Sequencing capacity in a veterinary diagnostic laboratory

Virginia Polytechnic Inst And St Univ, Blacksburg VA

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Abstract

As technologies become available for better pathogen identification and characterization, challenges arise in standardizing use of these technologies. Illumina is offering a new platform, the iSeq, for less than $20,000 making this a viable option for diagnostic laboratories. A nanopore-based sequencer from Oxford Nanopore Technologies, MinION, complements and potentially replaces Sanger and Illumina sequencing because of the long reads (up to 1 megabase) and low cost of the instrument. We are in the unique position of having used this sequencer for the last 3 years and are able to compare ?affordable? sequencing instruments and standardize sequencing and analysis approaches. Key Project Areas 1. Validation of nucleotide sequence-based pathogen comparisons: Virginia Tech Animal Laboratory Services has been sequencing animal specimens for pathogen detection and characterization for 3 years since entry in the MinION ?Early Access Program?. We have used their mobile sequencer to accurately detect and genotype viral pathogens and perform whole genome sequencing of bacteria and viruses. As this technology matures, there is a need to identify common practices for pathogen sequencing for identification and characterization. We will compare nanopore-based sequencing to Illumina sequencing as well as to hybrid assembly using both. 2. based pathogen analysis: With new technologies come the need for new methods of analysis. ViTALS is currently using python-based open source programs to analyze data. We are working with our local Galaxy.org instance to implement these programs into a pipeline which standardizes the sequence analysis and allows other laboratories to follow the same protocol. These pipelines will be shared with other veterinary diagnostic laboratories which use MinION and Illumina sequencing. 3. Participation in additional projects: ViTALS has the intellectual infrastructure in place to conduct method development and validation as well as matrix extension as needed. If funding is received for this project, funds will be used enhance molecular diagnostic testing capabilities and are excited to investigate disease outbreaks as requested.