Test V2 Research Articles

Liquid Biopsy: A Multi-Parametric Analysis of Mutation Status, Circulating Tumor Cells and Inflammatory Markers in EGFR-Mutated NSCLC.

The liquid biopsy has the potential to improve patient care in the diagnostic and therapeutic setting in non-small cell lung cancer (NSCLC). Consented patients with epidermal growth factor receptor (EGFR) positive disease (n = 21) were stratified into two cohorts: those currently receiving EGFR tyrosine kinase inhibitor (TKI) therapy (n = 9) and newly diagnosed EGFR TKI treatment-naïve patients (n = 12). Plasma genotyping of cell-free DNA was carried out using the FDA-approved cobas® EGFR mutation test v2 and compared to next generation sequencing (NGS) cfDNA panels. Circulating tumor cell (CTC) numbers were correlated with treatment response and EGFR exon 20 p.T790M. The prognostic significance of the neutrophil to lymphocyte ratio (NLR) and lactate dehydrogenase (LDH) was also investigated. Patients in cohort 1 with an EGFR exon 20 p.T790M mutation progressed more rapidly than those with an EGFR sensitizing mutation, while patients in cohort 2 had a significantly longer progression-free survival (p = 0.04). EGFR exon 20 p.T790M was detected by liquid biopsy prior to disease progression indicated by computed tomography (CT) imaging. The cobas® EGFR mutation test detected a significantly greater number of exon 20 p.T790M mutations (p = 0.05). High NLR and derived neutrophil to lymphocyte ratio (dNLR) were associated with shorter time to progression and worse survival outcomes (p < 0.05). High LDH levels were significantly associated with shorter time to disease progression (p = 0.03). These data support the use of liquid biopsy for monitoring EGFR mutations and inflammatory markers as prognostic indicators in NSCLC.

UTILITY OF MINI-POOL NAT STRATEGY FOR IMPROVING BLOOD SAFETY BY DETECTING OCCULT HEPATITIS B VIRUS INFECTION : A 5 YEAR STUDY

Introduction: The prevalence of transfusion transmitted infections (TTIs) is high in India. The aim of our study was to evaluate the sero-prevalence of TTIs using Nucleic acid technology (NAT) and detection of Occult Hepatitis B virus infection by Minipool NAT Strategy. A total of 89,639 units of blood donated at Dhanvanta Materials and Methods: ri Voluntary Blood Bank, Rajahmundry during the period from January 2012 to July 2016. The sero-prevalence for HIV, HBV and HCV was tested by 4th generation ELISA. Only sero-negative samples were tested on mini pool nucleic acid test (MP-NAT) to detect HIV1, HIV2, HCV and HBV viral nucleic acids. Combined NAT yield was calculated and compared the NAT yield with MPX test and MPX V2.0. We also evaluated the optical density (OD) values of ELISA for MP-NAT reactive donor samples to evaluate the efcacy of NAT in detecting window period cases. The Results: overall sero-prevalence of TTIs was 2.41% and HBV was predominantly present (66%). Total 29 ELISA negative blood donor samples were found reactive on NAT. All NAT reactive donors were of HBV only. Out of 29 cases, 12 were detected by MPX test from 26,008 donations and 17 by MPX V2.0 from 25,619 donations, providing NAT yield of 1:2169 and 1:1507 respectively. OD and Signal cut off values of ELISA for NAT reactive samples were found to be much below extended grey zone value (&lt;0.3). Additiona Conclusion: l testing of nucleic acids by MP-NAT in combination of mandated primary serology by ELISA provides 99.99% of safe blood to needy patients; thus signicantly reduces the risk of TTIs by identifying the window period cases.

LBA51 Osimertinib treatment based on plasma T790M monitoring in patients with EGFR-mutant non-small cell lung cancer (NSCLC): EORTC Lung Cancer Group 1613 APPLE phase II randomized clinical trial

