Abstract
Purpose
Cell-free circulating tumor DNA (ctDNA) in plasma enables rapid and repeat testing of actionable mutations. Next-generation sequencing (NGS) is an attractive platform for multiplex sequencing capabilities compared to traditional methods such as PCR. The purpose of this study is to evaluate the value of the NGS-based ctDNA assay and to identify the genomic alteration profile of ctDNA in real-world Chinese non-small cell lung (NSCLC) patients.
Methods
In total, 294 Chinese patients with pathological diagnosis of Phase III-IV NSCLC were enrolled. 3–4 mL peripheral blood was collected and NGS-based analysis was carried out using a 20-gene panel. The analytical sensitivity and specificity of ctDNA NGS-based assay was validated using droplet digital PCR (ddPCR).
Results
We have tested 570 sites from 286 samples using ddPCR, which included 108 positive sites and 462 negative sites from NGS results, and the concordance rate was 99.8% (418/419) for single-nucleotide variants (SNVs) and 96.7% (146/151) for insertions and deletions (InDels). The most frequent genes were TP53 (32%), EGFR (31.97%), KRAS (6.46%), PIK3CA (4.76%), and MET (4.08%). Exon 19 deletion (19del) was the most common alteration in EGFR and G12C was the most common alteration in KRAS. Furthermore, the detection rate of TP53 was higher in the male and patients with squamous cell carcinoma. We also found the prevalence of TP53 in L858R was higher than in 19del (61.29% vs. 40%; p = 0.1115).
Conclusion
The results indicate that the results of NGS-based ctDNA assay are highly consistent with ddPCR. In Chinese NSCLC patients, TP53 mutation was more frequently associated with male and squamous cell carcinoma. The prevalence of concomitant mutations in L858R may be different from that in 19del.
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Data availability
The datasets generated and analyzed during the current study are available from the corresponding author on reasonable request.
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Acknowledgements
We thank all the patients who participated in this study, and colleagues who contributed to this work.
Funding
This work was supported by “Four Batches” of the Science And Technology Innovation Plan of Shanxi Provincial Health Commission (No. 2020TD07).
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WC, WB and XJ designed the study. YX, ZB, JG, ZZ and HZ are responsible for sample collection and experiments. SG, LQ, BX, WW, GS headed all computational and analytical aspects. SG wrote the manuscript, and all authors participated in proofreading. All authors contributed to editorial changes in the manuscript. All authors read and approved the final manuscript.
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This study was performed in line with the principles of the Declaration of Helsinki. Approval was granted by the Clinical Trial Ethics Committee for Drugs and Medical Devices of Shanxi Cancer Hospital.
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Xi, Y., Bai, Z., Gao, S. et al. Genomic profiling of NGS-based ctDNA from Chinese non-small cell lung cancer patients. J Cancer Res Clin Oncol 149, 8573–8580 (2023). https://doi.org/10.1007/s00432-023-04794-z
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DOI: https://doi.org/10.1007/s00432-023-04794-z