DNA Quality Indicators for Downstream Application Sample Selection


Biorepositories are the raw materials that fuel many important research projects in translational medicine. The availability of these human tissue samples facilitates progress into the progression and diagnosis of many important diseases. Biorepositories provide an important service to the research community by collecting large numbers of high quality annotated samples of diseased and normal tissue for clinical and basic science applications. Biorepositories must ensure the integrity and long term functionality of the samples collected. For this purpose, biorepositories use quality indicators. In the case of DNA, purity and integrity determination are most heavily used. We summarize a study that analyzed the quality indicators for 118 frozen human tissue samples, 68 formalin-fixed paraffin embedded (FFPE) samples, 119 frozen blood samples and 26 saliva samples. DNA quality results and their impact on various downstream methods are discussed and will determine the best source of DNA for various applications. Quantification and quality of DNA was determined by spectrophotometry, integrity analysis by electrophoresis, and quantification and integrity estimation by PicoGreen.

DNA banks provide researchers with high quality annotated DNA from a large number of sources. Research on the genetic determinants of disease as well as interactions with lifestyle and environmental factors would not be possible without these sources of samples. A wide variety of samples can be used in downstream applications. As such, DNA qualification is an essential process to guarantee the suitability of the material for research. In the paper the researchers analyzed usability, purity and integrity of the DNA as potential material for molecular testing.

Frozen tissues provide the best source of quality DNA; the usability and integrity of FFPE samples is questionable. Methods for using FFPE samples are improving, which opens up new avenues given the limited samples available. When a premium is placed on the quality of the extracted DNA, samples sourced from blood are the best option. However, collecting blood involves an invasive procedure. An alternative source of samples that does not suffer this problem is saliva. The disadvantage is that nonhuman DNA in the saliva must be discarded. The integrity of the DNA sourced from saliva is high, more so than the DNA from blood.

When choosing a source material for human tissue, the correct choice depends on availability and the target study in question. Blood offers the highest availability as frozen tissue depends on diagnostic interventions. Saliva can also be chosen when noninvasive methods are a crucial variable. DNA from biorepositories must be carefully considered with respect to downstream applications. This must be decided upon prior to consideration of distribution of samples. This allows for the availability of appropriate DNA such as frozen tissue for restrictive technologies.