APPLE is a randomized, non-comparative, open-label, 3-arm, phase II study in patients with common EGFR-mutant, treatment-naïve NSCLC, aimed to evaluate the feasibility of longitudinal plasma EGFR T790M monitoring and the best sequencing strategy from gefitinib to osimertinib. We report the results of arm B (gefitinib until the emergence of circulating tumor DNA (ctDNA) EGFR T790M mutation by cobas EGFR Test v2 or progression (PD) by RECIST) and arm C (gefitinib until PD by RECIST), and then switch to osimertinib in both arms. Primary endpoint is Progression Free Survival rate (by RECIST 1.1) “on osimertinib” at 18 months (PFSR-OSI-18). The study was designed to reject a PFSR-OSI-18 of ≤40% in Arm B with 1-sided α = 0.08 and 92% power under a PFSR-OSI-18 of 60%. Arm C was an internal control arm. Secondary endpoints: response rate, overall survival (OS) and Brain PFS (BPFS). The primary analysis was performed in per-protocol (PP) population. From Nov 2017 to Feb 2020, 52 and 51 patients in 6 countries were randomized to Arm B and C. Most patients were females (75% and 65%), never smokers (71% and 59%) and had EGFR Del19 (64% and 65%), respectively. Median age was 69 and 61 years. One-third of patients had baseline brain metastases. In arm B, 17% of patients (8/47) switched to osimertinib based on ctDNA T790M-positive before RECIST PD. Median follow-up was 30 months. The study met its primary endpoint - PFSR-OSI-18 was 67.2% (84%CI 56.4-75.9%) in arm B vs. 53.5% (84% CI 42.3-63.5%) in arm C, with a median PFS of 22.0 months (95% CI 18.6-NR) vs. 20.2 months (95% CI 14.6-35.0), respectively. The median OS was not reached in arm B vs. 42.8 months (95%CI 27.0-NR) in arm C. Median BPFS in arm B and C were 24.4 months (95% CI 17.9-28.6) and 21.4 months (95% CI 14.5-42.8). Toxicity was as expected for both drugs. Serial monitoring of ctDNA T790M status in patients with advanced EGFR mutant-NSCLC by Cobas v2.0 PCR test treated with first-generation EGFR inhibitors is feasible, and a molecular progression before RECIST PD led to earlier switch to osimertinib in 17% of patients with satisfactory PFS and OS outcomes.

Paper 77: Only a Minority of Patients with Rotator Cuff Tear Achieve MCID for PROMIS Pain and Function Measures Following Initial Non-Operative Treatment

Objectives:It is still unclear which patients benefit from nonoperative treatment of rotator cuff tear versus those who benefit from early intervention. The purpose of our study was to determine which patients benefit from conservative therapy and establish the MCID of patients undergoing nonoperative treatment for partial and full-thickness rotator cuff tears (RCT).Methods:We performed a retrospective cohort study evaluating non-operatively managed patients with MRI-confirmed partial-thickness and full-thickness RCT (PTRCT, FTRCT). We included patients who underwent initial course consisting of rest, activity modification, physical therapy, and/or injection for their condition. In our institution, all patients complete National Institutes of Health (NIH) Patient-Reported Outcomes Measurement Information System (PROMIS) assessments for physical function and pain interference. In patients with shoulder conditions, this consists of the PROMIS Upper Extremity Computer Adaptive Test (CAT) v2.0 (“PROMIS UE”) and the PROMIS Pain Interference CAT v1.1 (“PROMIS PI”). Treatment modalities and follow-up PROMIS scores at least 6 weeks after initial visit were recorded. Using a distribution technique, the minimum clinically important difference (MCID) was calculated, and the proportion of patients achieving MCID for each tear group for both function and pain was determined. Chi-square tests were used to compare MCID achievement between PTRCT and FTRCT patients for both PROMIS UE and PROMIS PI.Results:A total of 100 FTRCT and 90 PTRCT patients were included in this analysis. Average age was 61.2 years, with 59% (n=112) female patients. The MCID for PROMIS UE was determined to be 3.9 and 3.9 for PTRCT and FTRCT patients, respectively. For PROMIS PI, MCID was 3.1 and 3.7 for PTRCT and FTRCT, respectively. In patients with PTRCT, the baseline score improved slightly from 31.4 to 34.9 for PROMIS UE, compared to a score change of 30.1 to 32.8 for patients with FTRCT. In total, 46% of PTRCT and 38% of FTRCT achieved MCID for PROMIS UE. In patients with PTRCT, the baseline score improved slightly from 63.1 to 60.0 for PROMIS PI, compared to a score change of 63.4 to 61.1 for patients with FTRCT. In total, 33% of PTRCT and 36% of FTRCT achieved MCID for PROMIS PI. When comparing PROMIS UE scores between PTRCT and FTRCT patients, there was no statistically significant difference in achievement of MCID (p=0.288). This was also the case for PROMIS PI (p=0.727).Conclusions:The present study identified MCID for PROMIS UE and PROMIS PI in both PTRCT and FTRCT undergoing conservative management. Only a minority of patients achieved MCID for pain (33% for PTRCT and 36% for FTRCT). A slightly higher proportion of patients achieved MCID for physical function (46% for PTRCT and 38% for FTRCT). The results of this study indicate that, while function may be more likely improved than pain, neither domains are significantly improved following initial nonoperative management in this patient population.

