Wilmington, NC February 2016. Dr. James Willey presents AccuGenomics NGS quality control method at the Public Workshop – Next Generation Sequencing-Based Oncology Panels.
The FDA held a public meeting to gather input on strategies for establishing performance characteristics for NGS-based oncology panels for rare variants across tumor types. This need has become important as more NGS companion diagnostic oncology tests are being developed. Companion Diagnostics are those tests that provide information that is essential for the safe and effective use of a corresponding drug or biological product.
Dr. Willey described his approach to providing unique quality controls for NGS of rare mutations. The approach uses StarSeq, synthetic internal standards as process controls to establish performance characteristics for each NGS-based rare variant test and results in every mutation in each patient sample receiving a confidence measurement. This approach provides “three performance characteristics that contribute to measurement confidence and the use of synthetic internal standards to control for them. This information is incorporated into the analytical pipeline to assess the confidence for each measurement. An LoD defined as 3 sigma above the background would be quantifiable for each measurement,” says Dr. Willey.
Detection of rare mutations can be affected by the quality of sample, the NGS library construction and NGS instrument read. The StarSeq approach combines two pieces of information unique to the StarSeq method, input target abundance and NGS introduced mutation rate, with the NGS sequence counts to come up with a quality score for every mutation in every patient sample. This approach was described in a 2015 BDQ Article.
About Standardized Testing
Deployable molecular tests based on transcript abundance signatures has proven unreliable due to its sensitivity to variations in reagent handling, reagent specificity, instrument drift, and specimen quality. The predictive performance of complex transcript abundance signatures is reduced by the method variation and drift. AccuGenomics offers several transcript abundance methodologies that control for these variations to ensure every measurement was made correctly. These methods are ideal for development of kits that make many abundance measurements from limited degraded samples.
Next–generation sequencing refers to non-Sanger-based high-throughput DNA sequencing technologies. Millions or billions of DNA strands can be sequenced in parallel, yielding substantially more throughput and minimizing the need for the fragment-cloning methods that are often used in Sanger sequencing of genomes.