Resolution of Optimal Mitochondrial and Nuclear DNA Enrichment in Target-Panel Sequencing and Physiological Mitochondrial DNA Copy Number Estimation in Liver Cancer and Non-Liver Cancer Subjects
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Method
2.1. Sample Collection, DNA Extraction, Library Construction
2.2. Next-Generation Sequencing and Data Preprocessing
2.3. Data Processing and Sequencing Quality Estimation
3. Results
3.1. Sequencing Read Count under Different Dilutions of mtDNA Probes
3.2. Average Sequencing Depth under Different Dilutions of mtDNA Probes
3.3. Coverage of Targeted Regions under Different Dilutions of mtDNA Probes
3.4. Normal Physiological Range of Variation in mtDNA:ncDNA Copy Ratio
3.5. Physiological Range of Variation in mtDNA:ncDNA Copy Ratio in HCC Patients
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Lyu, X.-Y.; Tsui, Y.-M.; Tam, I.K.-K.; Li, P.-M.; Cheung, G.C.-H.; Lee, J.M.-F.; Ng, I.O.-L.; Ho, D.W.-H. Resolution of Optimal Mitochondrial and Nuclear DNA Enrichment in Target-Panel Sequencing and Physiological Mitochondrial DNA Copy Number Estimation in Liver Cancer and Non-Liver Cancer Subjects. Cancers 2024, 16, 3012. https://doi.org/10.3390/cancers16173012
Lyu X-Y, Tsui Y-M, Tam IK-K, Li P-M, Cheung GC-H, Lee JM-F, Ng IO-L, Ho DW-H. Resolution of Optimal Mitochondrial and Nuclear DNA Enrichment in Target-Panel Sequencing and Physiological Mitochondrial DNA Copy Number Estimation in Liver Cancer and Non-Liver Cancer Subjects. Cancers. 2024; 16(17):3012. https://doi.org/10.3390/cancers16173012
Chicago/Turabian StyleLyu, Xue-Ying, Yu-Man Tsui, Ivan Ka-Kit Tam, Po-Man Li, Gary Cheuk-Hang Cheung, Joyce Man-Fong Lee, Irene Oi-Lin Ng, and Daniel Wai-Hung Ho. 2024. "Resolution of Optimal Mitochondrial and Nuclear DNA Enrichment in Target-Panel Sequencing and Physiological Mitochondrial DNA Copy Number Estimation in Liver Cancer and Non-Liver Cancer Subjects" Cancers 16, no. 17: 3012. https://doi.org/10.3390/cancers16173012