PMID- 35600407
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220716
IS  - 2234-943X (Print)
IS  - 2234-943X (Electronic)
IS  - 2234-943X (Linking)
VI  - 12
DP  - 2022
TI  - Comprehensive Evaluation and Application of a Novel Method to Isolate Cell-Free 
      DNA Derived From Bile of Biliary Tract Cancer Patients.
PG  - 891917
LID - 10.3389/fonc.2022.891917 [doi]
LID - 891917
AB  - 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, as bile directly contacts tumors in the 
      biliary tract system. However, there is no commercial kit or widely acknowledged 
      method for bile cfDNA extraction. In this study, we established a 
      silica-membrane-based method, namely 3D-BCF, for bile cfDNA isolation, exhibiting 
      effective recovery of DNA fragments in the spike-in assay. We then compared the 
      3D-BCF method with four other commercial kits: the BIOG cfDNA Easy Kit (BIOG), 
      QIAamp DNA Mini Kit (Qiagen), MagMAX(TM) Cell-Free DNA Isolation Kit (Thermo 
      Fisher), and NORGEN Urine Cell-Free Circulating DNA Purification Mini Kit (Norgen 
      Biotek). The proposed 3D-BCF method exhibited the highest cfDNA isolation 
      efficiency (p < 0.0001) from patient bile samples, and bile cfDNA of short, 
      medium or long fragments could all be extracted effectively. To test whether the 
      extracted bile cfDNA from patients carries tumor-related genomic information, we 
      performed next-generation sequencing on the cfDNA and verified the gene-mutation 
      results by polymerase chain reaction (PCR)-Sanger chromatograms and 
      copy-number-variation (CNV) detection by fluorescence in situ hybridization 
      (FISH) of tumor tissues. The 3D-BCF method could efficiently extract cfDNA from 
      bile samples, providing technical support for bile cfDNA as a promising liquid 
      biopsy for BTC patient diagnosis and prognosis.
CI  - Copyright (c) 2022 Shen, Zhu, Zhang, Nian, Xu, Yu, Ruan, Chen, Liu, Cao, Shi, Li, 
      Huang, Wang, Chen, Xiong, Zhang, Fu and Zhang.
FAU - Shen, Ningjia
AU  - Shen N
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Zhu, Bin
AU  - Zhu B
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Zhang, Wei
AU  - Zhang W
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Nian, Baoning
AU  - Nian B
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Xu, Xiaoya
AU  - Xu X
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Yu, Lianghe
AU  - Yu L
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Ruan, Xiang
AU  - Ruan X
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Chen, Sheng
AU  - Chen S
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Liu, Yang
AU  - Liu Y
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Cao, Xinkai
AU  - Cao X
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Shi, Xintong
AU  - Shi X
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Li, Zhikuan
AU  - Li Z
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Huang, Xingfeng
AU  - Huang X
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Wang, Xiang
AU  - Wang X
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Chen, Caifu
AU  - Chen C
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Xiong, Lei
AU  - Xiong L
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Zhang, Dadong
AU  - Zhang D
AD  - 3D Medicines Inc., Shanghai, China.
FAU - Fu, Xiaohui
AU  - Fu X
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
FAU - Zhang, Yongjie
AU  - Zhang Y
AD  - Department of Biliary Surgery, Shanghai Eastern Hepatobiliary Surgery Hospital, 
      Second Military Medical University/Navy Medical University, Shanghai, China.
LA  - eng
PT  - Journal Article
DEP - 20220504
PL  - Switzerland
TA  - Front Oncol
JT  - Frontiers in oncology
JID - 101568867
PMC - PMC9116272
OTO - NOTNLM
OT  - bile
OT  - cell-free DNA
OT  - extraction
OT  - liquid biopsy
OT  - yield
COIS- Authors WZ, BN, XX, SC, XC, ZL, CC, LX, and DZ are/were employed by 3D Medicines 
      Inc. The remaining authors declare that the research was conducted in the absence 
      of any commercial or financial relationships that could be construed as a 
      potential conflict of interest.
EDAT- 2022/05/24 06:00
MHDA- 2022/05/24 06:01
PMCR- 2022/01/01
CRDT- 2022/05/23 03:53
PHST- 2022/03/08 00:00 [received]
PHST- 2022/03/29 00:00 [accepted]
PHST- 2022/05/23 03:53 [entrez]
PHST- 2022/05/24 06:00 [pubmed]
PHST- 2022/05/24 06:01 [medline]
PHST- 2022/01/01 00:00 [pmc-release]
AID - 10.3389/fonc.2022.891917 [doi]
PST - epublish
SO  - Front Oncol. 2022 May 4;12:891917. doi: 10.3389/fonc.2022.891917. eCollection 
      2022.