Because of this, there is always a chance that more than one copy of the original DNA molecule will get sequenced. It’s well known that the best way to limit the generation of PCR duplicates is to use as few PCR cycles as possible, and the most efficient way to do that is to increase the concentration of DNA going into your library preparation.

PCR Duplicates in Downstream NGS Data

In our most recent application note we compare the proportion of PCR duplicates in libraries prepared from FFPE samples purified by the Ionic system to libraries prepared from the same samples using a column-based kit. We not only demonstrate the correlation between PCR amplification cycles during library preparation and PCR duplicates in downstream sequencing data, but we also demonstrate the potential to reduce PCR duplicates with higher yields when performing extraction and purification using the Ionic system.