Abstract

Efficient, Automated Purification of ccfDNA From Plasma

Douglas Horejsh, Senior Research Scientist,, Promega Corporation

While circulating cell-free DNA (ccfDNA) is one of the most promising sources of DNA-based information for oncology research available today, scientists continue to look for better ways to actively target the precious small fragment DNA necessary for liquid biopsy applications.

The use of ccfDNA as a sample type is not without its challenges. The low concentration and highly fragmented nature of ccfDNA, coupled with the low frequency of biomarkers of interest, present many challenges to the adoption of ccfDNA monitoring. Variations inherent to the sample type, as well as sample handling, can affect the amount of contaminating high molecular weight gDNA. Presence of high levels of contaminating gDNA may result in difficulty detecting low-level mutations present in the minor component ccfDNA

We have developed novel nucleic acid purification chemistries that improve upon current manual and automated methods for the purification of DNA from plasma and demonstrate their use in downstream assays. In addition, we seek to provide tools to assess DNA quantity to understand the composition of the nucleic acid obtained.  In those cases where samples have been contaminated by gDNA, we have created applications where we can enrich for the ccfDNA component of a sample, thereby eliminating larger material and effectively decreasing background without affecting levels of the 170bp fragment.