FFPE tissue samples are known to produce low yields of nucleic acid that is often of a lower quality by comparison to nucleic acid from freshfrozen tissue, particularly samples that have been stored for several years or longer. When FFPE tissue is limited, conventional extraction and purification technologies may not produce enough high-quality DNA to meet the recommended library preparation input requirements for next-generation sequencing (NGS). To compensate for this, most library preparation methods use additional PCR cycles to create enough copies of the original DNA. This results in a higher number of PCR duplicates that reduce sequencing efficiency. Improving the quality and quantity of DNA extracted and purified from FFPE samples can greatly improve sequencing results and interpretation by reducing the number of PCR cycles needed during library preparation yielding more usable high-quality sequencing reads.
To compare the efficiency of DNA extraction and purification from FFPE samples, DNA was purified from a single 10 μm thick section from eight FFPE tissue blocks (18 years of age) containing breast, colon, or lung tissue using the Purigen Ionic® Purification System and a commercially available column-based kit. Adjacent scrolls were harvested from each block and processed separately by each method. The DNA purified by each method was quantified prior to NGS. The Ionic system produced a higher average yield from each sample to enable library preparation without additional PCR amplification with a resulting lower rate of PCR duplicates during next generation sequencing.
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