Analytical Validation of a Hybrid Capture–Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA
| Autor: | Jason D. Hughes, Michael Coyne, Doron Lipson, Jie He, Erica B. Schleifman, Philip J. Stephens, Mark Bailey, Allison Welsh, Jeffrey S. Ross, Jill M. Spoerke, Travis A. Clark, Vincent A. Miller, Eric Peters, Jeffrey P. Gregg, Garrett M. Frampton, Daniel S. Lieber, Dean Pavlick, Amy Donahue, Steven Roels, Tim Brennan, Jon Chung, Geneva Young, Tariq I Mughal, Siraj M. Ali, Mark Kennedy, Geoff Otto, Mark R. Lackner, Niru Chennagiri, Mandy Zhao, Bernard Fendler, Steven Gendreau, Virginia Breese, Shan Zhong, Alyssa Tsiros, Lauren Young |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Concordance Gene Dosage Biology Gene dosage DNA sequencing Article Pathology and Forensic Medicine Circulating Tumor DNA 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine INDEL Mutation Gene duplication medicine Humans Allele frequency Gene Rearrangement Gene Amplification Cancer High-Throughput Nucleotide Sequencing Gene rearrangement Genomics medicine.disease Molecular biology 030104 developmental biology chemistry 030220 oncology & carcinogenesis Molecular Medicine DNA |
| Zdroj: | The Journal of Molecular Diagnostics : JMD |
| ISSN: | 1943-7811 1525-1578 |
| Popis: | Genomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a noninvasive method for detecting 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 short variants (base substitutions, short insertions/deletions) and genomic re-arrangements at low allele frequencies (AFs), and copy number amplifications. Analytical validation was performed on 2666 reference alterations. The assay achieved >99% overall sensitivity (95% CI, 99.1%–99.4%) for short variants at AF >0.5%, >95% sensitivity (95% CI, 94.2%–95.7%) for AF 0.25% to 0.5%, and 70% sensitivity (95% CI, 68.2%–71.5%) for AF 0.125% to 0.25%. No false positives were detected in 62 samples from healthy volunteers. Genomic alterations detected by FoundationACT demonstrated high concordance with orthogonal assays run on the same clinical cfDNA samples. In 860 routine clinical FoundationACT cases, genomic alterations were detected in cfDNA at comparable frequencies to tissue; for the subset of cases with temporally matched tissue and blood samples, 75% of genomic alterations and 83% of short variant mutations detected in tissue were also detected in cfDNA. On the basis of analytical validation results, FoundationACT has been approved for use in our Clinical Laboratory Improvement Amendments–certified/College of American Pathologists–accredited/New York State–approved laboratory. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|