Abstract
A good DNA quality and quantity from a formalin-fixed paraffin-embedded (FFPE) tissue sample is crucial for a better downstream genomic analysis. Previous research has focused on comparing FFPE DNA extraction kits, but the improvement in kit outcome has yet to be studied. This study aimed to make some modifications to a selected Qiagen DNA extraction manual protocol using a manual macrodissected FFPE colorectal cancer (CRC) tissue sample. A variety of DNA extraction protocol-related variables, such as washing steps, tissue sections, and FFPE tissue age have been investigated to determine the DNA quality and quantity of the FFPE tissues. The prechilled absolute ethanol washing step showed the highest DNA concentration with good purity ratios. One, two, or four tissue sections using the washing step were sufficient to obtain adequate DNA concentrations with acceptable DNA purity ratios. 1% or 2% agarose gel electrophoresis with the pre-casting method allowed better visualisation of FFPE DNA. Based on the ideal quality and quantity, we chose a manual macrodissected DNA extraction protocol employing 4 x 10 µm FFPE tissue sections generated in recent years with an optimised prechilled absolute ethanol washing step.