Application of an Ultrasensitive NGS-Based Blood Test for the Diagnosis of Early-Stage Lung Cancer: Sensitivity, a Hurdle Still Difficult to Overcome

Abstract

Diagnosis of lung cancer requires histological examination of a tissue sample, which in turn requires an invasive procedure that cannot always be obtained. Circulating tumor DNA can be reliably detected in blood samples of advanced-stage lung cancer patients and might also be a minimally invasive alternative for early-stage lung cancer detection. We wanted to explore the potential of targeted deep sequencing as a test for the diagnosis of early-stage lung cancer in combination with imaging. Mutation detection on cell-free DNA from pretreatment plasma samples of 51 patients with operable non-small cell lung cancer was performed and results were compared with 12 control patients undergoing surgery for a non-malignant lung lesion. By using a variant allele frequency threshold of 1%, somatic variants were detected in 23.5% of patients with a median variant allele fraction of 3.65%. By using this threshold, we could almost perfectly discriminate early-stage lung cancer patients from controls. Our study results are discussed in the light of those from other studies. Notwithstanding the potential of today’s techniques for the use of liquid biopsy-based cell-free DNA analysis, sensitivity of this application for early-stage lung cancer detection is currently limited by a biological background of somatic variants with low variant allele fraction.

Matched tissue and liquid biopsies for advanced non-small cell lung cancer patients A potentially indispensable complementary approach

“…One major challenge is certainly to be able to detect ctDNA in early-stage lung cancer, notably in stage I lung cancer, due to the low level of shedding of tumor cells into the blood stream. So, very sensitive methods of ctDNA detection need to be developed in the near future [72] . Some studies using CTCs in early-stage NSCLC gave controversial and discrepant results, emphazing the variability of the specificity and sensitivity of the methods used [73] .…”

A novel approach for the non-invasive diagnosis of pulmonary nodules using low-depth whole-genome sequencing of cell-free DNA

“…However, it is difficult to reliably detect mutated ctDNA in early-stage non-small cell lung cancer (NSCLC) due to the low abundance of ctDNA in cfDNA, which is estimated to be less than 0.01% in 50% of patients with stage I NSCLC (17,18). Mutationbased cfDNA tests, which included the whole-exome sequencing (WES) and targeted multiple gene sequencing (Panel-seq) in early-stage NSCLC require ultra-deep coverage that are costly and technically challenging due to sequencing artifacts, vast mutational heterogeneity between patients, and the frequent occurrence of non-malignant somatic mutations in cfDNA, e.g., those that drive clonal hematopoiesis (12,(19)(20)(21)(22). Therefore, new non-invasive approaches other than mutation-based cfDNA tests should be explored.…”