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Published on: April 11, 2016
Analytical Validation of a Plasma-Based Rapid Liquid Biopsy Assay Using Next-Generation Sequencing
Sinchita Roy-Chowdhuri1, Ana Galan-Cobo2, Nitin Agarwal2
1Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Molecular Diagnostic Laboratory, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
This study validates a rapid, two-day next-generation sequencing (NGS) liquid biopsy assay using cell-free total nucleic acid (cfTNA). The assay accurately detects genetic variants, potentially reducing time to cancer treatment.
Area of Science:
- Molecular Diagnostics
- Oncology
- Genomics
Background:
- Liquid biopsy (LBx) using cell-free total nucleic acid (cfTNA) provides a minimally invasive alternative to tissue biopsy for next-generation sequencing (NGS).
- Traditional NGS-based LBx assays often have long turnaround times (TAT), delaying treatment decisions.
Purpose of the Study:
- To validate a rapid NGS-based cfTNA liquid biopsy assay with a two-day TAT.
- To assess the assay's performance for detecting single nucleotide variants (SNVs), insertion deletions (indels), and fusions.
Main Methods:
- Validation of the Oncomine Precision Assay on the Genexus Sequencer using patient plasma samples.
- Optimization of fusion detection through manual extraction using the QIAamp cfTNA Kit.
- Analytical validation in synthetic controls and clinical samples, comparing results with orthogonal assays.
Main Results:
- High analytical sensitivity and specificity for SNVs (>99%) and indels (95-100%) in both synthetic and clinical samples.
- Manual extraction improved overall performance for fusion detection.
- Achieved an average TAT of ≤2 days with high precision (>99%).
Conclusions:
- A two-day TAT NGS-based cfTNA liquid biopsy assay is feasible and validated.
- This rapid assay has the potential to significantly reduce the time to cancer treatment initiation.
