The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma
Background The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequen...
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PeerJ Inc.
2022-05-01
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| Online Access: | https://peerj.com/articles/13473.pdf |
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| author | Yubo Ding Jingwei Yao Meiling Wen Xiong Liu Jialu Huang Minghui Zhang Yu Zhang Yufan Lv Zhuoyi Xie JianHong Zuo |
| author_facet | Yubo Ding Jingwei Yao Meiling Wen Xiong Liu Jialu Huang Minghui Zhang Yu Zhang Yufan Lv Zhuoyi Xie JianHong Zuo |
| author_sort | Yubo Ding |
| collection | DOAJ |
| description | Background The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing. Methods We used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein–protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan–Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer. Results Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further analysis, four genes significantly related to the prognosis of liver cancer were identified. Conclusion In this study, our findings indicate that ctDNA can be used for sequencing. Our results provide some molecular data for the mapping of genetic variation in Chinese patients with liver cancer, which enriches the understanding of HCC pathogenesis and provides new ideas for the diagnosis and prognosis of HCC patients. |
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| language | English |
| last_indexed | 2024-03-09T06:41:00Z |
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| spelling | doaj.art-2584ae5e7a4b46a899a40d6e5915e1d22023-12-03T10:50:10ZengPeerJ Inc.PeerJ2167-83592022-05-0110e1347310.7717/peerj.13473The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinomaYubo Ding0Jingwei Yao1Meiling Wen2Xiong Liu3Jialu Huang4Minghui Zhang5Yu Zhang6Yufan Lv7Zhuoyi Xie8JianHong Zuo9The Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, ChinaThe Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, ChinaThe First Affiliated Hospital, University of South China, Hengyang, ChinaDepartment of Otolaryngology-Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, ChinaUniversity of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, ChinaUniversity of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, ChinaUniversity of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, ChinaThe Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, ChinaUniversity of South China, Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, Hengyang, Hunan, ChinaThe Affiliated Nanhua Hospital of University of South China, Hengyang, Hunan, ChinaBackground The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing. Methods We used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein–protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan–Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer. Results Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further analysis, four genes significantly related to the prognosis of liver cancer were identified. Conclusion In this study, our findings indicate that ctDNA can be used for sequencing. Our results provide some molecular data for the mapping of genetic variation in Chinese patients with liver cancer, which enriches the understanding of HCC pathogenesis and provides new ideas for the diagnosis and prognosis of HCC patients.https://peerj.com/articles/13473.pdfLiver cancerNext-generation sequencingGene mutationPathway analysisCirculating tumor DNA |
| spellingShingle | Yubo Ding Jingwei Yao Meiling Wen Xiong Liu Jialu Huang Minghui Zhang Yu Zhang Yufan Lv Zhuoyi Xie JianHong Zuo The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma PeerJ Liver cancer Next-generation sequencing Gene mutation Pathway analysis Circulating tumor DNA |
| title | The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma |
| title_full | The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma |
| title_fullStr | The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma |
| title_full_unstemmed | The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma |
| title_short | The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma |
| title_sort | potential analysis and prospect of ctdna sequencing in hepatocellular carcinoma |
| topic | Liver cancer Next-generation sequencing Gene mutation Pathway analysis Circulating tumor DNA |
| url | https://peerj.com/articles/13473.pdf |
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