Performance of the OncomineTM Lung cfDNA Assay for Liquid Biopsy by NGS of NSCLC Patients in Routine Laboratory Practice

Luca, Giuseppa De; Lastraioli, Sonia; Conte, Romana; Mora, Marco; Genova, Carlo; Rossi, Giovanni; Tagliamento, Marco; Coco, Simona; Bello, Maria Giovanna Dal; Zupo, Simona; Dono, Mariella

doi:10.3390/app10082895

Cited by 7 publications

(7 citation statements)

References 33 publications

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“…Thus, reporting from various studies by independent groups may help to determine the performance of the assay. The previous study using the Oncomine Lung Cell-Free DNA Assay, the same platform with the different assay, demonstrated a sensitivity of 81% with <20 ng of cfDNA at a VAF of 0.1%, whereas our data showed a sensitivity of 50% under the same condition [21]. In the report by the manufacturer, the same assay in the present study showed a sensitivity of 80% at a VAF of 0.1% for SNV [22].…”

Section: Discussionsupporting

confidence: 49%

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

Park

Kim

et al. 2021

Diagnostics

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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.

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Section: Discussionsupporting

confidence: 49%

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

Park

Kim

et al. 2021

Diagnostics

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“…These include the droplet digital PCR (ddPCR) method with an estimated LOD of 0.05% for the exon 19 deletion and L858R mutations and 0.1% for T790M mutations 24 and the OncoBEAM (beads, emulsion, amplification and magnetics) approach with a LOD of nearly 0.02% for T790M mutation 25 . The conventional NGS-based approaches are considered less sensitive, however the implementation of a molecular tagging strategies in NGS technology in the last years allows to significantly reduce the sequencing artifacts and reach sensitivities similar to those observed with the other approaches (up to 0.1%) 26 , 27 .…”

Section: Discussionmentioning

confidence: 94%

Evaluation of the Idylla ctEGFR mutation assay to detect EGFR mutations in plasma from patients with non-small cell lung cancers

Gilson

Saurel

Salleron

et al. 2021

Sci Rep

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The assessment of EGFR mutations is recommended for the management of patients with non-small cell lung cancer (NSCLC). Presence of EGFR mutation is associated with response or resistance to EGFR tyrosine kinase inhibitors (EGFR-TKI). Liquid biopsy is nowadays widely used for the detection of resistance to EGFR-TKI. We evaluated here the performance of the Idylla ctEGFR mutation assay for the detection of EGFR mutations in circulating tumour DNA (ctDNA) in plasma from patients with NSCLC. Previously characterized plasma samples from 38 patients with NSCLC were analysed using 2 different analytical conditions (C1 and C2). The limit of detection (LOD) was evaluated using 2 mL of healthy donor plasma spiked with commercial DNA controls. Overall agreement, sensitivity and specificity were 92.1%, 86.7% and 95.7% for C1 condition respectively and 94.7%, 86.7% and 100% for C2 condition respectively. The T790M secondary resistance mutation was detected in two samples out of 3. The Idylla system was able to detect the exon 19 deletion from 6 copies/mL and up to 91 copies/mL for the G719S mutation. These results support that the Idylla ctEGFR mutation assay is a rapid option for the detection of EGFR hotspots mutations in plasma samples, however a particular attention is needed for its interpretation.

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“…Firefly assay demonstrated superior sensitivity and specificity with a 98.89% detection rate at an allele frequency of 0.2% [ 30 ]. Oncomine ™ Lung cell-free DNA Assay (OLcfA) NGS panel has been shown to be effective in detecting mutations in NSCLC patients with a detection limit of 0.1% [ 31 ]. In this proof-of-concept pilot study, we aim to develop and validate a custom 15-gene ctDNA NGS panel for detecting single nucleotide variants and small indels in lung cancer, with primary focus on EGFR mutation analysis in NSCLC.…”

Section: Discussionmentioning

confidence: 99%

“…Overall, our custom NGS panel showed comparable performance to the real time PCR based assays (Cobas and Therascreen) and achieved 100% analytical sensitivity and specificity for detecting EGFR mutations with at least 1% allelic frequencies. However, the assay is suboptimal when compared to droplet digital PCR or NGS-based assays which can achieve detection limits of below 1% [ 18 , 31 , 41 ].…”

Section: Discussionmentioning

confidence: 99%

Analytical and clinical validation of a custom 15-gene next-generation sequencing panel for the evaluation of circulating tumor DNA mutations in patients with advanced non-small-cell lung cancer

Chow

Abidin²,

Kow

et al. 2022

PLoS ONE

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Background This is a pilot proof-of-concept study to evaluate the utility of a custom 15-gene circulating tumor DNA (ctDNA) panel as a potential companion molecular next-generation sequencing (NGS) assay for identifying somatic single nucleotide variants and indels in non-small-cell lung cancer (NSCLC) patients. The custom panel covers the hotspot mutations in EGFR, KRAS, NRAS, BRAF, PIK3CA, ERBB2, MET, KIT, PDGFRA, ALK, ROS1, RET, NTRK1, NTRK2 and NTRK3 genes which serve as biomarkers for guiding treatment decisions in NSCLC patients. Method The custom 15-gene ctDNA NGS panel was designed using ArcherDX Assay Designer. A total of 20 ng or 50 ng input ctDNA was used to construct the libraries. The analytical performance was evaluated using reference standards at different allellic frequencies (0.1%, 1%, 5% and parental). The clinical performance was evaluated using plasma samples collected from 10 treatment naïve advanced stage III or IV NSCLC patients who were tested for tissue EGFR mutations. The bioinformatics analysis was performed using the proprietary Archer Analysis Software. Results For the analytical validation, we achieved 100% sensitivity and specificity for the detection of known mutations in the reference standards. The limit of detection was 1% allelic frequency. Clinical validation showed that the clinical sensitivity and specificity of the assay for detecting EGFR mutation were 83.3% and 100% respectively. In addition, the NGS panel also detected other mutations of uncertain significance in 6 out of 10 patients. Conclusion This preliminary analysis showed that the custom 15-gene ctDNA NGS panel demonstrated good analytical and clinical performances for the EGFR mutation. Further studies incorporating the validation of other candidate gene mutations are warranted.

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Performance of the OncomineTM Lung cfDNA Assay for Liquid Biopsy by NGS of NSCLC Patients in Routine Laboratory Practice

Cited by 7 publications

References 33 publications

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

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

Evaluation of the Idylla ctEGFR mutation assay to detect EGFR mutations in plasma from patients with non-small cell lung cancers

Analytical and clinical validation of a custom 15-gene next-generation sequencing panel for the evaluation of circulating tumor DNA mutations in patients with advanced non-small-cell lung cancer

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