Theranostics 2019; 9(7):2056-2070. doi:10.7150/thno.28119

Research Paper

Non-invasive diagnosis of early-stage lung cancer using high-throughput targeted DNA methylation sequencing of circulating tumor DNA (ctDNA)

Wenhua Liang1*, Yue Zhao2*, Weizhe Huang1*, Yangbin Gao2, Weihong Xu2, Jinsheng Tao2, Meng Yang2, Lequn Li3, Wei Ping 3, Hui Shen4, Xiangning Fu3, Zhiwei Chen2, Peter W. Laird4, Xuyu Cai2✉, Jian-Bing Fan5,2✉, Jianxing He1✉

1. First Affiliated Hospital of Guangzhou Department of Thoracic Surgery/Oncology, the First Affiliated Hospital of Guangzhou Medical University; Guangzhou Institute of Respiratory Disease & Health; China State Key Laboratory and National Clinical Research Center for Respiratory Disease, Guangzhou, China;
2. AnchorDx Medical Co., Ltd., Guangzhou, China;
3. Tongji Hospital, Tongji Medical College Huazhong University of Science & Technology, Wuhan, China;
4. Van Andel Research Institute (VARI), Grand Rapids, MI, USA;
5. Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China.
*These authors contributed equally to the paper.

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions.
Citation:
Liang W, Zhao Y, Huang W, Gao Y, Xu W, Tao J, Yang M, Li L, Ping W, Shen H, Fu X, Chen Z, Laird PW, Cai X, Fan JB, He J. Non-invasive diagnosis of early-stage lung cancer using high-throughput targeted DNA methylation sequencing of circulating tumor DNA (ctDNA). Theranostics 2019; 9(7):2056-2070. doi:10.7150/thno.28119. Available from https://www.thno.org/v09p2056.htm

File import instruction

Abstract

Rational: LDCT screening can identify early-stage lung cancers yet introduces excessive false positives and it remains a great challenge to differentiate malignant tumors from benign solitary pulmonary nodules, which calls for better non-invasive diagnostic tools.

Methods: We performed DNA methylation profiling by high throughput DNA bisulfite sequencing in tissue samples (nodule size < 3 cm in diameter) to learn methylation patterns that differentiate cancerous tumors from benign lesions. Then we filtered out methylation patterns exhibiting high background in circulating tumor DNA (ctDNA) and built an assay for plasma sample classification.

Results: We first performed methylation profiling of 230 tissue samples to learn cancer-specific methylation patterns which achieved a sensitivity of 92.7% (88.3% - 97.1%) and a specificity of 92.8% (89.3% - 96.3%). These tissue-derived DNA methylation markers were further filtered using a training set of 66 plasma samples and 9 markers were selected to build a diagnostic prediction model. From an independent validation set of additional 66 plasma samples, this model obtained a sensitivity of 79.5% (63.5% - 90.7%) and a specificity of 85.2% (66.3% - 95.8%) for differentiating patients with malignant tumor (n = 39) from patients with benign lesions (n = 27). Additionally, when tested on gender and age matched asymptomatic normal individuals (n = 118), our model achieved a specificity of 93.2% (89.0% - 98.3%). Specifically, our assay is highly sensitive towards early‐stage lung cancer, with a sensitivity of 75.0% (55.0%-90.0%) in 20 stage Ia lung cancer patients and 85.7% (57.1%-100.0%) in 7 stage Ib lung cancer patients.

Conclusions: We have developed a novel sensitive blood based non‐invasive diagnostic assay for detecting early stage lung cancer as well as differentiating lung cancers from benign pulmonary nodules.

Keywords: Early-stage lung cancer, circulating tumor DNA, high-throughput targeted DNA methylation sequencing