Epidemiology and clinical impact of EGFR mutation in patients with lung cancer after radical surgical treatment.

8552 Background: The epidemiology of epidermal growth factor receptor (EGFR) mutation in lung adenocarcinoma and its clinical impact are well-known. However, most studies have focused on advanced-stage inoperable cancer. Data on the frequency of EGFR mutation in surgically resected lung cancer are limited. Recent studies have shown a promising effect of Osimertinib in adjuvant settings. Hence, the need to estimate the target population in the real-world data. This study aimed to assess the occurrence of EGFR mutation in patients after radical surgical treatment of lung adenocarcinoma and explore its prognostic impact compared to EGFR negative group. Methods: This single-center retrospective analysis included the group of 732 consecutive Caucasian patients with histopathologically confirmed lung adenocarcinoma, evaluated for EGFR mutations expression, who underwent anatomical resection between January 2016, and December 2020. EGFR status was assessed by cobas EGFR mutation test v2. The frequency of EGFR mutations, disease-free survival (DFS) and overall survival (OS) in EGFR positive and EGFR negative groups were analyzed. Results: EGFR mutations were found in 65 surgical patients (8.9%) and did not differ from patients with advanced stages of lung adenocarcinoma (7.9%). EGFR mutations occurred more frequently in females than males, 48 out of 344 (14%) and 17 out of 388 (4.4%), respectively. Deletions within exon 19 and the L858R mutation in exon 21 constituted 49.2% and 24.6% of all mutations, respectively, while others comprised 26.2%. One case of L858R mutation coincided with T790M in exon 20 mutation. Detailed results divided by stages are presented in the Table. The occurrence of EGFR mutation had no significant influence on DFS and OS in patients after radical resection. Conclusions: The frequency of EGFR mutation in postoperative lung cancer was comparable to the occurrence in the general lung cancer population. EGFR mutation did not affect DFS and OS in patients after radical resection. [Table: see text]

Analytical and clinical validation of an amplicon-based next generation sequencing assay for ultrasensitive detection of circulating tumor DNA.

Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA (cfDNA). The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (Epstein-Barr virus (EBV) and hepatitis B virus (HBV)) and microsatellite instability (MSI). Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF. In non-cancer samples, a high specificity (≥99.9999% per-base) was observed. The limit of detection for copy number alterations, EBV, HBV, and MSI were also empirically determined. Orthogonal comparison of epidermal growth factor receptor (EGFR) variant calls made by LiquidHALLMARK and a reference allele-specific polymerase chain reaction (AS-PCR) method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% circulating tumor DNA (ctDNA)-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.

Efficacy of liquid biopsy for disease monitoring and early prediction of tumor progression in EGFR mutation-positive non-small cell lung cancer.

15–40% of non-small cell lung cancer (NSCLC) patients harbor epidermal growth factor receptor (EGFR)-sensitizing mutations. Tyrosine kinase inhibitors (TKIs) provide significant clinical benefit in this population, yet all patients will ultimately progress. Liquid biopsy can reliably identify somatic tumor-associated EGFR mutations in plasma. This study aimed to assess the feasibility and value of the quantitative assessment of EGFR driver mutations in plasma in EGFR-mutated NSCLC patients treated with EGFR-TKIs as a tool to evaluate therapeutic response to TKIs and monitor for disease progression. The study included 136 patients with tissue biopsy-confirmed EGFR-sensitizing, mutation-positive lung adenocarcinoma with plasma collected prior to TKI treatment and at least two post-initiation TKI treatment/follow-up blood samples. Plasma samples were tested with the cobas® EGFR Mutation Test v2 (cobas EGFR Test), and semi-quantitative index (SQI) values for each identified mutation were reported by the assay software. The most common baseline EGFR mutations detected in tissue were L858R (53.7%) and exon 19 deletion (39.7%). Plasma cell-free DNA analysis detected EGFR mutations in 74% of the baseline samples. Objective response rate by RECIST 1.1 was achieved in 72% of patients, while 93% had a molecular response (defined as disappearance of the EGFR mutation from plasma). 83% of patients had molecular progression (MP; 1.5X SQI increase or new T790M mutation), and 82% who had a clinical response had clinical progression. On average, MP occurred 42 days prior to clinical progression. Patients who progressed while on first-line TKI showed MP of the original EGFR-sensitizing mutations prior to the emergence of a T790M mutation, which was detected in 27% of the EGFR plasma-positive patients. Longitudinal monitoring of EGFR mutational load in plasma is feasible and can predict both response and clinical progression in EGFR-mutated NSCLC patients treated with EGFR-TKIs, as well as detect treatment-emergent EGFR mutations.

