Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor...

Area of Science:

• Molecular Diagnostics
• Genomics
• Cancer Research

Background:

• Next-generation sequencing (NGS) is revolutionizing precision medicine, but diagnostic accreditation lacks standardized validation criteria due to platform and process variability.
• Ensuring high-quality DNA and RNA from formalin-fixed paraffin-embedded (FFPE) samples is critical for accurate and cost-effective molecular diagnostic testing.
• Challenges with FFPE sample integrity necessitate robust quality control (QC) measures throughout the library preparation process.

Purpose of the Study:

• To establish a benchmark for QC metrics specifically for FFPE samples used in molecular diagnostic laboratories.
• To guide the development of good clinical laboratory practices for targeted NGS panels.
• To ensure successful library preparation and high-quality NGS data output from FFPE specimens.

Main Methods:

• Processed 144 DNA and 103 RNA samples from various cancer types, stored for a maximum of 2 years.
• Utilized targeted NGS panels focusing on 52 genes.
• Implemented extensive QC check parameters at multiple checkpoints during DNA and RNA library preparation.

Main Results:

• Demonstrated the feasibility of imposing stringent QC measures on FFPE samples for NGS.
• Identified critical QC checkpoints for successful library preparation.
• A decision tree approach was developed as a proposed benchmark for FFPE sample QC.

Conclusions:

• Stringent QC of DNA and RNA is essential for reliable NGS results from FFPE samples.
• The proposed decision tree approach can serve as a benchmark for molecular diagnostic laboratories.
• Implementing these QC metrics supports good clinical laboratory practice for targeted NGS panels.