Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma EGFR Mutations

Yong Gon Cho; Joonhong Park; Ji Yoon Han; Tae Yun Kim

doi:10.3390/genes14061219

Evaluation of the Analytical Performance of Oncomine Lung cfDNA Assay for Detection of Plasma EGFR Mutations

Genes (Basel). 2023 Jun 2;14(6):1219. doi: 10.3390/genes14061219.

Authors

Yong Gon Cho^{1

2}, Joonhong Park¹, Ji Yoon Han³, Tae Yun Kim⁴

Affiliations

¹ Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea.
² Research Institute of Clinical Medicine, Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea.
³ Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea.
⁴ Department of Thoracic and Cardiovascular Surgery, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea.

Abstract

Background: The clinical utility of circulating tumor DNA (ctDNA) in the early detection of tumor mutations for targeted therapy and the monitoring of tumor recurrence has been reported. However, the analytical validation of ctDNA assays is required for clinical application.

Methods: This study evaluated the analytical performance of the Oncomine Lung cfDNA Assay compared with the cobas^®EGFR Mutation Test v2. The analytical specificity and sensitivity were estimated using commercially pre-certified reference materials. The comparative evaluation of the two assays was carried out using reference materials and plasma derived from patients diagnosed with lung cancer.

Results: Using 20 ng of input cell-free DNA (cfDNA), the analytical sensitivities for EGFR mutations with variant allele frequencies (VAFs) of 1% and 0.1% were 100% and 100%, respectively. With VAFs of 1.2% and 0.1% using 20 ng of input cfDNA, seven out of nine different mutations in six driver genes were identified in the Oncomine Lung cfDNA Assay. The two assays showed 100% concordance in 16 plasma samples clinically. Furthermore, various PIK3CA and/or TP53 mutations were identified only in the Oncomine Lung cfDNA Assay.

Conclusions: The Oncomine Lung cfDNA Assay can be used to identify plasma EGFR mutations in patients with lung cancer, although further large-scale studies are required to evaluate the analytical validity for other types of aberrations and genes using clinical samples.

Keywords: Oncomine Lung cfDNA Assay; analytical performance; cobas® EGFR Mutation Test v2; next-generation sequencing; plasma EGFR mutations.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell-Free Nucleic Acids* / genetics
ErbB Receptors / genetics
Humans
Lung / pathology
Lung Neoplasms* / diagnosis
Lung Neoplasms* / genetics
Lung Neoplasms* / pathology
Mutation
Neoplasm Recurrence, Local

Substances

Cell-Free Nucleic Acids
ErbB Receptors
EGFR protein, human

Grants and funding

This paper was supported by Fund of Biomedical Research Institute, Jeonbuk National University Hospital. This paper was supported by research funds for newly appointed professors of Jeonbuk National University in 2022.