DNA Experts Warn Against Misuse of Next-Generation DNA Sequencing in AHPA Article

Photo © iStockphoto.com/Сергей Хакимуллин

An article published this week on the website of the American Herbal Products Association (AHPA; Silver Spring, MD) cautions the supplements industry and regulators against falling for a few perilous pitfalls associated with DNA testing herbal ingredients with Next-Generation Sequencing (NGS) techniques. While the authors note that NGS can be a useful tool, it can also provide dramatically misleading findings on the identity of an herbal ingredient based only on trace amounts of incidental DNA fragments.

“As the industry struggles to make use of DNA testing amid widely divergent claims and opinions on the readiness of this new technology to enter the pantheon of reliable testing methods, examining the strengths and limitations adds an important component to the conversation,” said Michael McGuffin, president of AHPA, in a press statement.

The article is authored by Steven Newmaster, PhD, professor of botany and genetics/genomics at the University of Guelph; Subramanyam Ragupathy, PhD, senior scientist, MHP molecular diagnostics at the Biodiversity Institute of Ontario, and Robert Hanner, chief technology officer at TRU-ID.

One of the biggest problems with NGS, the authors write, is that it “may indicate presence of species in a sample due only to detection of incidental DNA, and may also over-estimate the amounts of incidental DNA.” Incidental DNA, such as the negligible amount of DNA from weeds that may appear in a collected crop, is a somewhat inevitable guest in any plant harvest.

What’s more, the authors point out, “pharmacopeial botanical monographs specifically allow some small amount-usually 2 to 5 percent-of “foreign organic matter,” which may reasonably include other plant parts of the target species, or inadvertent but minimal presence of other species that may be co-mingle in a harvested crop.” Unfortunately, NGS testing cannot quantify the amount of different plant DNA appearing in a sample, therefore making it easy to mistake incidental DNA with a more serious contaminant issue.

Furthermore, the article authors also note that the foodborne pathogen industry has not adopted NGS technology because it has “not yet been able to overcome the above issues in order to provide a statistically valid test; and when applied to detection of food pathogens, the possibility of a false positive result can cause significant business disruption, while any chance of a false negative is well understood to be an unacceptable threat to public health.”

The authors conclude that NGS testing might be made more accurate with certain improvements, such as the development of “bioinformatics algorithms that adjust the estimates of sequence abundance from NGS per species” or other necessary research and development initiatives, but that such validated methods are still “likely to be several years away.” Even then, the use of NGS will still require expensive equipment operated by highly-trained personnel, the researchers note.

“NGS is a powerful research tool, as it is very useful for detecting multiple sources of DNA in a single analysis, a quality that can be useful in answering certain research questions,” the authors explain. “But the published literature indicates there are considerable problems with NGS that present an immediate impediment to generating scientifically valid test results, as are necessary for commercial use of this tool to verify herbal ingredient identity, and that therefore require additional research.”

Read more:

New DNA Test Method Lets Probiotic Firms Test Multistrain Blends: SupplySide West Report

Now Foods Begins DNA Testing Probiotics

Next-Generation DNA Testing for Botanicals

Michael Crane
Associate Editor
Nutritional Outlook Magazine
michael.crane@ubm.com