"Incidental DNA fragments" may be misinterpreted using Next Generation Sequencing (NGS)

"Incidental DNA fragments" may be misinterpreted using Next Generation Sequencing (NGS)

October 19. 2016: A caution to industry and regulators

Published: Wednesday, October 19, 2016

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This article by leading DNA experts details challenges and pitfalls of DNA analysis used to verify the identity of herbal ingredients.

"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 AHPA President Michael McGuffin.

The article, "A caution to industry and regulators - 'Incidental DNA fragments' may be misinterpreted using Next Generation Sequencing (NGS)," is authored by Dr. Steven Newmaster, Professor, Botany & Genetics/Genomics at the University of Guelph, Dr. Subramanyam Ragupathy, Senior Scientist, NHP Molecular Diagnostics at the Biodiversity Institute of Ontario, and Dr. Robert Hanner, Chief Technology Officer (CTO) at TRU-ID Ltd.

"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 article states. "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."

The authors write that NGS results 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. This can result in conclusions that are irrelevant at best and potentially misleading, and in fact may only point to a trace amount of an inconsequential taxon that has no real relevance to the analysis or underlying research.

"During the past year we have responded to industry concerns that commercial NGS test results are reporting confusing results including considerable weed species in samples," the authors note. "This is not surprising since farm operations encounter considerable amounts of incidental DNA from agricultural weeds in every field; NGS is so sensitive it is possible it is detecting very small numbers of DNA fragments from weeds on a farm that are in only negligible amounts in the harvested crop."

The DNA experts conclude that NGS is a promising technology that will be commercially available for the food, supplement, and Natural Health Product (NHP) industries once the libraries and pipelines have been developed, validated, and published in peer-reviewed scientific journals. Their research team is contributing to the necessary research and development initiatives for NHPs, but community accepted methodological validation of such methods is still likely to be several years away.

"Even when completely validated, the use of NGS approaches will still require relatively expensive equipment operated by highly qualified personnel in ISO accredited test labs, or perhaps on-site by manufacturers with sufficient Quality Assurance/Quality Control (QA/QC) budgets," the authors write.

About the authors

Dr. Steven G. Newmaster

Professor, Botany & Genetics/Genomics
University of Guelph, 50 Stone Rd., Guelph, Ontario N1G2W1
Dr Newmaster is a botany professor specializing in plant diversity, medicinal plants and identification systems using DNA, analytical chemistry and morphometrics. He has more than 100 publications including numerous scientific journal articles and books. He has supervised over 220 HQP including visiting scientists from around the globe and he lectures to over 2000 university students every year. His research program has generated over $8 million dollars in research, funded by National and International funding agencies. His research lab is situated within the Centre for Biodiversity Genomics (CBG) at the Biodiversity Institute of Ontario. Currently he is conducting leading international research on genomic diversity in biodiversity and the development of molecular diagnostic tools for plant identification. His R&D has impacted Canadian policy on biodiversity, and international trade of herbal products including product authentication and certification standards within the food and natural product industry within Canada, USA, E.U. and Asia. He advises on the authentication of herbal products to regulators and is developing new QA/QC industry standards for testing natural ingredient authenticity. He is one of the founders for the world’s first international certification program (TRU-ID) of natural biological ingredients used in Food and NHP.

Dr Subramanyam Ragupathy (“Ragu”)

Senior Scientist, Molecular Diagnostics Lab
Biodiversity Institute of Ontario, University of Guelph, 50 Stone Rd., Guelph, Ontario N1G2W1
Ragu attained my PhD in botany and genetics followed by a post doctorate in ethnobotany genomics. His has over 80 publications including books and journal papers on genomic diversity and molecular diagnostic tools for plant identification. He has discovered and described several new plant species (in India and China), and plant based medicine and food; currently he is working on DNA-based tools for the identification of coffee, tea and chocolate.  Ragu is the curator of the Biodiversity Institute of Ontario’s BIO Herbarium, and has developed Standard Biological Reference Material (SBRMs) DNA libraries for 1500 herbal products. He has co-developed TRU-ID commercial DNA probes (TRU-ID.net) and lab SOPs for new industry standards in natural ingredient identification and authentication.  He also has over 25 years experience in herbal industry raw material procurement and supply chain sources of NHPs in India & North America. His research has identified a number of problems with the mislabeling of food and natural health products in North America and Asis and has impacted policy on biodiversity, and international trade of herbal products including product authentication and certification standards within the food and natural product industry within Canada, USA, E.U. and Asia.

Dr Robert Hanner

Chief Technology Officer (CTO), TRU-ID Ltd
Research Park Centre, Suite 102, 150 Research Lane, Guelph, Ontario N1G 4T2
Robert holds a PhD degree in biology and has worked in the field of DNA – based species recognition for over 20 years. He is an Associate Professor in the department of Integrative Biology at the University of Guelph. He is also the Campaign Coordinator for the Fish Barcode of Life Initiative and has published widely on the molecular identification of fish. Previously he served as the Scientific Program Director for cell repositories at the Coriell Institute for Medical Research and as Curatorial Associate at the American Museum of Natural History. There he spearheaded the establishment of the Ambrose Monell Collection for Molecular and Microbial Research. His research has pioneered the use of molecular diagnostic tools to detect market adulteration in the seafood supply chain and the development of molecular probes. These can be utilized to drive forward the in-client product testing capabilities demanded by the industry.

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