Do you recommend any QC assays to perform on the input cfDNA prior to library preparation?
We recommend analyzing the size distribution of the input cfDNA with a gel electropherogram assay, such as Bioanalyzer High Sensitivity DNA kit (Agilent), to ensure it is free from high molecular weight (HMW) DNA that may be carried over from cfDNA extraction. HMW DNA will negatively impact the accurate quantification of cfDNA input amounts (Figure 1). We also recommend quantifying input cfDNA with a Qubit high-sensitivity dsDNA assay (Thermo Fisher Scientific) for accurate DNA quantification.
| cfDNA With HMW Carryover | Remediated cfDNA |
|---|---|
 |
 |
Figure 1. Capillary gel electropherogram from Bioanalyzer High Sensitivity Assay (Agilent) comparing cfDNA containing HMW carryover versus clean cfDNA.
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