Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing

Sandra V. Fernandez, Yin Fei Tan, Shilpa Rao, Patricia Fittipaldi, Fathima Sheriff, Hossein Borghaei, Efrat Dotan, Jennifer S. Winn, Martin J. Edelman, Joseph Treat, Julia Judd, R. Katherine Alpaugh, Y. Lynn Wang, Jian Q. Yu, Mariusz Wasik, Donald Baldwin

Research output: Contribution to journalArticlepeer-review

Abstract

A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions (indels) in 33 target genes using fragmented genomic DNA extracted from plasma. The analytical performance of this assay was assessed with reference standard DNA and 29 samples from cancer patients and detected 66 SNVs and 23 indels. Using 50 ng of input DNA, the sensitivity was 95.5% to detect SNVs at 0.5% allele frequency, and the specificity was 92.3%. The sensitivity to detect indels at 1% allele frequency was 70.4%. A cutoff of 0.25% variant allele frequency (VAF) was set up for diagnostic reporting. An inter-laboratory study of concordance with an orthologous test resulted in a positive percent agreement (PPA) of 91.7%.

Original languageEnglish
Article number15779
JournalInternational Journal of Molecular Sciences
Volume24
Issue number21
DOIs
StatePublished - Nov 2023

Keywords

  • assay performance assessment
  • cfDNA
  • clinical cancer genotyping
  • ctDNA
  • laboratory-developed test
  • Circulating Tumor DNA/genetics
  • Humans
  • INDEL Mutation
  • Biomarkers, Tumor/genetics
  • High-Throughput Nucleotide Sequencing/methods
  • Molecular Diagnostic Techniques
  • Neoplasms/diagnosis
  • Mutation
  • Pathology, Molecular

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