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Updated: Aug 7, 2025
Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
Paired Comparison of Routine Molecular Screening of Patient Samples with Advanced Non-Small Cell Lung Cancer in
David Barthelemy1,2,3,4, Gaelle Lescuyer2,3,4, Florence Geiguer2,3,4
1Institut of Pharmaceutical and Biological Sciences (ISPB), Claude Bernard Lyon I, 69373 Lyon, France.
Introduction:
Progressive advanced non-small cell lung cancer (NSCLC) accounts for about 80-85% of all lung cancers. Approximately 10-50% of patients with NSCLC harbor targetable activating mutations, such as in-frame deletions in Exon 19 (Ex19del) of EGFR. Currently, for patients with advanced NSCLC, testing for sensitizing mutations in EGFR is mandatory prior to the administration of tyrosine kinase inhibitors.
Patients And Methods:
Plasma was collected from patients with NSCLC. We carried out targeted NGS using the Plasma-SeqSensei™ SOLID CANCER IVD kit on cfDNA (circulating free DNA). Clinical concordance for plasma detection of known oncogenic drivers was reported. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with our custom validated NGS assay. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis for our custom validated NGS assay.
Results:
In the plasma samples, driver targetable mutations were studied, with a mutant allele frequency (MAF) ranging from 0.00% (negative detection) to 82.25%, using the targeted next-generation sequencing Plasma-SeqSensei™ SOLID CANCER IVD Kit. In comparison with the OncoBEAMTM EGFR V2 kit, the EGFR concordance is 89.16% (based on the common genomic regions). The sensitivity and specificity rates based on the genomic regions (EGFR exons 18, 19, 20, and 21) were 84.62% and 94.67%. Furthermore, the observed clinical genomic discordances were present in 25% of the samples: 5% in those linked to the lower of coverage of the OncoBEAMTM EGFR V2 kit, 7% in those induced by the sensitivity limit on the EGFR with the Plasma-SeqSensei™ SOLID CANCER IVD Kit, and 13% in the samples linked to the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit. Most of these somatic alterations were cross validated in our orthogonal custom validated NGS assay, used in the routine management of patients. The concordance is 82.19% in the common genomic regions (EGFR exons 18, 19, 20, 21; KRAS exons 2, 3, 4; BRAF exons 11, 15; and PIK3CA exons 10, 21). The sensitivity and specificity rates were 89.38% and 76.12%, respectively. The 32% of genomic discordances were composed of 5% caused by the limit of coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit, 11% induced by the sensitivity limit of our custom validated NGS assay, and 16% linked to the additional oncodriver analysis, which is only covered by our custom validated NGS assay.
Conclusions:
The Plasma-SeqSensei™ SOLID CANCER IVD kit resulted in de novo detection of targetable oncogenic drivers and resistance alterations, with a high sensitivity and accuracy for low and high cfDNA inputs. Thus, this assay is a sensitive, robust, and accurate test.
Insights
The Plasma-SeqSensei™ SOLID CANCER IVD kit accurately detects targetable oncogenic drivers in non-small cell lung cancer (NSCLC) patients. This sensitive and robust assay is effective for both low and high circulating free DNA (cfDNA) inputs.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genomics
Background:
- Non-small cell lung cancer (NSCLC) is a prevalent malignancy, with a significant proportion of patients harboring actionable EGFR mutations.
- Testing for sensitizing EGFR mutations is crucial for guiding tyrosine kinase inhibitor therapy in advanced NSCLC.
Purpose of the Study:
- To evaluate the performance of the Plasma-SeqSensei™ SOLID CANCER IVD kit for detecting targetable oncogenic drivers in NSCLC patient plasma.
- To assess the clinical concordance and accuracy of this targeted next-generation sequencing (NGS) assay compared to orthogonal methods.
Main Methods:
- Targeted NGS was performed on circulating free DNA (cfDNA) from NSCLC patient plasma using the Plasma-SeqSensei™ SOLID CANCER IVD kit.
- Results were validated against an orthogonal OncoBEAM™ EGFR V2 assay and a custom validated NGS assay, with filtering for clonal hematopoiesis.
Main Results:
- The Plasma-SeqSensei™ kit detected targetable mutations with mutant allele frequencies ranging from 0.00% to 82.25%.
- Concordance with the OncoBEAM™ EGFR V2 assay was 89.16% for EGFR, with sensitivity and specificity of 84.62% and 94.67%, respectively.
- Concordance with the custom NGS assay was 82.19% across multiple genes, with sensitivity of 89.38% and specificity of 76.12%.
Conclusions:
- The Plasma-SeqSensei™ SOLID CANCER IVD kit demonstrates high sensitivity and accuracy for detecting oncogenic drivers and resistance alterations in cfDNA.
- This assay is a sensitive, robust, and accurate tool for molecular profiling in NSCLC, suitable for various cfDNA input levels.
