Bile cell‑free DNA as a novel and powerful liquid biopsy for detecting somatic variants in biliary tract cancer

Shen,Ningjia; Zhang,Dadong; Yin,Lei; Qiu,Yinghe; Liu,Jian; Yu,Wenlong; Fu,Xiaohui; Zhu,Bin; Xu,Xiaoya; Duan,Anqi; Chen,Zishuo; Wang,Xiang; Cao,Xinkai; Zhao,Teng; Zhou,Zisong; Yu,Lianghe; Qin,Hao; Fang,Zheng; Li,Jing‑Yu; Liu,Yuanjin; Xiong,Lei; Yuan,Bo; Li,Fugen; Zhang,Yongjie

doi:10.3892/or.2019.7177

Bile cell‑free DNA as a novel and powerful liquid biopsy for detecting somatic variants in biliary tract cancer

Authors:
- Ningjia Shen
- Dadong Zhang
- Lei Yin
- Yinghe Qiu
- Jian Liu
- Wenlong Yu
- Xiaohui Fu
- Bin Zhu
- Xiaoya Xu
- Anqi Duan
- Zishuo Chen
- Xiang Wang
- Xinkai Cao
- Teng Zhao
- Zisong Zhou
- Lianghe Yu
- Hao Qin
- Zheng Fang
- Jing‑Yu Li
- Yuanjin Liu
- Lei Xiong
- Bo Yuan
- Fugen Li
- Yongjie Zhang
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Affiliations: Department of Biliary II, Shanghai Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China, Research and Development Institute of Precision Medicine, 3D Medicines, Inc., Pujiang Hi‑tech Park, Shanghai 201114, P.R. China
Published online on: May 31, 2019 https://doi.org/10.3892/or.2019.7177
Pages: 549-560
Copyright: © Shen et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Tissue sampling of biliary tract carcinomas (BTCs) for molecular characterization is challenging. The aim of this study was to investigate the possibility of identifying individual actionable mutations derived from bile cell‑free DNA (cfDNA) using targeted deep sequencing. Ten BTC patients, four with gallbladder carcinomas and six with cholangiocarcinomas, were enrolled in the present study. Using targeted deep sequencing with a panel of 150 tumor‑related genes, paired bile cfDNA and tumor DNA were analyzed for mutational variants individually and then compared. The present study, to the best of our knowledge, is the first to reveal that bile cfDNA is predominantly comprised of long DNA fragments, which is not the case for plasma cfDNA. Herein, paired bile cfDNA and tumors from ten BTC patients were examined using targeted deep sequencing. When comparing bile cfDNA and tumor DNA for single nucleotide variation (SNV)/insertion and deletion (Indel), the results using targeted deep sequencing revealed high sensitivity (94.7%) and specificity (99.9%). Additionally, the sensitivity of detecting a copy number variation (CNV) was 75.0%, with a specificity of 98.9%. When comparing two bile extraction methods, including percutaneous transhepatic cholangial drainage and operation, no significant difference in SNV/Indel or CNV detection sensitivity was noted. Moreover, when examining the tumor stage and incidence site, AJCC stage II and the distal bile duct both had significantly decreased CNV detection sensitivities. The present study revealed that targeted deep sequencing can reliably detect mutational variants within bile cfDNA obtained from BTC patients. These preliminary results may shed light on bile cfDNA as a promising liquid biopsy for BTC patients.

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