News Article

Does Your DNA Purification Method for NGS Really Matter?

Maureen Montogomery

Maureen Montgomery
Sr. Technical Training Specialist
Thermo Fisher Scientific

"it’s imperative to consider all the downstream applications when incorporating a new extraction method"

Tell us a bit about your job and journey in the field of HLA?

I am the Sr. Technical Training Specialist for our One Lambda branded NGS products. Before joining Thermo Fisher’s Transplant Diagnostics business, I spent 20 years working in the HLA Clinical Laboratories at the University of North Carolina and LabCorp using a variety of One Lambda products. I worked mainly on the molecular side with the validation of NGS assays and some R&D work as well.

Why is DNA Purification so important?

The quality of your DNA is critical to the results of your assay. If you have genomic DNA that is not intact (has small fragment sizes), it will greatly limit the quality of results and how successful they are. Ensuring a quality starting material is key to obtaining the best results possible.

Are all DNA extraction methods the same?

No - all DNA extraction methods are not the same. There are several ways to extract DNA, such as magnetic beads, spin columns and filter plates, among several others. It is crucial to the success of molecular assays that the DNA does not contain PCR inhibitors. When evaluating a DNA extraction method, it is a good idea to run several samples through all the assays in your laboratory to ensure the extracted DNA is suitable for all your methodologies.

Is the source of DNA (blood, etc.) important?

Generally speaking, you should be able to yield high-quality DNA from most sample sources for use in molecular assays. For HLA typing, most samples come from peripheral blood or buccal swabs. Blood samples tend to yield a higher concentration and longer fragments of DNA. Buccal swabs can sometimes be challenging since this type of sample doesn’t always yield DNA that’s intact and highly concentrated. The objective is to find an extraction method that works for your samples and gives you enough DNA to perform your assays successfully and consistently.

Based on manual or automated extraction, is there a difference in the quality of DNA?

The quality of DNA from the manual and automated extractors is typically within what would be considered normal variation between extractions. There are also cost and hand-on time differences to be measured between the two methods. Once again, just make sure that the final DNA is suitable to be used in your molecular assays.