Resectable lung lesions malignancy assessment and cancer detection by ultra-deep sequencing of targeted gene mutations in plasma cell-free DNA

Muyun Peng, Yuancai Xie, Xiaohua Li, Youhui Qian, Xiaonian Tu, Xumei Yao, Fangsheng Cheng, Feiyue Xu, Deju Kong, Bing He, Chaoyu Liu, Fengjun Cao, Haoxian Yang, Fenglei Yu, Chuanbo Xu, Geng Tian, Muyun Peng, Yuancai Xie, Xiaohua Li, Youhui Qian, Xiaonian Tu, Xumei Yao, Fangsheng Cheng, Feiyue Xu, Deju Kong, Bing He, Chaoyu Liu, Fengjun Cao, Haoxian Yang, Fenglei Yu, Chuanbo Xu, Geng Tian

Abstract

Background: Early detection of lung cancer to allow curative treatment remains challenging. Cell-free circulating tumour (ct) DNA (ctDNA) analysis may aid in malignancy assessment and early cancer diagnosis of lung nodules found in screening imagery.

Methods: The multicentre clinical study enrolled 192 patients with operable occupying lung diseases. Plasma ctDNA, white cell count genomic DNA (gDNA) and tumour tissue gDNA of each patient were analysed by ultra-deep sequencing to an average of 35 000× of the coding regions of 65 lung cancer-related genes.

Results: The cohort consists of a quarter of benign lung diseases and three quarters of cancer patients with all histopathology subtypes. 64% of the cancer patients are at stage I. Gene mutations detection in tissue gDNA and plasma ctDNA results in a sensitivity of 91% and specificity of 88%. When ctDNA assay was used as the test, the sensitivity was 69% and specificity 96%. As for the lung cancer patients, the assay detected 63%, 83%, 94% and 100%, for stages I, II, III and IV, respectively. In a linear discriminant analysis, combination of ctDNA, patient age and a panel of serum biomarkers boosted the overall sensitivity to 80% at a specificity of 99%. 29 out of the 65 genes harboured mutations in the patients with lung cancer with the largest number found in TP53 (30% plasma and 62% tumour tissue samples) and EGFR (20% and 40%, respectively).

Conclusion: Plasma ctDNA was analysed in lung nodule assessment and early cancer detection, while an algorithm combining clinical information enhanced the test performance.

Trial registration number: NCT03081741.

Keywords: circulating tumor DNA; liquid biopsy; lung cancer detection; lung nodule malignancy; targeted gene NGS sequencing.

Conflict of interest statement

Competing interests: None declared.

© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.

Figures

Figure 1
Figure 1
Lung cancer gene mutation burden in benign and various stages of patients. Mutation types: C1: no mutation found; C2: one non-driver mutation found; C3: one driver mutation found; C4: both driver mutation and non-driver mutation found; C5: more than one non-driver mutation found.
Figure 2
Figure 2
Driver mutation distribution in patients with lung cancer patients. (A) Plasma ctDNA. (B) FFPE gDNA. ctDNA, circulating tumour DNA; gDNA, genomic DNA.
Figure 3
Figure 3
Lung cancer detection rate by ctDNA, serum biomarkers and LDA model per stage. Model=LDA model. ctDNA, circulating tumour DNA; LDA, linear discriminant analysis.

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