Analytical validation of an error-corrected ultra-sensitive ctDNA next-generation sequencing assay.

Autor:	Fettke H; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia., Steen JA; Precision Medicine, School of Clinical Sciences at Monash Health, Melbourne, Australia., Kwan EM; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.; Department of Medical Oncology, Monash Health, Melbourne, Australia., Bukczynska P; Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia., Keerthikumar S; Computational Cancer Biology Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia., Goode D; Computational Cancer Biology Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia., Docanto M; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia., Ng N; Walter & Eliza Hall Institute of Medical Research, Melbourne, Australia., Martelotto L; Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia., Hauser C; Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia., Southey MC; Precision Medicine, School of Clinical Sciences at Monash Health, Melbourne, Australia.; Department of Clinical Pathology, The University of Melbourne, Melbourne, Australia.; Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia., Azad AA; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.; Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia., Nguyen-Dumont T; Precision Medicine, School of Clinical Sciences at Monash Health, Melbourne, Australia.; Department of Clinical Pathology, The University of Melbourne, Melbourne, Australia.
Jazyk:	angličtina
Zdroj:	BioTechniques [Biotechniques] 2020 Aug; Vol. 69 (2), pp. 133-140. Date of Electronic Publication: 2020 Jul 13.
DOI:	10.2144/btn-2020-0045
Abstrakt:	Plasma circulating tumor DNA (ctDNA) analysis has emerged as a minimally invasive means to perform molecular tumor typing. Here we developed a custom ultra-sensitive ctDNA next-generation sequencing assay using molecular barcoding technology and off-the-shelf reagents combined with bioinformatics tools for enhanced ctDNA analysis. Assay performance was assessed via a spike-in experiment and the technique was applied to analyze 41 plasma samples from men with advanced prostate cancer. Orthogonal validation was performed using a commercial assay. Sensitivity and specificity of 93 and 99.5% were recorded for ultra-rare somatic variants (<1%), with high concordance observed between the in-house and commercial assays. The optimized protocol dramatically improved the efficiency of the assay and enabled the detection of low-frequency somatic variants from plasma cell-free DNA (cfDNA).
Databáze:	MEDLINE
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