Noninvasive detection of tumor-associated mutations from circulating cell-free DNA in hepatocellular carcinoma patients by targeted deep sequencing

Oncotarget. 2016 Jun 28;7(26):40481-40490. doi: 10.18632/oncotarget.9629.


Background: Detection of circulating cell-free DNA (cfDNA) has potential clinical value for assessing tumor biology in patients with hepatocellular carcinoma (HCC), yet many traditional assays lack robustness. This study was the first to apply a high-throughput sequencing platform to detect tumor-associated mutations in HCC from circulating tumor-derived DNA (ctDNA) and to evaluate the utility and feasibility of this approach.

Methods: Using the MiSeq™ system, plasma and matched tumor DNA samples were analyzed for hotspot mutations in the TERT, CTNNB1, and TP53 genes that had been verified as the most prevalent mutations in HCC. We compared tumor and plasma data and prospectively investigated the association between significant mutations detected in ctDNA and the patients' clinical outcomes.

Results: In 41 patients, we detected tumor-associated mutations for HCC in 8 (19.5%) plasma samples. Among them, one showed a tumor-associated mutation in ctDNA but not in the tumor tissue which we used to detect. We also found that ctDNA with mutations could be detected more easily in patients who suffered vascular invasion (P=0.041) and predicted a shorter recurrence-free survival time (P<0.001). There was no relationship between detectable mutations and concentration of cfDNA (P=0.818).

Conclusions: The results of our study suggest that tumor-associated mutations detected in plasma are associated with vascular invasion and might be used to predict a shorter recurrence-free survival time for HCC patients. This kind of biomarker can overcome the limitations of tumor heterogeneity. Moreover, the diagnostic performance is improved if multiple mutations in different genes are combined.

Keywords: MiSeq sequencing; circulating cell-free DNA; circulating tumor DNA; hepatocellular carcinoma; tumor-associated mutation.

MeSH terms

  • Aged
  • Biomarkers, Tumor / genetics
  • Carcinoma, Hepatocellular / genetics*
  • Cell-Free Nucleic Acids / blood
  • Cell-Free Nucleic Acids / genetics*
  • DNA Mutational Analysis
  • DNA, Neoplasm / genetics
  • Disease-Free Survival
  • Female
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Liver Neoplasms / genetics*
  • Male
  • Middle Aged
  • Mutation*
  • Neoplasm Recurrence, Local
  • Telomerase / genetics
  • Tumor Suppressor Protein p53 / genetics
  • beta Catenin / genetics


  • Biomarkers, Tumor
  • CTNNB1 protein, human
  • Cell-Free Nucleic Acids
  • DNA, Neoplasm
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • beta Catenin
  • TERT protein, human
  • Telomerase