Authors:
D Gale, ARJ Lawson, K Howarth, M Madi, B Durham, S Smalley, J Calaway, S Blais, G Jones, J Clark, P Dimitrov, M Pugh, S Woodhouse, M Epstein, A Fernandez-Gonzalez, AS Whale, JF Huggett, CA Foy, GM Jones, H Raveh-Amit, K Schmitt, A Devonshire, E Green, T Forshew, V Plagnol, N Rosenfeld
Journal name: 
PLoS One
Citation info: 
13(3):e0194630
Abstract: 
INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes. MATERIALS AND METHODS: We present analytical validation of the eTAm-Seq technology across two laboratories to determine the reproducibility of mutation identification. We assess the quantitative performance of eTAm-Seq technology for analysis of single nucleotide variants in clinically-relevant genes as compared to digital PCR (dPCR), using both established DNA standards and novel full-process control material. RESULTS: The assay detected mutant alleles down to 0.02% AF, with high per-base specificity of 99.9997%. Across two laboratories, analysis of samples with optimal amount of DNA detected 94% mutations at 0.25%-0.33% allele fraction (AF), with 90% of mutations detected for samples with lower amounts of input DNA. CONCLUSIONS: These studies demonstrate that eTAm-Seq technology is a robust and reproducible technology for the identification and quantification of somatic mutations in circulating tumor DNA, and support its use in clinical applications for precision medicine.
DOI: 
http://doi.org/10.1371/journal.pone.0194630
Research group: 
Rosenfeld Group
E-pub date: 
16 Mar 2018