374 Therapeutic Class Labeling of EGFR Companion Diagnostics (CDxs)

OBJECTIVES/GOALS: Review all approved companion diagnostics (CDxs) labeling for therapeutic class language. Examine the regulatory pathways of CDx products whose labels contain therapeutic class labeling. Develop recommendations for pharmaceutical industry professionals on best practices in the co-development of CDxs and oncology therapeutic products. METHODS/STUDY POPULATION: Literature discussing companion diagnostics was reviewed from EBSCOhost, PubMed, and OVID. The Intended Use language within CDx labels on the Food and Drug Administrations “List of Cleared or Approved Companion Diagnostic Devices (In Vitro and Imaging Tools)” website were reviewed on November 1, 2021 for therapeutics class language. For CDx products with therapeutic class label language, the regulatory history was evaluated to determine the development approach taken to achieve the language. RESULTS/ANTICIPATED RESULTS: A total of 45 CDxs were identified, of which only 2 contained therapeutic class labeling, both of which were devices for the identification of epidermal growth factor receptor (EGFR) mutations for the treatment of non-small cell lung cancer (NSCLC). Three additional EGFR CDxs were approved; however, they did not contain therapeutic class labeling. The first CDx was the Cobas EGFR Mutation Test V2, which received therapeutic group label language as an update on October 27, 2020; however, prior to the therapeutic class labeling, three oncology products were named in the Intended Use: Tarceva (erlotinib), Tagrisso (osimertinib), and Iressa (gefitinib). The second CDx to incorporate therapeutic class labeling was the ONCO/Reveal Diagnostic Lung and Colon Cancer Assay upon initial approval on July 30, 2021. DISCUSSION/SIGNIFICANCE: EGFR CDxs are the first to shift towards therapeutic class labeling. Indication, molecular alterations, and mechanism of action of the approved therapeutic class products, number of products approved, as well as CDx analytical and clinical validation influence class label relevance. Discussions with the FDA are encouraged early in development.

Final report on plasma ctDNA T790M monitoring during EGFR-TKI treatment in patients with EGFR mutant non-small cell lung cancer (JP-CLEAR trial).

Osimertinib is active against T790M-positive epidermal growth factor receptor mutant non-small cell lung cancer. We enrolled 122 sensitive epidermal growth factor receptor mutant non-small cell lung cancer patients who were planned to receive or were receiving first-/second-generation epidermal growth factor receptor tyrosine kinase inhibitors without disease progression and monitored plasma T790M every 1–2 months using the cobas® EGFR Mutation Test v2. We previously reported the concordance between T790M status in plasma and tissue. This is the final report on the sensitivity of plasma T790M and the efficacy of sequential osimertinib. The sensitivity was 21.1% (95% confidence interval: 6.1–45.6%). The best overall response was 25.0% (95% confidence interval: 9.8–46.7) in the plasma T790M-positive group and 28.6% (95% confidence interval: 8.4–58.1) in the plasma T790M-negative but tissue T790M-positive group. Median progression-free survival was 7.9 months (95% confidence interval: 4.7–17.5) for the former and 4.4 months (95% confidence interval: 3.0–N.E.) for the latter, with no statistically significant difference (P = 0.74).

Effects of Different Centrifugation Protocols on the Detection of EGFR Mutations in Plasma Cell-Free DNA.

ObjectivesVarious preanalytical factors, including the collection tube, storage conditions, and centrifugation, affect the detection results of plasma cell-free DNA (cfDNA). We compared the effect of different centrifugation protocols on the detection of EGFR mutations in cfDNA.MethodsWe analyzed 117 plasma specimens from 110 patients with non–small cell lung cancer using the cobas EGFR Mutation Test v2 (Roche Diagnostics). We compared the identified EGFR mutations and semiquantitative index values from the 1- and 2-step centrifugation groups and confirmed the clinical impact of differences in the results after further high-speed centrifugation.ResultsWe detected EGFR mutations in 44 (37.6%) and 47 (40.2%) samples that were centrifuged once and twice, respectively; the 2 groups showed an 89.7% (105/117) concordance and a strong correlation in their semiquantitative index values (r = 0.929). Among the 12 inconsistent result pairs, 9 samples of 2-step centrifugation (75%) were consistent with the results of a recent tissue biopsy.ConclusionsAdditional high-speed centrifugation has been shown to increase the sensitivity of EGFR mutation detection in a commercial in vitro diagnostic real-time polymerase chain reaction device and is an optimal preanalytical factor for detecting low-allele frequency gene mutations using low concentrations of cfDNA.

