Technology Platforms

Ontario Genomics facilitates access to genomics technologies to support the genomics research community.

Ontario Genomics has historically funded several primary genomics and proteomics platform technology services utilizing Genome Canada funds, service revenues, the Ontario government (MRI-ORF, ORDCF, OIT, etc.) and other funders such as CFI.

As part of the Genomics Technology Platforms (GTP), the following four technology platforms provide researchers with access to cutting-edge genomics technologies to advance genomics research in Ontario.

The Centre for Applied Genomics

Project leaders: Stephen Scherer, Lisa Strug (The Hospital for Sick Children)
Genome Center: Ontario Genomics
Total Funding: $11.6 million

The Centre for Applied Genomics (TCAG), founded in 1998, has been a Genome Canada Science and Technology Platform since 2001. TCAG provides genomics support and analysis to more than 800 Principal Investigator labs per year, a total of more than 2,000 over its lifetime, spanning 45 countries, 317 academic institutions, 150 companies and 46 government agencies and non-governmental organizations. Through its work, TCAG has catalyzed many significant scientific advances. TCAG developed and hosts the Database of Genomic Variants and the Ontario Population Genomics Platform repository, leads the “MSSNG” autism genome sequencing project and the Canadian Personal Genome Project, and is the Toronto node of Canada’s Genomics Enterprise (CGEn), a national network of whole genome sequencing centres.

With additional funding from Genome Canada, TCAG will continue to actively develop novel methodologies for whole genome sequencing, genome assembly and statistical analysis of genome-wide data. These activities will complement the development and implementation of additional pipelines and methods for generating and analyzing genomic data. TCAG will continue to work with national and international partners to advance the utilization of genomics to address many facets of multidisciplinary science, including a strong focus on human diseases and neurodevelopmental disorders.

The Centre for Phenogenomics

Project leaders: Colin McKerlie, (The Hospital for Sick Children) Silvia Vidal (McGill University)
Genome Center: Ontario Genomics, Génome Québec
Total Funding: $7.5 million

Discovering and understanding the function of genes and abnormalities in genes (“mutations”) that cause disease in children and adults remains a major challenge. Researchers use mouse models to evaluate the impact of these mutations, but need access to state-of-the-art services to enable their research. Since 2007, The Centre for Phenogenomics (TCP) has been providing these services, designing and producing customized mouse models, determining the functional consequences of genetic abnormalities, validating a phenotype (”observable characteristics that result from a mutation”) comparable to the human disorder, and investigating the underlying molecular pathways. It also supports translational services to reverse the effect of the mutations through genetic or pharmaceutical approaches. In the past five years, TCP has provided more than 40,000 services to 615 clients, generating nearly $13 million in revenue. A Canada Foundation for Innovation review panel called TCP “the best facility of its kind in Canada and … among the top five in the world.” TCP brings together a unique Canadian critical mass of infrastructure, expertise, interaction and technology. Over the coming five years, it will expand its research services to infectious diseases and inflammatory conditions, both of which are common and major health and economic burdens to Canada. To support Canadian scientists’ efforts to understand gene function and the genetic changes that cause disease, TCP will provide Canadian scientists with unparalleled access to leading-edge genomic services in disease model production and evaluation. TCP will also continue to develop new technologies and enhance existing ones to deliver state-of-the-art services, thereby maintaining its competitiveness and that of its users.

Network Biology Collaborative Centre

Project leaders: Jeff Wrana, Anne-Claude Gingras (Lunenfeld-Tanenbaum Research Institute, Sinai Health System)
Genome Center: Ontario Genomics
Total Funding: $6.7 million

The Network Biology Collaborative Centre (NBCC) at the Lunenfeld-Tanenbaum Research Institute was founded in 2014 to assist scientists with coupling the vast understanding of genomic and phenotypic variation in health and disease with a functional understanding of how gene products convey biological information and how their alterations drive disease.

The NBCC is built on one of Canada’s first proteomics mass spectrometry facilities and one of the first academic screening centres, which date back to 1999. Since that time, the Centre and its precursors have provided critical support for high-impact research and the translation of that research into an understanding of disease mechanisms, increased economic activity and potential new treatments and improved health outcomes.

The NBCC currently operates through multiple complementary nodes: proteomics, high-throughput screening including next-generation sequencing, and high-content to high-resolution imaging. The NBCC provides not only its extensive expertise in the design and application of sophisticated screening strategies through these nodes, but also its ability to integrate these screens with each other to drive biological insights.

