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Data-driven solutions - the power of bioinformatics

Color coded DNA sequence on touch pad illuminated by light (Istock credit jxfzsy)Technological advances have led to an explosion in the amount of biologic, genetic and health data available to veterinary scientists.

The power of informatics to analyze and interpret this information has opened new avenues of discovery in veterinary medicine, providing opportunities to advance animal health and better understand and combat disease. Coined in the 1960s, the term informatics is by definition the science of processing data for storage and retrieval. Essentially, it uses computational techniques to bring together information from multiple sources of data.

A recent scoping review of veterinary medical and animal health literature conducted by Ben Ouyang (PhD candidate in epidemiology) with guidance from Jan Sargeant and Theresa Bernardo, researchers in the Ontario Veterinary College’s Department of Population Medicine at the University of Guelph, found the term informatics has trended upward over time with ‘bioinformatics’ first appearing in 1999 and rising rapidly since then. Bioinformatics studies tend to use genetic or protein data sources, compared to informatics studies which use a wider variety of data sources, such as electronic medical records, sensors and global positioning systems, she notes.

For Brenda Coomber and Geoff Wood, cancer researchers at the Ontario Veterinary College (OVC), bioinformatics helps them understand more about cancer genetics to potentially impact clinical treatment. Along with OVC researchers Paul Woods and Dorothee Bienzle, Coomber and Wood are studying canine lymphoma trying to determine why some dogs respond well to a four-chemotherapy combination called CHOP (a treatment also used in human lymphoma patients) while others do not.

Finding those answers began with a clinical study where they isolated and sequenced RNA and DNA collected from dogs who had been diagnosed with naturally- occurring lymphoma. The researchers wanted to look at RNA expressed by the dogs’ tumours and also compare differences in DNA between normal and cancerous tissues, an enormous amount of data.

“If you think of DNA as a string of four different letters, sequencing essentially takes all the DNA in a sample and makes a very long list of letters,” says Coomber. “Bioinformatics is able to take that enormous file of letters and make it into the equivalent of words and sentences.”

That’s really the power of bioinformatics, she adds. It translates information from biological systems and uses computer tools to make sense of it.

With this information, researchers can look for similarities and differences in genetic data, or identify where chunks of data are missing or moved around. Ultimately, from thousands of genes, they identified differences in eight genes that, collectively, seem to separate dogs that did well on the chemotherapy from those that did poorly.

The researchers hope study results will help better predict which dogs will respond to the CHOP treatment.

Wood has used bioinformatics in a number of studies, most recently in a collaboration with Wellcome Sanger Institute in the United Kingdom in the first ever cross-species DNA sequencing study to compare cancer genomes across human, canine and equine tumours. The tri-species study was designed to pinpoint key genes that are mutated in mucosal melanoma, a rare subtype in humans that is much more common in dogs, which can occur in non-skin locations such as nasal passages and mouth. The researchers sequenced the genomes of mucosal melanoma tumours from 46 humans, 65 dogs and 28 horses. Numerous canine and equine samples were provided by Wood and the Companion Animal Tumour Sample Bank, part of the Institute for Comparative Cancer Investigation at the University of Guelph.

“From a bioinformatic point of view it is meaningful to look at cancer genetics across species,” says Wood, “the differences and similarities can inform biology. Finding mutations that are common across species can help determine the most biologically relevant drug targets.”

The advanced availability of DNA sequencing is also impacting disease informatics, allowing researchers to sequence the entire genomes of both bacteria and the host animals they target to better understand when disease may occur.

Lots of animals may carry a pathogen but whether or not disease occurs depends on a number of factors – the pathogen, the animal host and the environment which together make up the disease triangle, says Nicole Ricker, a professor in pathogenomics and disease informatics at OVC. The microbiome, a collection of bacteria, viruses and other microorganisms that live in and on our bodies, is impacted by all three, she adds.

“We can look at a particular pathogen’s genomics and compare it to the genomics of the host animal and the microbiome so we can see which animals get disease versus which animals carry a pathogen but don’t show any evidence of disease,” says Ricker. Environmental factors, such as how many animals are housed together or if the host animal received antibiotics, are also important.

“Disease informatics brings all this information together to understand when a pathogen is going to be able to be successful and helps researchers identify ways to combat disease,” says Ricker.

The wide variety of data sources available also can enhance preventative medicine.

Health informatics is relatively new territory for veterinary medicine, but offers immense opportunities for veterinarians to offer new services to pets and their families, managing chronic diseases such as obesity, says Bernardo, IDEXX Chair in Emerging Technologies and Bond Centered Animal Healthcare.

She points to weight management for companion animals as an up-and-coming area with activity monitors for pets gathering information, similar to their human companions’ fitbits.

She envisions a future where pet owners can access an interactive app with a dashboard holding historical data about their pet, such as genomic and microbiome data, which will aid their veterinarians in defining diagnosis and treatment, as well as preventative approaches.

Adds Bernardo: “I think this is going to change the nature of what veterinarians do and presents new possibilities for them to offer a preventative medicine approach and ongoing coaching over the life of the pet.”

Originally published in The Crest, Summer-Fall 2019 issue. The Crest is the research, teaching and health care magazine of the Ontario Veterinary College, University of Guelph.