As the cost of sequencing continues to drop, the throughput and complexity of next generation (NGS) assays have risen precipitously. At the same time, the types of samples being used for these assays have expanded as researchers find value in studying low-input, degraded biological samples, such as cell-free DNA (cfDNA). Obtaining actionable information from clinical samples is challenging due to loss during extraction, low conversion during NGS library preparation, drop in complexity during target enrichment, and sequencing and PCR errors that lead to low limits of detection.
Here, we present a complete workflow for effective analysis of ultra-low-frequency variants in cfDNA. Our magnetic bead-based extraction kit provides complex, high-yield recovery of cfDNA. A novel library prep chemistry delivers higher complexity and coverage than conventional TA-ligation-based workflows, enabling highly sensitive, low-frequency variant detection. By combining the high conversion of our extraction and library preparation chemistry with our efficient hybridization capture technology, we demonstrate an effective approach to extracting information from low-quantity, challenging samples.