Comprehensive Evaluation and Application of a Novel Method to Isolate Cell-Free DNA Derived From Bile of Biliary Tract Cancer Patients

• DOI: 10.3389/fonc.2022.891917
• Publication Date: 2022-05-04T14:06:52Z
• Authors: Ningjia Shen; Bin Zhu; Wei Zhang; Baoning Nian; Xiaoya Xu; Lianghe Yu; Xiang Ruan; Sheng Chen; Yang Liu; Xinkai Cao; Xintong Shi; Zhikuan Li; Xingfeng Huang; Xiang Wang; Caifu Chen; Lei Xiong; Dadong Zhang; Xiaohui Fu; Yongjie Zhang
• Keywords: Cell-free fetal DNA; Liquid biopsy; genomic DNA; Sanger sequencing

Cell-free DNA (cfDNA) exists in various types of bodily fluids, including plasma, urine, bile, and others. Bile cfDNA could serve as a promising liquid biopsy for biliary tract cancer (BTC) patients, bile directly contacts tumors the system. However, there is no commercial kit or widely acknowledged method extraction. In this study, we established silica-membrane-based method, namely 3D-BCF, isolation, exhibiting effective recovery fragments spike-in assay. We then compared 3D-BCF with four other kits: BIOG Easy Kit (BIOG), QIAamp Mini (Qiagen), MagMAX TM Cell-Free Isolation (Thermo Fisher), NORGEN Urine Circulating Purification (Norgen Biotek). The proposed exhibited highest isolation efficiency (p < 0.0001) from patient samples, short, medium long all be extracted effectively. To test whether patients carries tumor-related genomic information, performed next-generation sequencing on verified gene-mutation results by polymerase chain reaction (PCR)-Sanger chromatograms copy-number-variation (CNV) detection fluorescence situ hybridization (FISH) tumor tissues. efficiently extract providing technical support BTC diagnosis prognosis.