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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
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Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene
Matthew C Hiemenz1, Stephan Kadauke2, David B Lieberman1
1Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Plos One
|April 5, 2016
Summary
Next-generation sequencing (NGS) reliably detects cancer mutations. Implementing quality control metrics ensures accurate NGS results for clinical oncology, facilitating broader adoption.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Next-generation sequencing (NGS) is crucial for identifying cancer mutations.
- Clinical implementation of NGS necessitates robust quality control (QC) metrics for accuracy.
- Evaluating NGS pipeline performance is vital for routine clinical use.
Purpose of the Study:
- To assess the robustness and reliability of a clinical NGS pipeline.
- To compare NGS results with targeted single-gene tests in solid tumors and hematologic malignancies.
- To validate the effectiveness of QC metrics in ensuring accurate NGS detection of cancer mutations.
Main Methods:
- Analysis of 304 solid tumor and hematologic malignancy specimens.
- Simultaneous testing using NGS and targeted single-gene assays (EGFR, KRAS, BRAF, NPM1, FLT3, JAK2).
- Evaluation of concordance and identification of clinically significant mutations, considering validated tumor percentage and DNA quality thresholds.
Main Results:
- Perfect concordance between NGS and targeted tests for samples meeting QC thresholds.
- Two FLT3 internal tandem duplications detected by NGS but below the initial reporting limit.
- NGS identified additional clinically relevant mutations beyond single-gene panels.
- The study confirmed NGS reliability with appropriate QC measures.
Conclusions:
- NGS is a dependable platform for clinical cancer mutation identification.
- Implementing stringent QC metrics, including tumor percentage and DNA quality, is essential for accurate NGS results.
- The proposed workflow can aid other institutions in adopting clinical oncologic NGS services.
