A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits.

Abstract

DNA isolation from formalin-fixed paraffin-embedded (FFPE) tissues for molecular analysis has become a frequent procedure in cancer research. However, the yield or quality of the isolated DNA is often compromised, and commercial kits are used to overcome this to some extent. We developed a new protocol (IARCp) to improve the quality and yield of DNA from FFPE tissues without using any commercial kit. To evaluate the IARCp's performance, we compared the quality and yield of DNA with two commercial kits, namely NucleoSpin® DNA FFPE XS (MN) and QIAamp DNA Micro (QG) isolation kit. Total DNA yield for QG ranged from 120.0 to 282.0ng (mean 216.5ng), for MN: 213.6-394.2ng (mean 319.1ng), and with IARCp the yield was much higher ranging from 775.5 to 1896.9ng (mean 1517.8ng). Moreover, IARCp has also performed well in qualitative assessments by spectrophotometer, fluorometer, and real-time PCR assay. Overall, IARCp represents a novel approach to DNA isolation from FFPE which results in good quality and significant amounts of DNA suitable for many downstream genome-wide and targeted molecular analyses. This protocol does not require the use of any commercial kits or phenol for isolating DNA from FFPE tissues, making it suitable to implement in low-resource settings such as low and middle-income countries.