Pediatric Respiratory Virus Infections During the COVID-19 Pandemic in a Region Without Active Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Circulation.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were not prevalent in Yonago and its vicinity during autumn 2020, and the relative frequencies of pathogen-induced respiratory infections during this period are unclear. We collected 109 nasopharyngeal swabs from 93 pediatric patients who visited Tottori University Hospital between October 1, 2020, and March 31, 2021. These samples were comprehensively tested for 18 pathogens with the FilmArray® respiratory panel test (v2.1) using nested real-time polymerase chain reaction, and the frequency of pathogens detected per month was calculated. In addition, we compared the duration of fever and the blood test results of patients infected with each pathogen or multiple pathogens. Of the 109 samples, 42 were obtained from female patients and 67 from male patients (median age, 3 years; range, 0-15 years). Overall, 62 patients (56.9%) had a fever ≥ 38 °C at the time of examination, and the median duration of fever ≥ 38 °C was 2 days (1-12). During the study period, the highest number of samples (22) were collected in November 2020. Among samples that tested positive, the most common pathogens were rhino/enteroviruses (52 samples; 76.5%), followed by adenoviruses (7 samples; 10.3%), coronavirus NL63 (6 samples; 8.8%), coronavirus OC43, parainfluenza virus type 1, and parainfluenza virus type 2 (1 sample each; 1.5% each). The duration of fever was significantly longer in adenovirus-infected patients than in patients infected with other viruses (P < 0.05). Hemoglobin and sodium levels were also significantly lower among the adenovirus-infected patients. However, these variations were mostly within the normal range. No clinically meaningful differences were found between rhino/enterovirus-infected and non-rhino/enterovirus-infected cases, between coronavirus NL63-infected and non-coronavirus NL63-infected cases, and between cases with multiple- and single-pathogen infections. Rhino/enteroviruses were the most common viruses causing respiratory tract infections in areas without endemic SARS-CoV-2.

Monitoring of the presence of EGFR-mutated DNA during EGFR-targeted therapy may assist in the prediction of treatment outcome

The aim of our trial was to evaluate the prognostic significance of qualitative ctDNA analysis on different stages of EGFR mutated non-small cell lung cancer (NSCLC) treatment.We included 99 patients amendable for the first line treatment with either gefitinib/erlotinib (n = 87), afatinib (n = 10) or osimertinib (n = 2). Sequential qualitative analysis of ctDNA with cobas® EGFR Mutation Test v2 were performed before first dose, after 2 and 4 months of treatment, and on progression.Our analysis showed clinically significant heterogeneity of EGFR-mutated NSCLC treated with 1st line tyrosine kinase inhibitors (TKIs) in terms of progression-free and overall survival. When treated with conventional approach, i.e. monotherapy with TKIs, the patients falls into three subgroups based on ctDNA analysis before and after 2 months of treatment. Patients without detectable ctDNA at baseline (N = 32) possess the best prognosis on duration of treatment (PFS: 24.07 [16.8–31.3] and OS: 56.2 [21.8–90.7] months). Those who achieve clearance after two months of TKI (N = 42) have indistinguishably good PFS (19.0 [13.7 – 24.2]). Individuals who retain ctDNA after 2 months (N = 25) have the worst prognosis (PFS: 10.3 [7.0 – 13.5], p = 0.000). 9/25 patients did not develop ctDNA clearance at 4 months with no statistical difference in PFS from those without clearance at 2 months.Prognostic heterogeneity of EGFR-mutated NSCLC should be taken into consideration in planning further clinical trials and optimizing the outcome of patients.

Application of liquid biopsy-based targeted capture sequencing analysis to improve the precision treatment of non-small cell lung cancer by tyrosine kinase inhibitors

BackgroundTargeted therapy of patients with non-small cell lung cancer (NSCLC) who harbour sensitising mutations by tyrosine kinase inhibitors (TKIs) has been found more effective than traditional chemotherapies. However, target genes...

Investigation of EGFR mutations in non-small cell lung cancer usually undetectable by PCR methods.

