The FFPE yield is lower than expected, how can I improve the yield?
The FFPE yield observed will vary significantly depending on method and user. If you observe no yield or less than 50 ng total recovered DNA it is likely that the cell pellet was lost during the xylene deparaffinization and subsequent wash steps. During the xylene treatment it is important to be able to locate and visualize the clear cell pellet (a small cell disc) in your tube to ensure no cells are aspirated at this initial stage. If you are experiencing total DNA yields of 50 - 200 ng per FFPE section then it is possible that some of your DNA remains on the column during the elution. Performing multiple elution steps may be beneficial. From our experience, dual 50 μl elutions provide a greater total DNA yield compared to a single 100μl elution.