May 6th, 2020

// Alberta Bioinformatics Expertise at Work in Health and Agriculture

Alberta Bioinformatics Expertise at Work in Health and Agriculture

CALGARY, May 6, 2020 /CNW/ - We are surrounded by data. Lots of it.  It is particularly true for genomics data, and the interpretation of complex sets of information have a significant role in improving the speed and effectiveness of applying genomic data in a number of areas.  

When the Enabling Bioinformatics Solutions funding competition was first announced, we identified agriculture and human health as two key areas that were generating large amounts of genomics data. Applicants were asked to submit proposals that would support the development of bioinformatic and computational approaches to help users overcome limitations in understanding, analyzing, and drawing conclusions from the genomic data being collected.  An independent panel reviewed the proposals and we are pleased to announce that a total of $1.1 million has been awarded to 5 projects.  

One of the successful projects is led by Tarah Lynch, Clinical Assistant Professor in the Department of Pathology & Laboratory Medicine at the University of Calgary.  Her project will help store and organize the terabytes worth of data generated by new high-throughput sequencing technology. HTS is used to gather all the genetic information contained within a microorganism. This provides a high-resolution genetic fingerprint to characterize and compare isolates to each other which is important for surveillance and infection control (e.g. outbreak investigations or antimicrobial resistance trends).

The resulting database from the project can be used by researchers in public health and clinical settings and will be compatible with Alberta Precision Laboratories current databases.  Tara Lynch said about her work, "This project focuses on building a strong foundation for genomics use in Alberta Precision Laboratories by creating infrastructure to organize, analyze and interpret genomic data from microorganisms such as bacteria and viruses. This project is co-led by collaborators in Calgary and Edmonton with the intention that these tools will be open source to extend their use for other genomic applications in the province."

In addition to the project led by Tara Lynch at the University of Calgary, 4 other projects were selected:

  1. Jason de Koning, University of Calgary, "An Open Platform for Rapid, Reproducible, Phenotype-Centric Variant Prioritization in Poorly Characterized Rare Genetic Disease" 
  2. Quan Long, University of Calgary, "Computational tools for viral pathogenesis and epidemiology using third-generation sequencing" 
  3. Rodrigo Ortega-Polo, Agriculture and Agri-Food Canada, "BeeBiome Data Portal" 
  4. Graham Plastow, University of Alberta, "Development and deployment of a computational tool for efficient whole-genome sequence association and prediction analyses"

David Bailey, President and CEO of Genome Alberta sees Alberta as home to global leaders in both health and agriculture genomics and said "Investments in bioinformatics will allow researchers to better understand and derive meaning from large, complex, genomic data sets. This will not only maximize the utility of previously generated data, but also help grow Alberta's capacity for big-data analyses. This is extremely relevant for improving the quality of care for Albertans in the era of precision medicine, as well as advancing Alberta's agricultural productivity and economy."

The Enabling Bioinformatics Solutions funding was made possible through a partnership involving Genome Alberta, Genome Canada, the Government of Alberta, and Alberta Innovates. 


1. An Open Platform for Rapid, Reproducible, Phenotype-Centric Variant Prioritization in Poorly Characterized Rare Genetic Disease
Total budget - $200,000
Project lead: Jason de Koning, University of Calgary

In rare disease research, identifying the genetic variants that cause an individual patient's disease can be like looking for a needle in a haystack by making informed guesses about where the needle may be. This project is intended to help enable more systematic, reproducible, and objective guesses via probabilistic reasoning and systematic prioritization models. 
The translational software platform developed by Dr. Jason de Koning, PhD, and team will allow these models to be customized, evaluated, and shared. It will be based on a variety of state-of-the-art and highly discriminating predictors derived from open data sources. Predictions will be made in the context of what scientists think they know about a patient's disease, and on measures of confidence in those beliefs.

2.  Computational tools for viral pathogenesis and epidemiology using third-generation sequencing
Total budget: $200,000
Project lead: Quan Long, University of Calgary

Third-Generation Sequencing (TGS) technology offers an exciting breakthrough opportunity for virology researchers. TGS can sequence the whole genome (including methylation status) in a single read, thereby, offering unprecedented opportunities to answer clinical and scientific questions related to viral evolution, transmission and pathogenesis. 
Dr. Quan Long, PhD, and his team will develop novel tools for the TGS and apply them to human immunodeficiency viruses (HIV). These tools will enhance our understanding of HIV, and will be widely applicable to study other viruses. 

3.  From sequencer to results: enabling routine genomics use for clinical and public health microbiology in Alberta
Total budget: $201,750
Project Lead: Tarah Lynch, University of Calgary

Academic scientists in Alberta currently use high-throughput sequencing (HTS) to gather vast amounts of data, such as detailed sets of genomic information in plants and animals. For public health, the data from microbial genomes can be used to enhance virus outbreak surveillance, patient treatment plans and infection prevention programs in hospitals.
Dr. Tarah Lynch, PhD, and her team are building a database to better organize and share HTS data across the province. The project also aims to improve the process used to interpret data and the way the analyzed data is displayed, ensuring it is in a format that is easier to interpret.

4. Sustaining bee population health for Alberta's agriculture system. BeeBiome Data Portal
Total budget: $384,288
Project lead: Rodrigo Ortega-Polo, Agriculture and Agri-Food Canada

Bees are fundamental to Alberta's agriculture, but are suffering severe declines worldwide due to multiple factors. The bee gut microbiome is the complex community of microorganisms living within the bee digestive system, and it directly impacts bee health and immunity. Now that a large amount of data on the bee microbiome is available, there is an urgent need for those data to be more accessible so that information can be applied for scientific discoveries and can be translated for stakeholder use.
The goal of this project is to advance the development of the BeeBiome Data Portal, which will allow analysis and sharing of information on the microorganisms and viruses associated with bees.
The outcome of the project will be greater accessibility to bee microbiome data and its use for new scientific discoveries and for translation efforts. This increased accessibility will benefit the scientific community, stakeholders and policy makers by enabling data-driven approaches to decision making regarding bee health.

5. Better cattle breeding predictions for Alberta producers
Total budget - $160,00
Project lead – Graham Plastow, University of Alberta

Results from the latest run of the 1000 bull genomes project, together with phenotypes and genotypes on tens of thousands of Alberta beef cattle, provides a vast amount of information that could greatly improve the accuracy of genomic prediction for economically important traits. 
The main challenge is to develop statistically powerful and efficient methods for largescale analysis of this information. The goal of this project is to develop a computing algorithm for such analysis. We plan to evaluate the algorithm for accuracy and develop a cloud-based platform that automatically runs the process.
This project will provide the Alberta beef industry and research institutions with a powerful tool for fast integration of sequence information into genomic research and applications. It should also improve the accuracy of genomic prediction compared to current methods.

About Genome Alberta
Genome Alberta is a publicly funded not-for profit corporation which invests primarily in large-scale genome sciences research projects and technology platforms focused on areas of strategic importance to the province (e.g. human health, forestry, plant and animal agriculture, energy, and environment).  By working collaboratively with government, universities, and industry, Genome Alberta is a catalyst for a vibrant life sciences cluster with far reaching social and economic benefits for Alberta and Canada. To date, the organization has managed a research portfolio with approved budgets totaling more than $255 million.  Please visit Genome Alberta's website for more information.

SOURCE Genome Alberta


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