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

doi:10.3390/ijms242115779

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

Fox Chase Cancer Center

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

A modified version of the PGDx elio^TM 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 language	English
Article number	15779
Journal	International Journal of Molecular Sciences
Volume	24
Issue number	21
DOIs	https://doi.org/10.3390/ijms242115779
State	Published - 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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.3390/ijms242115779

Cite this

Fernandez, S. V., Tan, Y. F., Rao, S., Fittipaldi, P., Sheriff, F., Borghaei, H., Dotan, E., Winn, J. S., Edelman, M. J., Treat, J., Judd, J., Alpaugh, R. K., Wang, Y. L., Yu, J. Q., Wasik, M., & Baldwin, D. (2023). Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing. International Journal of Molecular Sciences, 24(21), Article 15779. https://doi.org/10.3390/ijms242115779

@article{0ae1bc62bc184dc397448ab09f6950ec,

title = "Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing",

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%.",

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",

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

note = "Publisher Copyright: {\textcopyright} 2023 by the authors.",

year = "2023",

month = nov,

doi = "10.3390/ijms242115779",

language = "English",

volume = "24",

journal = "International Journal of Molecular Sciences",

issn = "1661-6596",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "21",

}

Fernandez, SV, Tan, YF, Rao, S, Fittipaldi, P, Sheriff, F, Borghaei, H, Dotan, E, Winn, JS, Edelman, MJ , Treat, J , Judd, J, Alpaugh, RK, Wang, YL , Yu, JQ , Wasik, M & Baldwin, D 2023, 'Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing', International Journal of Molecular Sciences, vol. 24, no. 21, 15779. https://doi.org/10.3390/ijms242115779

TY - JOUR

T1 - Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing

AU - Fernandez, Sandra V.

AU - Tan, Yin Fei

AU - Rao, Shilpa

AU - Fittipaldi, Patricia

AU - Sheriff, Fathima

AU - Borghaei, Hossein

AU - Dotan, Efrat

AU - Winn, Jennifer S.

AU - Edelman, Martin J.

AU - Treat, Joseph

AU - Judd, Julia

AU - Alpaugh, R. Katherine

AU - Wang, Y. Lynn

AU - Yu, Jian Q.

AU - Wasik, Mariusz

AU - Baldwin, Donald

PY - 2023/11

Y1 - 2023/11

N2 - 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%.

AB - 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%.

KW - assay performance assessment

KW - cfDNA

KW - clinical cancer genotyping

KW - ctDNA

KW - laboratory-developed test

KW - Circulating Tumor DNA/genetics

KW - Humans

KW - INDEL Mutation

KW - Biomarkers, Tumor/genetics

KW - High-Throughput Nucleotide Sequencing/methods

KW - Molecular Diagnostic Techniques

KW - Neoplasms/diagnosis

KW - Mutation

KW - Pathology, Molecular

UR - http://www.scopus.com/inward/record.url?scp=85176375451&partnerID=8YFLogxK

UR - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=purepublist2023&SrcAuth=WosAPI&KeyUT=WOS:001099491900001&DestLinkType=FullRecord&DestApp=WOS

U2 - 10.3390/ijms242115779

DO - 10.3390/ijms242115779

M3 - Article

C2 - 37958763

SN - 1661-6596

VL - 24

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

IS - 21

M1 - 15779

ER -

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

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Researcher from Fox Chase Cancer Center Reports Details of New Studies and Findings in the Area of Genetics (Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing)

Cite this

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

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Press/Media

Researcher from Fox Chase Cancer Center Reports Details of New Studies and Findings in the Area of Genetics (Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing)

Cite this