Circulating Tumor DNA Analysis for Liver Cancers and Its Usefulness as a Liquid Biopsy

Abstract

Background & AimsCirculating tumor DNA (ctDNA) carrying tumor-specific sequence alterations has been found in the cell-free fraction of blood. Liver cancer tumor specimens are difficult to obtain, and noninvasive methods are required to assess cancer progression and characterize underlying genomic features.MethodsWe analyzed 46 patients with hepatocellular carcinoma who underwent hepatectomy or liver transplantation and for whom whole-genome sequencing data was available. We designed personalized assays targeting somatic rearrangements of each tumor to quantify serum ctDNA. Exome sequencing was performed using cell-free DNA paired primary tumor tissue DNA from a patient with recurrent liver cancer after transcatheter arterial chemoembolization (TACE).ResultsWe successfully detected ctDNA from 100 μL of serum samples in 7 of the 46 patients before surgery, increasing with disease progression. The cumulative incidence of recurrence and extrahepatic metastasis in the ctDNA-positive group were statistically significantly worse than in the ctDNA-negative group (P = .0102 and .0386, respectively). Multivariate analysis identified ctDNA (OR 6.10; 95% CI, 1.11–33.33, P = .038) as an independent predictor of microscopic vascular invasion of the portal vein (VP). We identified 45 nonsynonymous somatic mutations in cell-free DNA after TACE and 71 nonsynonymous somatic mutations in primary tumor tissue by exome sequencing. We identified 25 common mutations in both samples, and 83% of mutations identified in the primary tumor could be detected in the cell-free DNA.ConclusionsThe presence of ctDNA reflects tumor progression, and detection of ctDNA can predict VP and recurrence, especially extrahepatic metastasis within 2 years. Our study demonstrated the usefulness of ctDNA detection and sequencing analysis of cell-free DNA for personalized treatment of liver cancer.

Circulating tumor DNA profiling reveals clonal evolution and real‐time disease progression in advanced hepatocellular carcinoma

“…Although peritumor is defined as cytological normal‐appearing cells from which tumor may arise, it already contains multiple genetic changes during early tumorigenesis comparing with PBMCs, while still lacks of mutations crucial for malignant transformation. At present, a number of researchers used PBMCs as control for tumor somatic mutation screening in HCC because of its germline character . However, our results suggest screening of somatic ctDNA alteration based on peritumor tissue rather than PBMCs would provide information of “real” somatic mutations to reflect majority of tumor lesions because of their origination during malignant transformation.…”

“…At present, a number of researchers used PBMCs as control for tumor somatic mutation screening in HCC because of its germline character. 12,13 However, our results suggest screening of somatic ctDNA alteration based on peritumor tissue rather than PBMCs would provide information of "real" somatic mutations to reflect majority of tumor lesions because of their origination during malignant transformation. These mutations are related to tumor development in HCC and thus have higher clinical potential for monitoring tumor burden.…”

“…As tumor burden and progression are accompanied with generation and accumulation of somatic mutations, the mutation spectrum in ctDNA should be of great importance for providing information of tumor burden and metastasis status . However, whether profiling of tumor mutations in ctDNA could reflect tumor burden during HCC progression still need further investigation.…”

“…As tumor burden and progression are accompanied with generation and accumulation of somatic mutations, the mutation spectrum in ctDNA should be of great importance for providing information of tumor burden and metastasis status. 12,13 However, whether profiling of tumor mutations in ctDNA could reflect tumor burden during HCC progression still need further investigation. Here we present extensive analysis of mutation profiles from 4 HCC patients to investigate the dynamics of cancer driven genomic mutations in serial plasma samples for evaluating ctDNA's clinical value.…”

Circulating nucleic acids: An analysis of their occurrence in malignancies

“…The presence of these circulating viral DNAs is observed in cases of healthy individuals, and in cases of malignancies associated with viral infection, such as nasopharyngeal carcinoma (11), cervical carcinoma (12) and hepatocellular carcinoma (29).…”