A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma

Oncogene. 2018 Jul;37(27):3740-3752. doi: 10.1038/s41388-018-0206-3. Epub 2018 Apr 9.


Cellular components of solid tumors including DNA are released into the bloodstream, but data on circulating-free DNA (cfDNA) in hepatocellular carcinoma (HCC) are still scarce. This study aimed at analyzing mutations in cfDNA and their correlation with tissue mutations in patients with HCC. We included 8 HCC patients treated with surgical resection for whom we collected paired tissue and plasma/serum samples. We analyzed 45 specimens, including multiregional tumor tissue sampling (n = 24), peripheral blood mononuclear cells (PMBC, n = 8), plasma (n = 8) and serum (n = 5). Ultra-deep sequencing (5500× coverage) of all exons was performed in a targeted panel of 58 genes, including frequent HCC driver genes and druggable mutations. Mutations detected in plasma included known HCC oncogenes and tumor suppressors (e.g., TERT promoter, TP53, and NTRK3) as well as a candidate druggable mutation (JAK1). This approach increased the detection rates previously reported for mutations in plasma of HCC patients. A thorough characterization of cis mutations found in plasma confirmed their tumoral origin, which provides definitive evidence of the release of HCC-derived DNA fragments into the bloodstream. This study demonstrates that ultra-deep sequencing of cfDNA is feasible and can confidently detect somatic mutations found in tissue; these data reinforce the role of plasma DNA as a promising minimally invasive tool to interrogate HCC genetics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adult
  • Aged
  • Carcinoma, Hepatocellular / genetics*
  • Carcinoma, Hepatocellular / pathology
  • Circulating Tumor DNA / blood*
  • Circulating Tumor DNA / genetics*
  • DNA Mutational Analysis / methods*
  • Discoidin Domain Receptor 2 / genetics
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Janus Kinase 1 / genetics
  • Liver Neoplasms / genetics*
  • Liver Neoplasms / pathology
  • Male
  • Middle Aged
  • Mutation / genetics
  • Pilot Projects
  • Telomerase / genetics
  • Tumor Suppressor Protein p53 / genetics


  • Circulating Tumor DNA
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • DDR2 protein, human
  • Discoidin Domain Receptor 2
  • JAK1 protein, human
  • Janus Kinase 1
  • TERT protein, human
  • Telomerase