QC Measurements for Predicting Downstream NGS Success with FFPE and Circulating Cell-Free DNA Plasma Samples

Abstract
Quantity and quality of DNA from formalin fixed, paraffin embedded (FFPE) tumor tissue samples is highly variable, with degradation and crosslinking due to the fixation process leading to issues with amplification and difficulty in NGS analysis. An alternative to FFPE is circulating cell-free DNA (ccfDNA) from plasma or other biological fluids. Compared to gDNA, ccfDNA yields are typically low, with tumor cell present at significantly lower frequencies. Due to the inherent variability of FFPE and ccfDNA, knowing the quantity of DNA is not in itself reliably predictive of downstream NGS success. In this presentation, we describe novel methods for predicting sequencing result quality utilizing a multiplexed qPCR assay.