Application of liquid biopsy to uncover critical cancer insights using the GeneReader NGS system.

Abstract

e13102 Background: NGS studies of cancer are primarily based on studies of FFPE samples, the use of which is limited by surgical feasibility, tissue availability and patient preference. An emerging field of study is focused on circulating-free DNA (cfDNA), sometimes termed “Liquid Biopsy”. While holding great promise as the future of cancer understanding and management, the liquid biopsy field is still nascent, lacking an integrated NGS workflow solution with proven performance. Methods: QIAGEN is an established expert in the field of sample preparation for liquid biopsy. The combination of the QIAamp Circulating Nucleic Acid Kit, the GeneReader NGS System using a new proprietary sequencing chemistry, and an optimized bioinformatics solution, provides the first fully integrated workflow specifically designed for analyzing cfDNA. A set of liquid biopsy samples from non-small cell lung cancer (NSCLC) patients and cfDNA reference standards (Horizon), with allelic frequency down to 1%, were used for this study. cfDNA was extracted from the liquid biopsy samples, and run through the QIAGEN GeneReader workflow. Variants were analysed using the QIAGEN Clinical Insight (QCI™) Analyze for liquid biopsy. Results: Expected mutations in all genes (EGFR, KRAS, NRAS, PI3KCA) were identified and verified, at 100% concordance with reported in ddPCR studies. Both single nucleotide and insertion-deletion variants were correctly detected down to a 1% allele frequency threshold which was reproducible between repeat runs. No significant difference was observed between cfDNA reference standards and clinical liquid biopsy samples. Conclusions: These data exhibit high sensitivity and performance consistency of liquid biopsy analysis with the GeneReader system. This study systematically demonstrates the accuracy of a cfDNA assay combined with the robustness of a fully integrated NGS system. As such, laboratories interested in conducting liquid biopsy studies can leverage this study and the system to implement an NGS workflow.