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

Part # PS312

Abstract

Doug Wieczorek, PhD, Spencer Hermanson, Curtis Knox, Jennifer Mook, Douglas Horejsh, PhD, Eric Vincent, PhD, Douglas Storts, PhD, Trista Schagat, PhD,
Promega Corporation, 2800 Woods Hollow Rd. Madison, WI

Formalin fixed, paraffin embedded (FFPE) tumor tissue samples have long been an important source of genetic material for mutational analysis. However, the quality of DNA from FFPE samples is often highly variable, and the resulting degradation and crosslinking due to the fixation process can lead to issues with amplifiability and difficulty in NGS analysis. An alternative to FFPE is obtaining circulating cell-free DNA (ccfDNA) from plasma or other biological fluids. Collecting ccfDNA samples from plasma is non-invasive and can be used when no tumor is accessible or detectable. Samples can be collected quickly and frequently and allows for the ability to monitor the disease or response to treatment over time. The drawbacks are that yields of ccfDNA are often very low and circulating tumor DNA is typically present at low frequencies.
We have developed novel nucleic acid purification chemistries that improve upon current manual and automated methods for the purification of DNA from FFPE and plasma and demonstrate their use in NGS applications.

Printed in USA.