Background: Liquid biopsy is considered a complementary and recently also an alternative method to surgical biopsy. It allows for the acquisition of valuable information regarding the potential presence of tumors, particularly through the analysis of circulating tumor DNA (ctDNA). CtDNA is a fraction of circulating free DNA (cfDNA) that can be extracted from various tissues, with blood being the most readily available. Results: To maximize the yield of plasma separation, specific Streck tubes are recommended for blood collection. The MagPurix CFC DNA Extraction Kit can be used for cfDNA extraction, and the TWIST Library Preparation protocol can be optimized for further analysis. Next-generation sequencing (NGS) can be employed to compare somatic and germline lineages, enabling the identification of somatic variants with a Variant Allele Frequency (VAF) of 5 % or higher, which are absent in the germline lineage. Conclusion: This analysis helps in the assessment of recurrence, analysis, and monitoring of cancer tissue.
Mareso, C., Crosta, M. L., De Vita, M. G., Cristofoli, F., Tanzi, B., Benedetti, S., Bonetti, G., Donofrio, C. A., Cominetti, M., Riccio, L., Fioravanti, A., Generali, D., Lucci Cordisco, E., Chiurazzi, P., Gatta, V., Stuppia, L., Cecchin, S., Bertelli, M., Marceddu, G., Assessing the efficacy of an innovative diagnostic method for identifying 5 % variants in somatic ctDNA, <<GENE>>, 2024; 928 (n/a): N/A-N/A. [doi:10.1016/j.gene.2024.148771] [https://hdl.handle.net/10807/304597]
Assessing the efficacy of an innovative diagnostic method for identifying 5 % variants in somatic ctDNA
Crosta, Maria Luigia;Generali, Daniele;Lucci Cordisco, Emanuela;Chiurazzi, Pietro;
2024
Abstract
Background: Liquid biopsy is considered a complementary and recently also an alternative method to surgical biopsy. It allows for the acquisition of valuable information regarding the potential presence of tumors, particularly through the analysis of circulating tumor DNA (ctDNA). CtDNA is a fraction of circulating free DNA (cfDNA) that can be extracted from various tissues, with blood being the most readily available. Results: To maximize the yield of plasma separation, specific Streck tubes are recommended for blood collection. The MagPurix CFC DNA Extraction Kit can be used for cfDNA extraction, and the TWIST Library Preparation protocol can be optimized for further analysis. Next-generation sequencing (NGS) can be employed to compare somatic and germline lineages, enabling the identification of somatic variants with a Variant Allele Frequency (VAF) of 5 % or higher, which are absent in the germline lineage. Conclusion: This analysis helps in the assessment of recurrence, analysis, and monitoring of cancer tissue.
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