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Development of a highly sensitive liquid biopsy platform to detect clinically-relevant cancer mutations at low allele fractions in cell-free DNA.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Lawson, Andrew RJ 
Howarth, Karen 
Madi, Mikidache 
Durham, Bradley 

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.

Description

Keywords

Adult, Alleles, Biomarkers, Tumor, Cell-Free Nucleic Acids, Circulating Tumor DNA, DNA Mutational Analysis, DNA, Neoplasm, Female, High-Throughput Nucleotide Sequencing, Humans, Liquid Biopsy, Male, Mutation, Neoplasms, Neoplastic Cells, Circulating, Polymerase Chain Reaction, Reproducibility of Results, Sensitivity and Specificity

Journal Title

PLoS One

Conference Name

Journal ISSN

1932-6203
1932-6203

Volume Title

13

Publisher

Public Library of Science (PLoS)
Sponsorship
Cancer Research UK (C14303/A17197)
Cancer Research UK (20240)