Epidermal growth factor receptor (EGFR) mutations are the most significant genomic drivers of non-small cell lung cancer (NSCLC) and determine the efficacy of EGFR tyrosine kinase inhibitor (EGFR-TKI) therapy. PCR methods are used clinically for the detection of EGFR mutations. The Scorpion Amplification Refractory Mutation System (Scorpion-ARMS) and the cobas® EGFR Mutation Test v2 (cobas v2) are widely used PCR methods. However, those PCR methods only selectively detect the common EGFR mutations. The aim of the present study was to reveal the true frequency of EGFR mutations in NSCLC by investigating EGFR mutations usually undetectable by PCR methods by using direct sequencing. A total of 70 Japanese patients who underwent lung resection for NSCLC between September 2016 and March 2019 were included in the present study. Subsequently, PCR methods and direct sequencing were performed. In total, 29 mutations were detected by cobas v2. In total, 41 patients were identified as EGFR wild-type by cobas v2, among whom direct sequencing detected mutations in 3 patients. Subsequent Scorpion-ARMS was performed in the 3 patients in whom direct sequencing detected mutations. In total, one exon 21 L858R + G863D compound mutation was identified as a L858R single mutation, and two other mutations were undetectable. Moreover, 1 patient who was ‘wild-type’ on cobas v2 but ‘EGFR mutation’ on direct sequencing developed recurrence after surgery and responded to EGFR-TKI treatment. In present study, the percentage of undetectable EGFR mutations by cobas v2 was 9.4% in 32 mutations. It was inferred that the cause of the discrepancy in the mutation type (L858R + G863D in exon 21, and L858R in exon 21) between cobas v2 and Scorpion ARMS was due to the different limit of detection between these two PCR methods. In conclusion, the findings of the present study suggested that a selective mutation detection method may decrease the opportunity of patients with NSCLC to receive EGFR-TKI therapy. Thus, the development of a screening test to determine the EGFR status as wild-type or mutant is required for EGFR-TKI therapy.

A large-scale, multicentered trial evaluating the sensitivity and specificity of digital PCR versus ARMS-PCR for detecting ctDNA-based EGFR p.T790M in non-small-cell lung cancer patients.

BackgroundDeveloping liquid biopsy technology with higher sensitivity and specificity especially for low-frequency mutations remains crucial. This study demonstrated superior performance of the newly developed digital PCR (dPCR) kit for ctDNA-based EGFR p.T790M detection in metastatic non-small-cell lung cancer (NSCLC) against ARMS-PCR.MethodsThis large-scale, multi-centered diagnostic study recruited 1,045 patients including 1,029 patients diagnosed with advanced NSCLC and 16 patients with specific samples between April 1st 2018 and November 30th 2019. EGFR p.T790M in plasma samples from mNSCLC patients were tested using dPCR with ADx-ARMS PCR and Cobas® EGFR Mutation Test V2 as comparator assays to confirm cut-off value for dPCR and evaluate its performance against ARMS-PCR-based assays. Efficacy was evaluated for patients with EGFR p.T790M detected by dPCR or ARMS-PCR, who underwent Osimertinib treatment.ResultsThe sensitivity, specificity, and concordance of dPCR against ADx-ARMS PCR was 98.15%, 88.66% and 90.16%, respectively for 1,026 plasma samples. Additional 9.26% patients were detected positive by dPCR. The majority of those samples had a mutation allele frequency between 0.1% and 1%. In 45 paired tissue and plasma samples, the sensitivity improved from 30.77% to 53.85% by dPCR with the specificity over 90%. The response of Osimertinib in 74 EGFR p.T790M-positive patients detected by dPCR, including 26 determined as negative by ARMS-PCR, were evaluated to have an ORR of 44.59% and a DCR of 90.54%.ConclusionsdPCR is a sensitive and accurate tool for ctDNA-based EGFR p.T790M detection due to its significantly improved sensitivity without compromising specificity, and dPCR is equivalent to ARMS-PCR as a companion diagnostic tool while benefiting more patients under Osimertinib treatment.Trial RegistrationChinese Clinical Trial Registry identifier: ChiCTR2100043147.

Evaluating the performance of the GeneXpert HIV-1 qualitative assay as a consecutive test for a new early infant diagnosis algorithm in South Africa.

