Analytical validation of an error-corrected ultra-sensitive ctDNA next-generation sequencing assay
- Author(s)
- Fettke, H; Steen, JA; Kwan, EM; Bukczynska, P; Keerthikumar, S; Goode, D; Docanto, M; Ng, N; Martelotto, L; Hauser, C; Southey, MC; Azad, AA; Nguyen-Dumont, T;
- Journal Title
- Biotechniques
- Publication Type
- Journal epub ahead of print
- Abstract
- 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).
- Publisher
- Future Science
- Research Division(s)
- Personalised Oncology
- PubMed ID
- 32654508
- Publisher's Version
- https://doi.org/10.2144/btn-2020-0045
- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2020-07-21 10:52:54
Last Modified: 2020-07-21 11:17:27