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.
Simple Summary: Mitochondria are important organelles in the human body, and they act as a source of chemical energy for different cellular processes. Multiple copies of mitochondria are normally detected in cells, and their copy number has also been reported to be aberrated in cancers, including li...
| Publicado en: | Cancers Vol. 16; no. 17; pp. 3012 - 3024 |
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| Autores principales: | , , , , , , , |
| Formato: | research tables/charts Journal Article |
| Publicado: |
MDPI
Sep2024
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=179645585&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 179645585 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 20726694 B74B jtl: Cancers issn: 20726694 maglogo: N pubinfo: dt: Sep2024 vid: 16 iid: 17 pid: 97109 pub: MDPI artinfo: ui: 179645585 179645585 179645585 10.3390/cancers16173012 179645585 ppf: 3012 ppct: 12 formats: tig: atl: 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. aug: au: Lyu, Xue-Ying Tsui, Yu-Man Tam, Ivan Ka-Kit Li, Po-Man Cheung, Gary Cheuk-Hang Lee, Joyce Man-Fong Ng, Irene Oi-Lin Ho, Daniel Wai-Hung affil: State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, China sug: subj: Liver Neoplasms Pathology Liver Neoplasms Diagnosis Cell-Free Nucleic Acids Analysis DNA, Mitochondrial Analysis Genetic Variation Sequence Analysis Methods Human Funding Source Male Female Aged Middle Age Adult DNA Probes Cost Effectiveness Analysis Aged: 65+ years Middle Aged: 45-64 years Adult: 19-44 years Male Female ab: Simple Summary: Mitochondria are important organelles in the human body, and they act as a source of chemical energy for different cellular processes. Multiple copies of mitochondria are normally detected in cells, and their copy number has also been reported to be aberrated in cancers, including liver cancer. Target-panel sequencing is frequently used in oncology studies, but the optimal pooling ratio of nuclear and mitochondrial probes has remained elusive. Therefore, it is necessary to determine the physiological mitochondrial DNA copy number in non-liver cancer subjects, which can serve as a useful reference for deciding the desirable ratio of nuclear and mitochondrial probes for a less biased target enrichment of nuclear and mitochondrial genomes and hence their even representation. In addition, it can also be used as a physiological basis that can distinguish normal physiological variations from the pathological conditions in liver cancer. Mitochondria generate energy to support cells. They are important organelles that engage in key biological pathways. The dysfunction of mitochondria can be linked to hepatocarcinogenesis, which has been actively explored in recent years. To investigate the mitochondrial dysfunction caused by genetic variations, target-panel sequencing is a flexible and promising strategy. However, the copy number of mitochondria generally exceeds nuclear DNA, which raises a concern that uneven target enrichment of mitochondrial DNA (mtDNA) and nuclear DNA (ncDNA) in target-panel sequencing would lead to an undesirably biased representation of them. To resolve this issue, we evaluated the optimal pooling of mtDNA probes and ncDNA probes by a series of dilutions of mtDNA probes in both genomic DNA (gDNA) and cell-free DNA (cfDNA) samples. The evaluation was based on read count, average sequencing depth and coverage of targeted regions. We determined that an mtDNA:ncDNA probe ratio of around 1:10 would offer a good balance of sequencing performance and cost effectiveness. Moreover, we estimated the median physiological mtDNA:ncDNA copy ratio as 38.1 and 2.9 in cfDNA and gDNA samples of non-liver cancer subjects, respectively, whereas they were 20.0 and 2.1 in the liver cancer patients. Taken together, this study revealed the appropriate pooling strategy of mtDNA probes and ncDNA probes in target-panel sequencing and suggested the normal range of physiological variation of the mtDNA:ncDNA copy ratio in non-liver cancer individuals. This can serve as a useful reference for future target-panel sequencing investigations of the mitochondrial genome in liver cancer. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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