Background. The proportion of HIV-exposed infants and young children infected with HIV in South Africa (SA) has declined markedly over the past decade as a result of the country’s comprehensive prevention of mother-to-child transmission programme. This decrease has in turn reduced the positive predictive value (PPV) of diagnostic assays, necessitating review of early infant diagnosis (EID) algorithms to ensure improved accuracy. Objectives. To evaluate the performance of the GeneXpert HIV-1 qualitative assay (Xpert EID) as a consecutive test for infants with an ‘HIV-detected’ polymerase chain reaction screening test at birth. Methods. We retrospectively analysed a longitudinal cohort of HIV-exposed infants on whom birth testing was performed, using whole-blood ethylenediaminetetra-acetic acid samples, from four tertiary sites in Gauteng Province between June 2014 and December 2019. Birth samples from all infants with a Cobas AmpliPrep/Cobas TaqMan HIV-1 Qualitative Test v2.0 (CAP/CTM v2.0) HIV-detected screening test, a concurrent Xpert EID test and a subsequent confirmatory CAP/CTM v2.0 test on a separate specimen were included. Performance of the Xpert EID in predicting final HIV status was determined as proportions with 95% confidence intervals (CIs). A comparison of indeterminate CAP/CTM v2.0 results, as per National Health Laboratory Service resulting practice, with discordant CAP/CTM v2.0 v. Xpert EID results was performed. Results. Of 150 infants who met the inclusion criteria, 6 (3.9%) had an Xpert EID result discordant with final HIV status: 5 (3.3%) were false negatives and 1 (0.7%) was false positive. As a consecutive test, the Xpert EID yielded a sensitivity of 96.5% (95% CI 92 - 98.9), specificity of 85.7% (95% CI 42.1 - 99.6), PPV of 99.3% (95% CI 95.7 - 99.9), negative predictive value of 54.5% (95% CI 32.5 - 74.9) and overall accuracy of 96.1% (95% CI 91.5 - 98.5). Using discordant CAP/CTM v2.0/Xpert EID results as criteria to verify indeterminate results instead of current practice would have reduced the number of indeterminate screening results by 42.1%, from 18 (12.6%) to 11 (7.2%), without increasing the false-positive rate. Conclusions. Addition of the Xpert EID as a consecutive test for specimens with an HIV-detected PCR screening result has the potential to improve the PPV and reduce the indeterminate rate, thereby reducing diagnostic challenges and time to final status, in SA’s EID programme.

Detection of EGFR mutations in liquid biopsy samples using allele-specific quantitative PCR: A comparative real-world evaluation of two popular diagnostic systems

PurposeThe detection of epidermal growth factor receptor (EGFR) mutations in plasma cell-free DNA (cfDNA) is an auxiliary tool for the molecular diagnosis of non-small cell lung cancer (NSCLC), especially when an adequate tumor tissue specimen cannot be obtained. We compared the diagnostic accuracy of two commonly used in vitro diagnostic-certified allele-specific quantitative PCR assays for detecting plasma cfDNA EGFR mutations. MethodsWe analyzed EGFR mutations in plasma cfDNA from 90 NSCLC patients (stages I–IV) before treatment (n ​= ​60) and after clinical progression on EGFR tyrosine kinase inhibitors (n ​= ​30) using the cobas EGFR mutation test v2 (Roche Molecular Systems, Inc.) and therascreen EGFR Plasma RGQ PCR kit (Qiagen GmbH). ResultsThere was higher concordance between plasma cfDNA and matched tumor tissue EGFR mutations with cobas (66.67%) compared with therascreen (55.93%). The concordance rate increased to 90.00% with cobas (Cohen's kappa coefficient, κ ​= ​0.80; p ​< ​0.0001) and 73.33% with therascreen (κ ​= ​0.49; p ​= ​0.0009) in advanced NSCLC patients. In treatment-naïve patients, cobas was superior to therascreen (sensitivity: 82.35% vs. 52.94%; specificity: 100% vs. 100%). In patients with clinical progression on EGFR tyrosine kinase inhibitors, EGFR exon 20 p.T790M was detected in 30% and 23% of cfDNA samples by cobas and therascreen, respectively. ConclusionsCobas was superior to therascreen for detection of plasma EGFR mutations in advanced NSCLC. Plasma cfDNA EGFR mutation analysis is complex; therefore, the diagnostic accuracy of commercially available assays should be validated.

Evaluation of the Aptima HIV-1 Quant Dx assay for HIV diagnosis at birth in South Africa

The increased coverage of antiretroviral therapy has resulted in a decrease in the positive predictive value (PPV) and diagnostic sensitivity of early infant diagnosis assays. To evaluate the diagnostic performance of the Aptima HIV-1 Quant DX assay (Aptima) in detecting HIV infection at birth. The study was a cross-sectional laboratory based evaluation using whole blood DBS specimens. Samples were collected from HIV-exposed neonates at birth at two paediatric facilities in Gauteng between 1st March 2018 - 31st January 2020. Performance of the Aptima compared to the Cobas® AmpliPrep/Cobas® TaqMan HIV-1 Qualitative Test v2.0 was calculated using a two-by-two table and reported as proportions with 95% confidence intervals. A total of 363 infants met the inclusion criteria of which 4 (1.1%) had an Aptima result discordant with CAP/CTM HIV status: two (50%) negative and two (50%) positive. The Aptima assay had a sensitivity of 93.75% (95% CI: 79.19%-99.23%), specificity of 99.4% (95% CI: 97.83%-99.93%), PPV of 93.75% (95% CI: 78.98%-98.36%), negative predictive value of 99.4% (95% CI: 97.73%-99.84%), and overall accuracy of 98.9% (95% CI: 97.2%-99.7%). The Aptima yielded an error code on 37 (10.19%) results, of which 35 (94.59%) were resolved on repeat testing. Of the 32 HIV-detected specimens, 20 had a plasma VL result available (18 on Abbott and 2 on Cobas). The absolute median difference was 0.66 log10 (IQR: 0.36-1.71). The Aptima demonstrated good EID performance and can be considered as a qualitative EID assay.

