We recommend using fluorescent-based DNA quantification tools such as the Qubit™ Fluorometer (Thermo Fisher Scientific) to determine the concentration of your DNA sample. Digital electrophoresis (i.e., Bioanalyzer™ instrument, Agilent) can be used to assess the input sample size distribution.
For formalin-fixed, paraffin-embedded (FFPE) samples, we recommend using standard quality control methods, including finding the Q-ratio with qPCR or the DNA Integrity Number (DIN) using size distribution (i.e., Bioanalyzer instrument). These methods can help you choose the appropriate number of PCR cycles for your sample. For cell-free DNA (cfDNA), we recommend assessing the size distribution with electrophoresis. Note, if large molecular weight DNA is present, an additional cleanup may be necessary to remove genomic DNA contamination.