Applications of molecular barcode sequencing for the detection of low-frequency variants in circulating tumour DNA from hepatocellular carcinoma

Hye Won Lee, Esl Kim, Kyung Joo Cho, Hye Jung Park, Jieun Seo, Hyeonah Lee, Eunha Baek, Jong Rak Choi, Kwang Hyub Han, Seung Tae Lee, Jun Yong Park

Research output: Contribution to journalArticlepeer-review

Abstract

Purpose: Liquid biopsy has emerged as a promising tool for minimally invasive and accurate detection of various malignancies. We aimed to apply molecular barcode sequencing to circulating tumour DNA (ctDNA) from liquid biopsies of hepatocellular carcinoma (HCC). Study Design: Patients with HCC or benign liver disease were enrolled between 2017 and 2018. Matched tissue and serum samples were obtained from these patients. Plasma cell-free DNA was extracted and subjected to targeted sequencing with ultra-high coverage and molecular barcoding. Results: The study included 143 patients: 102 with HCC, 7 with benign liver tumours and 34 with chronic liver disease. No tier 1/2 or oncogenic mutations were detected in patients with benign liver disease. Among the HCC patients, 49 (48%) had tier 1/2 mutations in at least one gene; detection rates were higher in advanced stages (75%) than in early stages (26%–33%). TERT was the most frequently mutated gene (30%), followed by TP53 (16%), CTNNB1 (14%), ARID2 (5%), ARID1A (4%), NFE2L2 (4%), AXIN1 (3%) and KRAS (1%). Survival among patients with TP53 mutations was significantly worse (p = 0.007) than among patients without these mutations, whereas CTNNB1 and TERT mutations did not affect survival. ctDNA testing combined with α-fetoprotein and prothrombin induced by vitamin K absence-II analyses improved HCC detection, even in early stages. Conclusions: ctDNA detection using molecular barcoding technology offers dynamic and personalized information concerning tumour biology, such information can guide clinical diagnosis and management. This detection also has the potential as a minimally invasive approach for prognostic stratification and post-therapeutic monitoring.

Original languageEnglish
Pages (from-to)2317-2326
Number of pages10
JournalLiver International
Volume42
Issue number10
DOIs
Publication statusAccepted/In press - 2022

Bibliographical note

Funding Information:
This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (NRF‐2018R1A2B2005901) and by the Research Scholars Program in liver disease by the Gilead Sciences. This study was also supported by a faculty research grant of Yonsei University College of Medicine (6‐2015‐082).

Funding Information:
This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (NRF-2018R1A2B2005901) and by the Research Scholars Program in liver disease by the Gilead Sciences. This study was also supported by a faculty research grant of Yonsei University College of Medicine (6-2015-082).

Publisher Copyright:
© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

All Science Journal Classification (ASJC) codes

  • Hepatology

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