Next-generation sequencing capacity and capabilities within the National Animal Health Laboratory Network |
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| Authors: | Beth Harris Jessica Hicks Melanie Prarat Susan Sanchez Beate Crossley |
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| Institution: | USDA-APHIS-VS-DB National Animal Health Laboratory Network, Ames, IA;USDA-APHIS-VS-DB National Veterinary Services Laboratories, Ames, IA;Ohio Department of Agriculture Animal Disease Diagnostic Laboratory, Reynoldsburg, OH;Athens Veterinary Diagnostic Laboratory, Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA;California Animal Health and Food Safety Laboratory, University of California–Davis, Davis, CA |
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| Abstract: | With the cost of next-generation sequencing (NGS) decreasing, this technology is rapidly being integrated into the workflows of veterinary clinical and diagnostic laboratories nationwide. The mission of the U.S. Department of Agriculture–National Animal Health Laboratory Network (NAHLN) is in part to evaluate new technologies and develop standardized processes for deploying these technologies to network laboratories for improving detection and response to emerging and foreign animal diseases. Thus, in 2018, the NAHLN identified the integration of NGS into the network as a top priority. In order to assess the current state of preparedness across NAHLN laboratories and to identify which have the capability for performing NGS, a questionnaire was developed by the NAHLN Methods Technical Working Group and submitted to all NAHLN laboratories in December 2018. Thirty of 59 laboratories completed the questionnaire, of which 18 (60%) reported having some sequencing capability. Multiple sequencing platforms and reagents were identified, and limited standardized quality control parameters were reported. Our results confirm that NGS capacity is available within the NAHLN, but several gaps remain. Gaps include not having sufficient personnel trained in bioinformatics and data interpretation, lack of standardized methods and equipment, and maintenance of sufficient computing capacity to meet the growing demand for this technology. |
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| Keywords: | animal diseases bioinformatics questionnaire whole-genome sequencing |
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