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Updated: Sep 30, 2025
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
FDA-led consortium studies advance quality control of targeted next generation sequencing assays for precision
Dan Li1, Rebecca Kusko2, Baitang Ning1
1Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
Abstract:
Cancer is the second leading cause of mortality worldwide despite tremendous advances in treatment. The promise of precision oncology depends on accurate characterization of tumor mutations and subsequent therapy selection. The lack of tumor reference samples along with the associated next generation sequencing (NGS) technical assessments has hindered the development of NGS assays and the realization of benefits for precision oncology. The summarized results and recommendations of several seminal SEQC2 studies along with a vision of the changing landscape of precision oncology and anticipated next steps by the SEQC2 consortium are reported. Importantly, these studies utilized a new robust reference sample material which was developed and constructed to support multiple DNA and RNA-based NGS assay studies. These studies focused on a wide variety of precision oncology assay scenarios and provided guidelines for standardized analyses and best practice recommendations. The evolving landscape of precision oncology requires insights into critical factors supporting the sensitivity and reproducibility of clinical NGS assays for continued improvement in patient outcomes. Persistent development of robust reference materials, quantitative performance metrics, and actionable data analysis recommendations are needed. This series of SEQC2 studies serve to advance NGS-based assays for precision oncology and support regulatory science endeavors.
Insights
This study introduces robust reference materials and guidelines to improve next-generation sequencing (NGS) assays for precision oncology. These advancements aim to enhance tumor mutation characterization and therapy selection, ultimately benefiting cancer patient outcomes.
Area of Science:
- Oncology
- Genomics
- Biotechnology
Background:
- Cancer is a leading cause of death globally, necessitating advanced diagnostic tools.
- Precision oncology relies on accurate tumor mutation profiling for effective therapy selection.
- Challenges in next-generation sequencing (NGS) assay development, including a lack of standardized reference samples, impede progress.
Purpose of the Study:
- To report findings and recommendations from SEQC2 studies on NGS assays for precision oncology.
- To introduce a novel reference sample material for DNA and RNA-based NGS assays.
- To provide guidelines for standardized analysis and best practices in precision oncology assays.
Main Methods:
- Development and utilization of a new, robust reference sample material.
- Evaluation of multiple DNA and RNA-based NGS assay scenarios.
- Analysis of SEQC2 consortium studies focusing on assay sensitivity and reproducibility.
Main Results:
- Establishment of guidelines for standardized analyses in precision oncology.
- Demonstration of a robust reference material supporting diverse NGS assay studies.
- Identification of critical factors for improving sensitivity and reproducibility of clinical NGS assays.
Conclusions:
- The SEQC2 studies advance NGS-based assays for precision oncology through robust reference materials and standardized guidelines.
- Continued development of reference materials, performance metrics, and data analysis recommendations is crucial.
- These efforts support regulatory science and aim to improve patient outcomes in precision oncology.
