As new and improved genotyping technologies become easier and easier to use, researchers and specialists are finding more and more applications for these tools. Dr. Armand Sanchez, professor of genetics at the Autonomous University of Barcelona, spoke to us about his work for VetGenomics, a company he spun off from the university that has offered veterinary genomics services for 10 years using Applied Biosystems technology. VetGenomics is in the process of bringing genotyping-by-sequencing (GBS) tools and protocols into its practice to update and replace older microsatellite-based genotyping methods.
Is SNP-based targeted GBS a good technique for companion animal genotyping?
VetGenomics currently uses gene panels for its work with dogs. They are involved in a project to control fecal samples in the streets of local communities. “As dogs often share waste deposition sites, VetGenomics’s canine panel is not only for paternity or individual identification, it also includes mitochondrial DNA markers to help them determine whether a particular sample contains DNA from multiple dogs and disambiguate the resulting data,” Dr. Sanchez explains.
The panel has been refined over two years and has been working well, but Dr. Sanchez hopes to switch to a GBS protocol for their work with dog feces for improved ease and efficiency. Moving from the existing panel to GBS is, according to him, “the next step that we need to do.” Applied Biosystems products, such as the AgriSeq Canine SNP Parentage & ID and AgriSeq Canine Traits and Disorders, are among the options available.
What kind of overall impact will ready-to-use GBS panels have on animal genotyping?
Prof. Sanchez is firmly convinced that GBS panels are the future of animal genotyping and that the rest of the genotyping community will not be far behind him in embracing this new technology. “Remember 15 to 20 years ago when microsatellites started to run in routine analyses in labs?” he asks, referencing the previous paradigm shift in applied genotyping. As GBS kits become more and more complete and ready out of the box, more and more labs will adopt them rather than put work into developing their own tools: “If there’s a tested kit that covers your needs, why not use it? This is one thing that I am sure that, at the commercial level, more labs will adopt.” Ready-to-use GBS panels make this technology more accessible to more labs, improving the reach of genotyping technology and creating space for more and more applications of genotype data.
How do you see this work evolving over time?
Many current genotyping labs do not have the equipment required for genotyping by sequencing, but this is guaranteed to change. When microsatellites and gene chips were new, there was a race to adopt these new technologies because of their clear benefits over their predecessors. GBS is no different, and that is the position that VetGenomics is in right now. Drawing an analogy to medical testing, Dr. Sanchez points out, “In most hospitals right now, they have high-throughput sequencing machines because they are routinely testing panels of markers for cancer and many other diseases. That’s exactly the same as is happening in our market. So, for companion animals, most animal genomics labs will adopt this technology,” especially as it becomes more affordable and the possibilities it offers become more and more standard and expected for even lower-end genotyping projects.
Do you have advice for a new lab that is starting to explore targeted GBS for companion animal genotyping and breeding?
Prof. Sanchez answers this question simply: “Don’t be afraid.” Migrating to new sequencing tools and platforms, including genotyping by sequencing, is easier than it seems, especially for labs that already have experience migrating to microsatellites and other recent developments in genotyping. Software for reading and translating results into usable data gets more and more user-friendly each generation, making each switch easier than the one before it. Starting with prebuilt GBS panels also means that other labs with relevant experience can assist with any difficulties one might experience, and Thermo Fisher Scientific is always available for more direct assistance.
How has Thermo Fisher Scientific helped VetGenomics?
Prof. Sanchez and VetGenomics have used Applied Biosystems technology for many years and consider themselves early adopters of many Applied Biosystems tools and platforms. They regard their relationship with Thermo Fisher Scientific as “excellent” and particularly appreciate the ongoing nature of this relationship when it comes to finding new approaches and solving new problems. Prof. Sanchez summarizes his experience: “I hope that we continue in the future.”
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io games says
“Remember 15 to 20 years ago when microsatellites started to run in routine analyses in labs?” i really surprise with this ques tion