testing of the EGFR gene is required to predict therapeutic response in non-small cell lung cancer (NSCLC). Although routinely performed, analysis of tumor tissue is subject to limitations. Analysis of circulating tumor DNA (ctDNA) in blood plasma may overcome these barriers, and techniques to detect and quantify variants in ctDNA are emerging. However, several key elements like sensitivity and specificity still need to be addressed. This study evaluates the inter-laboratory performance and reproducibility of the cobas® EGFR Mutation Test v2 for the detection of common EGFR variants in plasma. Fourteen laboratories from ten European countries received two identical panels of 27 single-blinded plasma members (Roche Molecular Systems, CA, USA). Samples were wild-type or spiked with plasmid DNA containing seven common EGFR variants at six predefined concentrations from 50-5000 target copies per mL (cp/mL). ctDNA was extracted by the Roche cobas® cfDNA Sample Preparation kit, followed by duplicate analysis with the Roche cobas® EGFR Mutation Test v2 kit. All sites received hands-on training and two obligatory proficiency samples to assure operator qualification. Statistical analyses were performed with SAS 9.4 (SAS Institute Inc., NC, USA). In total, 0.8% (12/1512) and 0.2% (3/1512) of runs were excluded due to protocol deviations or technical failures respectively. The sensitivity was lowest for the c.2156G>C; p.(G719A) variant with values of 80.4%, 69.6% and 89.1% at 50, 100 and 250 cp/mL respectively. Besides 88.7% for the c.2573T>G; p.(L858R) variant at 50 cp/mL, sensitivities for all other variants or concentrations varied between 96.3-100.0% and improved for increasing cp/mL. Specificities were all 98.8%-100.0%. Coefficients of variation (CV) indicate good intra-laboratory repeatability and inter-laboratory reproducibility, but increased for decreasing concentrations. Highest CV’s were reported for c.2156G>C; p.(G719A), c.2307_2308ins;Ex20Ins, and c.2582T>A; p.(L861Q) at 50 cp/mL. Prediction models reveal a significant correlation between the observed semi-quantitative index values (SQI) and copy numbers in plasma for all variants. A systematic over- and underestimation was observed for four different variants at 1000 and 5000 cp/mL respectively. This study demonstrates an overall robust performance of the cobas® EGFR Mutation Test v2 in plasma, suggesting a valuable and convenient addition to molecular tumor analysis in NSCLC. Repeated tests are advisable in case of low SQI values to reduce the average variation. Prediction models could be applied by future users to estimate the plasma tumor load from the observed SQI value, taking into account the possibility of systematic errors for high target copies.