As the saying goes, “garbage in, garbage out.” When it comes to DNA sample prep, the utility of DNA sequence data is directly dependent on the quality of the input material. As the cost per base pair of DNA sequence data continues to plummet, the breadth of applications for which sequencing is used continues to expand.
With this expansion comes an expanding list of input sample types (for example, formalin-fixed paraffin-embedded specimens), the need to separate target nucleic acids from complex mixtures, and attempts to generate high-quality data from diminishing amounts of material. In many cases, this is confounded by the fact that the laboratory performing the sample preparation and sequencing is not responsible for the extraction of the desired nucleic acid from the source material.
As samples navigate their way to becoming “sequencer-ready,” there is an increased investment of costly reagents, time, and resources with every process step. Thus, the ability to assess the quality of these samples prior to making this investment has become especially critical.
The factors that contribute to a nucleic acid’s viability for downstream applications include amount, purity, and degree of degradation. Nucleic acids often undergo a series of damaging processes as they are harvested from cells or tissue on their way to becoming purified. Improper storage, harsh extraction processes, and fixing processes for cells and tissues are all capable of inducing mechanical and chemical damage to DNA molecules. In the worst case, this degradation can cause irreversible damage and consequently reduce the fidelity of experimental results.