Single 10 μm slices of FFPE tissue were used to compare the results of DNA purification using standard and GeneRead protocols for FFPE samples. The wide range of DNA yields seen is due to the variation in the starting material. This is common for DNA purification from FFPE samples.
Double-stranded DNA was extracted from single 10 μm slices of FFPE tissue using the GeneRead DNA FFPE Kit and a product from an alternative supplier. Yields were measured by Qubit Fluorometric Quantitation.The GeneRead DNA FFPE Kit delivered up to 4-fold higher yields for the samples tested. A wide range of DNA yields is seen due to variation in the starting material, which is common for DNA extractions from FFPE samples.
Analysis of liver cancer samples was carried out. The GeneRead DNA FFPE Kit removed over 90% of low-frequency, novel mutations that are most likely to be artifactual in nature.
Analysis of liver cancer samples was carried out. High-frequency C>T|G>A transitions, whether novel or present in dbSNP, were retained when the GeneRead DNA FFPE protocol was used.
In FFPE samples, cytosine may become deaminated, leading to the cytosine pairing with adenine as uracil. In sequencing reactions, this will manifest as a C>T|G>A transition.
(Figure adapted from Klug and Cummings, 1997)