Cell-Free DNA Analysis by Whole-Exome Sequencing for Hepatocellular Carcinoma: A Pilot Study in Thailand
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Patient Characteristics and cfDNA Quantification
2.2. Somatic Mutation Profiling of cfDNA Using Whole-Exome Sequencing
2.3. Comparison of Top Frequently Mutated Genes across Studies, and Clinical Application
2.4. Copy Number Variants (CNVs) and Oxford Nanopore Application (Pilot Study)
3. Discussion
4. Materials and Methods
4.1. Patients and Study Overview
4.2. Sample Collection and DNA Extraction
4.3. Library Preparation and Whole-Exome Sequencing (WES)
4.4. WES Data Analysis
4.5. Library Preparation and Sequencing on an ONT Platform
4.6. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Baseline Characteristics | HCC (n = 30) * |
---|---|
Sex (male, %) | 25 (83.33) |
Age, years | 64.93 (51–86) |
Laboratory data | |
Aspartate aminotransferase, IU/L | 67.93 (11.0–151.0) |
Alanine aminotransferase, IU/L | 57.5 (11.0–152.0) |
Serum albumin, g/dL | 3.5 (2.2–4.4) |
Total bilirubin, mg/dL | 1.2 (0.3–2.2) |
Platelet, 109/L | 190.6 (28.0–685.0) |
Alpha-fetoprotein, IU/mL | 8102.9 (0.9–179,249.0) |
Liver disease status | |
HBV infection | 10 (33.33) |
HCV infection | 7 (23.33%) |
HBV and HCV infection | 1 (3.33%) |
Non-viral infection | 12 (40.00%) |
Cirrhosis | 19 (63.33%) |
BCLC stage | |
A | 9 |
B | 12 |
C | 9 |
Tumor number | |
Single | 19 |
Multiple | 11 |
Tumor size, cm | |
<5 | 14 |
≥5 | 16 |
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Kunadirek, P.; Chuaypen, N.; Jenjaroenpun, P.; Wongsurawat, T.; Pinjaroen, N.; Sirichindakul, P.; Nookaew, I.; Tangkijvanich, P. Cell-Free DNA Analysis by Whole-Exome Sequencing for Hepatocellular Carcinoma: A Pilot Study in Thailand. Cancers 2021, 13, 2229. https://doi.org/10.3390/cancers13092229
Kunadirek P, Chuaypen N, Jenjaroenpun P, Wongsurawat T, Pinjaroen N, Sirichindakul P, Nookaew I, Tangkijvanich P. Cell-Free DNA Analysis by Whole-Exome Sequencing for Hepatocellular Carcinoma: A Pilot Study in Thailand. Cancers. 2021; 13(9):2229. https://doi.org/10.3390/cancers13092229
Chicago/Turabian StyleKunadirek, Pattapon, Natthaya Chuaypen, Piroon Jenjaroenpun, Thidathip Wongsurawat, Nutcha Pinjaroen, Pongserath Sirichindakul, Intawat Nookaew, and Pisit Tangkijvanich. 2021. "Cell-Free DNA Analysis by Whole-Exome Sequencing for Hepatocellular Carcinoma: A Pilot Study in Thailand" Cancers 13, no. 9: 2229. https://doi.org/10.3390/cancers13092229