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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 
 LIVER INTERNATIONAL, Vol.42(10) : 2317-2326, 2022-10 
Journal Title
Issue Date
Biomarkers, Tumor / genetics ; Carcinoma, Hepatocellular* / diagnosis ; Carcinoma, Hepatocellular* / genetics ; Circulating Tumor DNA* / genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Liver Neoplasms* / diagnosis ; Liver Neoplasms* / genetics ; Mutation
circulating tumour DNA ; hepatocellular carcinoma ; liquid biopsy
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.
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1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
Park, Jun Yong(박준용) ORCID logo https://orcid.org/0000-0001-6324-2224
Lee, Seung-Tae(이승태) ORCID logo https://orcid.org/0000-0003-1047-1415
Lee, Hye Won(이혜원) ORCID logo https://orcid.org/0000-0002-3552-3560
Choi, Jong Rak(최종락) ORCID logo https://orcid.org/0000-0002-0608-2989
Han, Kwang-Hyub(한광협) ORCID logo https://orcid.org/0000-0003-3960-6539
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