Non-invasive detection of biliary tract cancer by low-coverage whole genome sequencing from plasma cell-free DNA: A prospective cohort study

Xiang Wang; Xiao-Hui Fu; Zi-Liang Qian; Teng Zhao; An-Qi Duan; Xiang Ruan; Bin Zhu; Lei Yin; Yong-Jie Zhang; Wen-Long Yu

doi:10.1016/j.tranon.2020.100908

Non-invasive detection of biliary tract cancer by low-coverage whole genome sequencing from plasma cell-free DNA: A prospective cohort study

Transl Oncol. 2020 Oct 12;14(1):100908. doi: 10.1016/j.tranon.2020.100908. eCollection 2021 Jan.

Authors

Xiang Wang¹, Xiao-Hui Fu¹, Zi-Liang Qian², Teng Zhao¹, An-Qi Duan¹, Xiang Ruan¹, Bin Zhu¹, Lei Yin¹, Yong-Jie Zhang³, Wen-Long Yu⁴

Affiliations

¹ Department of Biliary Tract Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Second Military Medical University/Navy Medical University, Shanghai 200438, China.
² Suzhou Hongyuan Biotech Inc, Biobay, Suzhou 215123, China; Prophet Genomics Inc, San Jose, CA 95131, United States.
³ Department of Biliary Tract Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Second Military Medical University/Navy Medical University, Shanghai 200438, China. Electronic address: yongjie_zh@outlook.com.
⁴ Department of Biliary Tract Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, Second Military Medical University/Navy Medical University, Shanghai 200438, China. Electronic address: Yu_wenlong@sina.com.

Abstract

Background: The diagnosis of biliary tract cancer (BTC) is challenging in clinical practice. We performed a prospective study to evaluate the value of plasma copy number variation (CNV) assays in diagnosing BTC.

Methods: 47 treatment-naïve patients with suspicious biliary lesions were recruited. Plasma samples were collected at admission. Cell-free DNA was analyzed by low coverage whole genome sequencing, followed by CNV analyses via a customized bioinformatics workflow, namely the ultrasensitive chromosomal aneuploidy detector.

Results: 29 patients were pathologically diagnosed as BTC, including 8 gallbladder cancers (GBCs) and 21 cholangiocarcinomas (CCs). Cancer patients had more CNV signals as compared with benign patients (26/29 vs. 2/18, P < 0.001). The most frequent copy number gains were chr3q (7/29) and chr8q (6/29). The most frequent copy number losses were chr7p (6/29), chr17p (6/29), and chr19p (6/29). The sensitivity and specificity of plasma CNV assays in diagnosing BTC were 89.7% and 88.9%, respectively. For CA 19-9 (cutoff: 37 U/ml), the sensitivity was 58.6% and the specificity was 72.2%. The diagnostic accuracy of CNV assays significantly outperformed CA 19-9 (AUC 0.91 vs. 0.62, P = 0.004). Compared with CA 19-9 alone, the adding of CNV profiles to CA 19-9 increased the sensitivity in diagnosing GBC (75.0% vs. 25.0%) and CC (100% vs. 52.4%). Higher CNV burden was also associated with decreased overall survival (Hazard ratio = 4.32, 95% CI 2.06-9.08, P = 0.033).

Discussion: Our results suggest that BTC harbors rich plasma CNV signals, and their assays might be useful for diagnosing BTC.

Keywords: BTC, biliary tract cancer; Biliary tract cancer; CC, cholangiocarcinoma; CEA, carcinoembryonic antigen; CIN, chromosomal instability; CNV, copy number variation; Cell-free DNA; Copy number variation; Diagnosis; GBC, gallbladder cancer; LCWG, low-coverage whole genome; Low-coverage whole genome; WGS, whole genome sequencing; cfDNA, cell-free DNA.