Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Analytic and clinical validation of a pan-cancer NGS liquid biopsy test for the detection of copy number amplifications, fusions and exon skipping variants.

Version 1 : Received: 23 January 2022 / Approved: 26 January 2022 / Online: 26 January 2022 (03:21:12 CET)

A peer-reviewed article of this Preprint also exists.

Audetat, A.; Tschida, C.; Kreston, S.; Stephen, A.; D’Alessio, B.; Bondy, M.; Jackson, L.; Mellert, H.; Givens, N.; Sathyanarayana, U.G.; Pestano, G.A. Analytic and Clinical Validation of a Pan-Cancer NGS Liquid Biopsy Test for the Detection of Copy Number Amplifications, Fusions and Exon Skipping Variants. Diagnostics 2022, 12, 729. Audetat, A.; Tschida, C.; Kreston, S.; Stephen, A.; D’Alessio, B.; Bondy, M.; Jackson, L.; Mellert, H.; Givens, N.; Sathyanarayana, U.G.; Pestano, G.A. Analytic and Clinical Validation of a Pan-Cancer NGS Liquid Biopsy Test for the Detection of Copy Number Amplifications, Fusions and Exon Skipping Variants. Diagnostics 2022, 12, 729.

Journal reference: Diagnostics 2022, 12, 729
DOI: 10.3390/diagnostics12030729

Abstract

Liquid biopsies are an integral part of the diagnosis of cancer. Here, we have extended previous validation studies of a new targeted NGS panel to include the detection of copy number amplifications (CNAs), fusions, and exon skipping variants. Detection of these gene classes included specimens from clinical and healthy donors and cell lines (fusions: ROS1, EML4-ALK, NTRK1), (exon skipping: MET exon 14), and (CNAs: HER2, CDK6, EGFR, MYC and MET). The limit of detection (LOD) for fusion/skipping was 42 copies (QC threshold = 3 copies) and was verified using 3 additional fusion/skipping variants. LOD for CNAs was 1.40-fold-change (QC threshold = 1.15-fold change) and was verified with 3 additional CNAs. In precision studies, all fusion/skipping variants were detected in all runs and all days of testing (n=18/18; 100%); average CV for repeatability was 20.5% (range 8.7% - 34.8%), and for reproducibility was 20.8% (range 15.7% - 30.5%). For CNAs, 28/29 (96.6%) copy gains were detected. For CNAs, average CV of 1.85% (range 0% to 5.49%) for repeatability and 6.59% (range 1.65% to 9.22%) for reproducibility. The test panel meets the criteria for being highly sensitive and specific and extends its utility for the detection of clinically relevant variants in cancer.

Keywords

non-small cell lung cancer (NSCLC); liquid biopsy; cell-free nucleic acid (cfNA); next generation sequencing (NGS); CNA (copy number amplifications); fusions, exon-skipping.

Subject

MEDICINE & PHARMACOLOGY, Oncology & Oncogenics

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