Analytical validation of a hybrid capture–based next-generation sequencing clinical assay for genomic profiling of cell-free circulating tumor DNA

Publication date: Available online 22 June 2018Source: The Journal of Molecular DiagnosticsAuthor(s): Travis A. Clark, Jon H. Chung, Mark Kennedy, Jason D. Hughes, Niru Chennagiri, Daniel S. Lieber, Bernard Fendler, Lauren Young, Mandy Zhao, Michael Coyne, Virginia Breese, Geneva Young, Amy Donahue, Dean Pavlick, Alyssa Tsiros, Timothy Brennan, Shan Zhong, Tariq Mughal, Mark Bailey, Jie HeAbstractGenomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a non-invasive method for the detection of genomic biomarkers to guide clinical decision-making for cancer patients. We developed a hybrid capture–based next-generation sequencing assay for genomic profiling of circulating tumor DNA from blood (FoundationACT®). High sequencing coverage and molecular barcode–based error detection enabled accurate detection of genomic alterations, including base substitutions, short insertions/deletions, and genomic rearrangements at low allele frequencies (AF), and copy number amplifications. Analytical validation was performed on 2,666 reference alterations. The assay achieved>99% overall sensitivity (95%CI:99.1% to 99.4%) for short variants at AF above 0.5%,>95% sensitivity for AF 0.25% to 0.5% (95%CI:94.2% to 95.7%), and 70% sensitivity (95%CI:68.2% to 71.5%) for AF 0.125% to 0.25%. No false-positives were detected in any samples from healthy volunteers (N=62). Genomic alterations detected by FoundationACT demonstrated high concordance with ortho...
Source: The Journal of Molecular Diagnostics - Category: Pathology Source Type: research