Targeted Next-Generation Sequencing of Plasma Cell-Free DNA in Korean Patients with Hepatocellular Carcinoma

Abstract

Background Hepatocellular carcinoma (HCC) is the second-most-common cause of cancer-related deaths worldwide, and an accurate and non-invasive biomarker for the early detection and monitoring of HCC is required. We assessed pathogenic variants of HCC driver genes in cell-free DNA (cfDNA) from HCC patients who had not undergone systemic therapy. Methods Plasma cfDNA was collected from 20 HCC patients, and deep sequencing was performed using a customized cfDNA next-generation sequencing panel, targeting the major HCC driver genes ( TP53 , CTNNB1 , TERT ) that incorporates molecular barcoding. Results In 13/20 (65%) patients, we identified at least one pathogenic variant of two major HCC driver genes ( TP53 and CTNNB1 ), including 16 variants of TP53 and nine variants of CTNNB1 . The TP53 and CTNNB1 variants showed low allele frequencies, with median values of 0.17% (range 0.06%–6.99%) and 0.07% (range 0.05%–0.96%), respectively. However, the molecular coverage of variants was sufficient, with median values of 5,543 (range 2,317–9,088) and 7,568 (range 2,400–9,633) for TP53 and CTNNB1 variants, respectively. Conclusions Our targeted DNA sequencing successfully identified low-frequency pathogenic variants in the cfDNA from HCC patients by achieving high coverage of unique molecular families. Our results support the utility of cfDNA analysis to identify somatic gene variants in HCC patients.

Tert C228t Mutation in Circulating Tumor Dna as a Clinical Marker in Hepatocellular Carcinoma Patients Attending a Tertiary Hospital in Egypt: A Case-Control Study

“…Therefore, the absence of C228T mutation in our study could also be attributed to the lower number of EHCC cases included in our study where only 12 patients had EHCC. Our results are in accordance with the results previously reported by Chae et al (2021) who investigated the presence of mutations in ctDNA derived from HCC patients. The authors used next-generation sequencing to target TERT, TP53, and CTNNB1 genes in Korean HCC patients who had not undergone systemic therapy.…”

“…None of the twenty patients included in the study had the C228T mutation or any other SNP in the TERT gene. The authors attributed the lack of TERT promoter mutations to the fact that they mainly investigated AHCC not EHCC cases (24) . Our results do not conform with the results of Jiao et al, 2018 where this study used sanger sequencing to detect TERT promoter mutations in ctDNA of HCC patients and found that overall prevalence of TERT promoter mutations, either C228T or C250T, was 47.7% in HCC patients.…”

Blood-based biomarkers for immune-based therapy in advanced HCC: Promising but a long way to go

“…Subsequent to tumor cell apoptosis and necrosis, ctDNA can be found in the blood stream of cancer patients ( 80 ) and provides an effective cancer ‘fingerprint’ as it has the tumor’s molecular characteristics. ctDNA can be differentiated from normal circulating DNA using various markers, including mutation signatures ( 80 , 81 ) and epigenetic alterations ( 82 ). The variation in the concentration of ctDNA in the blood provides a quantitative measure, whereas assessment of gene mutations, changes in DNA copy number, and methylation profiles provide a qualitative assessment of the disease condition.…”

“…The results highlight the value of incorporating ctDNA analysis for the diagnosis and prognosis of patients with HCC. Our recent study using targeted NGS technique identified at least one pathogenic variant of two major HCC driver genes (TP53 and CTNNB1), including 16 variants of TP53 and nine variants of CTNNB1 in 65% HCC patients (13/20) ( 81 ).…”

Clinical Practice Guidelines for Pre-Analytical Procedures of Plasma Epidermal Growth Factor Receptor Variant Testing

“…For many NSCLC patients, tumor tissue samples are not available for EGFR variant testing. Liquid biopsy using tumor-derived cell-free DNA (cfDNA) in patient blood is increasingly used for the molecular characterization of tumors [ 2 ]. Plasma EGFR variant testing for circulating tumor DNA (ctDNA) has been performed in Korea since 2017 to select patients in whom EGFR-TKIs may be effective [ 3 ].…”