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

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 targ...

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Bibliographic Details
Published in:International journal of molecular sciences 2023-11, Vol.24 (21), p.15779
Main Authors: Fernandez, Sandra V., Tan, Yin Fei, Rao, Shilpa, Fittipaldi, Patricia, Sheriff, Fathima, Borghaei, Hossein, Dotan, Efrat, Winn, Jennifer S., Edelman, Martin J., Treat, Joseph, Judd, Julia, Alpaugh, R. Katherine, Wang, Y. Lynn, Yu, Jian Q., Wasik, Mariusz, Baldwin, Don A.
Format: Article
Language:English
Subjects:
Bioinformatics
Breast cancer
DNA
Fulvestrant
Genes
Laboratories
Medical tests
Mutation
Plasma
Reference materials
Reproducibility
Software
Tumors
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Summary: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%.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms242115779