Background: Analysis of cell-free DNA (cfDNA) is promising for broad applications in clinical settings, but with significant bias towards late-stage cancers. Although recent studies have discussed the diverse and degraded nature of cfDNA molecules, little is known about its impact on the practice of cfDNA analysis.
Methods: We developed single-strand library preparation and hybrid-capture-based cfDNA sequencing (SLHCseq) to analysis degraded cfDNA fragments. Nextwe used SLHC-seq to performcfDNA profiling in 112 pancreatic cancer patients, and the results were compared with 13 previous reports. Extensive analysis was performed in terms of cfDNA fragments to explore the reasons for higher detection rate of KRAS mutations in the circulation of pancreatic cancers.
Findings: By applying the new approach, we achieved higher efficiency in analysis of mutations than previously reported using other detection assays. 791 cancer-specific mutations were detected in plasma of 88% patients with KRAS hotspots detected in 70% of all patients. Only 8mutationswere detected in 28 healthy controls without any known oncogenic or truncating alleles. cfDNA profiling by SLHC-seq was largely consistent with results of tissue-based sequencing. SLHC-seq rescued short or damaged cfDNA fragments along to increase the sensitivity and accuracy of circulating-tumour DNA detection.
Interpretation: We found that the small mutant fragments are prevalent in early-stage patients, which provides strong evidence for fragment size-based detection of pancreatic cancer. The new pipeline enhanced our understanding of cfDNA biology and provide new insights for liquid biopsy. (c) 2019 Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
[1]Fudan Univ, Dept Intervent Radiol, Zhongshan Hosp, Shanghai, Peoples R China;
[2]Shanghai Inst Med Imaging, Shanghai, Peoples R China;
[3]Chinese Acad Sci, Inst Neurosci, CAS Ctr Excellence Brain Sci & Intelligence Techn, State Kay Lab Neurosci, Shanghai, Peoples R China;
[4]Fudan Univ, Dept Pathol, Zhongshan Hosp, Shanghai, Peoples R China;
[5]Zhejiang Univ, Dept Hepatobiliary & Pancreat Surg, Sch Med, Affiliated Hosp 2, Hangzhou, Zhejiang, Peoples R China;
[6]Shanghai Univ Tradit Chinese Med, Dept Radiol, Shuguang Hosp, Shanghai, Peoples R China;
[7]Sichuan Univ, West China Hosp, Precis Med Ctr, Chengdu, Sichuan, Peoples R China;
[8]Qihan Bio Inc, Hangzhou, Zhejiang, Peoples R China;
[9]Stanford Genome Technol Ctr, Palo Alto, CA USA;
[10]Fudan Univ, Dept Radiol, Zhongshan Hosp, Shanghai, Peoples R China;
[11]Fudan Univ, Dept Pancreat Surg, Zhongshan Hosp, Shanghai, Peoples R China;
[12]Fudan Univ, Dept Gen Surg, Zhongshan Hosp, Shanghai, Peoples R China
(8.0+极速模式)