A Real-World, Observational, Prospective Study to Assess the Molecular Epidemiology of Epidermal Growth Factor Receptor (EGFR) Mutations upon Progression on or after First-Line Therapy with a First- or Second-Generation EGFR Tyrosine Kinase Inhibitor in EGFR Mutation-Positive Locally Advanced or Metastatic Non-Small Cell Lung Cancer: The 'LUNGFUL' Study.

Simple SummaryNon-small cell lung cancer (NSCLC) accounts for approximately 85% of lung cancer cases, with few patients carrying driver mutations in the gene encoding for epidermal growth factor receptor (EGFR). Advances in translational research have established EGFR tyrosine kinase inhibitors (TKIs) as the standard first-line therapy for NSCLC patients with activating EGFR mutations. The aim of our observational study was to assess the frequency of T790M acquired resistance and predictors of its presence, in patients with EGFR-mutated locally advanced or metastatic NSCLC who have progressed in the first-line EGFR-TKI treatment setting with first- or second-generation TKIs and have undergone molecular testing in tissue and/or plasma biopsy. The study highlights the challenges of performing tissue re-biopsy in routine care settings, which can lead to patients considered non-eligible for certain therapies from which they can benefit, and merits further actions from the healthcare community, in order to establish re-biopsy as a standard procedure.Background: Real-world data on the molecular epidemiology of EGFR resistance mutations at or after progression with first- or second-generation EGFR-TKIs in patients with advanced NSCLC are lacking. Methods: This ongoing observational study was carried out by 23 hospital-based physicians in Greece. The decision to perform cobas® EGFR Mutation Test v2 in tissue and/or plasma at disease progression was made before enrollment. For patients with negative/inconclusive T790M plasma-based results, tissue re-biopsy could be performed. Results: Ninety-six (96) eligible patients were consecutively enrolled (median age: 67.8 years) between July-2017 and September-2019. Of the patients, 98% were tested upon progression using plasma and 2% using tissue/cytology biopsy. The T790M mutation was detected in 16.0% of liquid biopsies. Tissue re-biopsy was performed in 22.8% of patients with a T790M-negative plasma result. In total, the T790M positivity rate was 21.9%, not differing between patients on first- or second-generation EGFR-TKI. Higher (≥2) ECOG performance status and longer (≥10 months) time to disease progression following EGFR-TKI treatment initiation were associated with T790M positivity. Conclusions: Results from plasma/tissue-cytology samples in a real-world setting, yielded a T790M positivity rate lower than previous reports. Fewer than one in four patients with negative plasma-based testing underwent tissue re-biopsy, indicating the challenges in routine care settings.

Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations.

Liquid biopsies have increasingly shown clinical utility. Although next-generation sequencing has been widely used for the detection of somatic mutations from plasma, performance characteristics vary by platform. Therefore, thorough validation is mandatory for clinical use. This study aimed to evaluate the analytical validity of the Oncomine Pan-Cancer Cell-Free Assay. A massively parallel sequencing for the assay was performed using the Ion S5 XL System with Ion 540 kit. The analytical sensitivity and precision were evaluated using pre-characterized reference materials. The specificity was evaluated using plasma from healthy subjects. A comparison with the Cobas EGFR Mutation Test v2 was performed using reference materials and plasma from lung cancer patients. For SNVs and short indels, the analytical sensitivities at variant allele frequencies (VAFs) of 0.1%, 0.5%, and 1% were 50%, 93.4%, and 100% with 20 ng of input, respectively. The overall precision of the true positive variants was 98% at a VAF of 1% with 20 ng input. The assay showed a similar sensitivity to that of the Cobas EGFR Mutation Test v2 at a VAF of 0.5% with 20 ng of input and 100% concordance on clinical samples. The Pan-Cancer Cell-Free Assay can be applied to detect EGFR mutations in advanced lung cancer patients, although follow-up studies will be needed to evaluate the analytical validity for other types of genes and aberrations using clinical samples.