Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays
Recently, liquid biopsy, as a promising approach was introduced for the analysis of different tumor-derived circulating markers including tumor DNA and cell free DNA (ct/cfDNA). Identification of mutations in cfDNA may allow the early detection of tumors, as well as predicting and monitoring treatme...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-02-01
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| Series: | Molecular and Cellular Probes |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0890850822000998 |
| _version_ | 1797788459645009920 |
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| author | István Szász Tímea Kiss Attila Mokánszki Viktória Koroknai János Deák Vikas Patel Krisztina Jámbor Róza Ádány Margit Balázs |
| author_facet | István Szász Tímea Kiss Attila Mokánszki Viktória Koroknai János Deák Vikas Patel Krisztina Jámbor Róza Ádány Margit Balázs |
| author_sort | István Szász |
| collection | DOAJ |
| description | Recently, liquid biopsy, as a promising approach was introduced for the analysis of different tumor-derived circulating markers including tumor DNA and cell free DNA (ct/cfDNA). Identification of mutations in cfDNA may allow the early detection of tumors, as well as predicting and monitoring treatment responses in a minimally invasive way. In the present study, we used commercially available gene panels to verify the mutation overlap between liquid biopsy and abnormalities detected in colorectal tumor tissue. The two panels (Archer®VariantPlex®Solid Tumor and LIQUIDPlexTM ctDNA) overlap in 23 genes, which enables a comprehensive view of tumor-plasma mutational status by next generation sequencing. We successfully analyzed 16 plasma and 16 tumor samples. We found that 87% of tumor tissues contained 44 mutations in 12 genes and 43.8% of cfDNA harbored 13 mutations in 5 genes. To verify whether the mutation pattern of the tumor DNA could be consistently detected in plasma cfDNA, we compared the alterations between cfDNA and matched tissue DNA in nine patients. Six of the 9 tumor tissues harbored mutations in TP53, KRAS or MET genes, those were not detectable by the ctDNA kit, even eventhough the exons of these genes overlap in both panels. Comparing the mutational patterns of the matched samples, we found that only one cfDNA had the same mutations (KRAS, SMAD4 and TP53) in the paired tissue. The results of the comparison between tumor tissue DNA and matched plasma cfDNA underline the importance of studying the paired solid tumor and plasma samples together. |
| first_indexed | 2024-03-13T01:36:51Z |
| format | Article |
| id | doaj.art-6456d77d8158409fa1084d18c8d8327a |
| institution | Directory Open Access Journal |
| issn | 0890-8508 |
| language | English |
| last_indexed | 2024-03-13T01:36:51Z |
| publishDate | 2023-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular and Cellular Probes |
| spelling | doaj.art-6456d77d8158409fa1084d18c8d8327a2023-07-04T05:09:06ZengElsevierMolecular and Cellular Probes0890-85082023-02-0167101888Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assaysIstván Szász0Tímea Kiss1Attila Mokánszki2Viktória Koroknai3János Deák4Vikas Patel5Krisztina Jámbor6Róza Ádány7Margit Balázs8ELKH-DE Public Health Research Group, University of Debrecen, 4032, Debrecen, Hungary; Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, HungaryELKH-DE Public Health Research Group, University of Debrecen, 4032, Debrecen, Hungary; Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, HungaryDepartment of Pathology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, HungaryELKH-DE Public Health Research Group, University of Debrecen, 4032, Debrecen, Hungary; Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, HungaryUniversity of Debrecen Clinical Center, Surgery Clinic, University of Debrecen, Debrecen, HungaryDoctoral School of Health Sciences, University of Debrecen, HungaryDepartment of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary; Doctoral School of Health Sciences, University of Debrecen, HungaryELKH-DE Public Health Research Group, University of Debrecen, 4032, Debrecen, Hungary; Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, HungaryELKH-DE Public Health Research Group, University of Debrecen, 4032, Debrecen, Hungary; Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary; Corresponding author. ELKH-DE Public Health Research Group, University of Debrecen, 4032, Debrecen, Hungary.Recently, liquid biopsy, as a promising approach was introduced for the analysis of different tumor-derived circulating markers including tumor DNA and cell free DNA (ct/cfDNA). Identification of mutations in cfDNA may allow the early detection of tumors, as well as predicting and monitoring treatment responses in a minimally invasive way. In the present study, we used commercially available gene panels to verify the mutation overlap between liquid biopsy and abnormalities detected in colorectal tumor tissue. The two panels (Archer®VariantPlex®Solid Tumor and LIQUIDPlexTM ctDNA) overlap in 23 genes, which enables a comprehensive view of tumor-plasma mutational status by next generation sequencing. We successfully analyzed 16 plasma and 16 tumor samples. We found that 87% of tumor tissues contained 44 mutations in 12 genes and 43.8% of cfDNA harbored 13 mutations in 5 genes. To verify whether the mutation pattern of the tumor DNA could be consistently detected in plasma cfDNA, we compared the alterations between cfDNA and matched tissue DNA in nine patients. Six of the 9 tumor tissues harbored mutations in TP53, KRAS or MET genes, those were not detectable by the ctDNA kit, even eventhough the exons of these genes overlap in both panels. Comparing the mutational patterns of the matched samples, we found that only one cfDNA had the same mutations (KRAS, SMAD4 and TP53) in the paired tissue. The results of the comparison between tumor tissue DNA and matched plasma cfDNA underline the importance of studying the paired solid tumor and plasma samples together.http://www.sciencedirect.com/science/article/pii/S0890850822000998Colorectal cancerTumor tissue and plasma samplescfDNANext generation sequencingLiquid biopsy |
| spellingShingle | István Szász Tímea Kiss Attila Mokánszki Viktória Koroknai János Deák Vikas Patel Krisztina Jámbor Róza Ádány Margit Balázs Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays Molecular and Cellular Probes Colorectal cancer Tumor tissue and plasma samples cfDNA Next generation sequencing Liquid biopsy |
| title | Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays |
| title_full | Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays |
| title_fullStr | Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays |
| title_full_unstemmed | Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays |
| title_short | Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays |
| title_sort | identification of liquid biopsy based mutations in colorectal cancer by targeted sequencing assays |
| topic | Colorectal cancer Tumor tissue and plasma samples cfDNA Next generation sequencing Liquid biopsy |
| url | http://www.sciencedirect.com/science/article/pii/S0890850822000998 |
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