By continually innovating, improving and implementing new technology, NBCC continues to offer the highest-calibre services. Over the next five years, the Centre will extend its proteomics and functional genomics screening into more sophisticated systems that will better model health and disease states, and continue to integrate data management and analytics across all of its nodes. Through its work, it will help to ensure that future scientists remain internationally competitive and drive their science to realize the greatest benefits for Canada.

Canadian Data Integration Centre

Project leaders: Philip Awadalla, Lincoln Stein, Vincent Ferretti, Jared Simpson, John Bartlett (Ontario Institute for Cancer Research)
Genome Center: Ontario Genomics
Total Funding: $7.8 million

The Canadian Data Integration Centre (CDIC) is an international leader in genomics, bioinformatics and translational research, supporting some of the world’s largest programs in genomic data analysis, genomic and clinical data hosting, cancer data analyses and access and the development of algorithms for advanced sequencing technology. The CDIC’s services range from small, bespoke data integration solutions to comprehensive large-scale genomic analyses and include the ability to handle difficult and small-volume biosamples, enabling investigators to maximize the utility of scant or rare clinical tissues. Its informatics and bio-computing core is the largest academic cancer informatics program in Canada and it is the only site in Canada to offer 3rd generation bioinformatics tools for researchers in genomics and functional and clinical genomics. In its first five years, CDIC has generated $87 millions in grants and $14 million in service revenue.

Over the next five years, CDIC will develop new technologies and methodologies for long-read sequencing, for research and clinical application; roll out translational biomarkers of therapeutics response and prognosis for clinical applications and services; and develop already-identified pan-cancer biomarkers for biopsy diagnoses to make them clinic- and industry-ready.

Platform Affiliates Program

As part of its mandate, Ontario Genomics has established the formal Ontario Genomics Platform Affiliates (OGPA) program and framework to increase access to genomics technology and resources, and further support the genomics research community.

Designation as Platform Affiliate (PA) facility is intended:

  • to increase the visibility and use of PAs by the research community;
  • to create greater leverage in negotiating access to or vendor discounts on leading-edge genomics technology and reagents; and
  • to facilitate the (mutually agreed upon) sharing of capacity, information and strategy among PAs.

Ontario Genomics’ strategic perspective in this program seeks to create greater connectivity, both among Ontario’s genomics platform technology service facilities and between them and their users (research scientists) and providers (vendors).

Advanced Analysis Centre Genomics Facility (AAC)

Guelph University’s AAC platform services include:

  • DNA sequencing and fragment analysis using an Applied Biosystems 3730 Capillary DNA Analyzer.
  • Microarray chip printing using a Virtek VersArray Chipwriter Pro.
  • Gene Expression Service including RNA labeling, hybridization and scanning of hybridized microarrays.
  • Microarray scanning using the Axon 4200A scanner.
  • Total RNA and mRNA quality and quantity assessment using an Agilent BioAnalyzer 2100.
  • Self or full service Real Time PCR analyses using an Applied Biosystems Step One Plus.
  • Access to software packages including CLCBio Main Workbench, Sequencher, Acuity, Gene Spring, Primer Express 3.0.

London Regional Genomics Centre (LRGC)

Robarts Research Institute’s LRGC platform services include:

  • Next-Generation Sequencing on the Illumina MiSeq and Ion Torrent PGM
  • Affymetrix GeneChip system services
  • Real-Time qPCR on Life Technologies ViiA7
  • Qualitative assessment of RNA via Agilent 2100 Bioanalyzer
  • DNA data analyses software (Partek Genomics Suite, Partek Pathway, CLC Genomics Workbench, Ingenuity Pathway Analysis)
  • DNA Sanger Sequencing using the ABI 3730

Princess Margaret Genomics Centre

The Princess Margaret Genomics Centre platform services include:

  • Microarrays (Affy, Agilent, Illumina, UHNMAC)
  • Validation Services (Nanostring, Xceed Ziplex)
  • Protein Profiling (Axela DotLab, Bio-Rad Bioplex)
  • RNA, DNA, Protein QC (BioAnalyzer, NanoDrop, Caliper)
  • Custom Arraying
  • Clone Production

Clinical Genomics Centre

The Clinical Genomics Centre platform services include:

  • Next generation DNA sequencing (Illumina/Solexa GAII)
  • SNP genotyping (Illumina Beadstation, Sequenom MassARRAYTM
  • Affymetrix GeneChip system
  • DNA sequencing ABI 3730xl Genetic Analyzer and ABI PRISM® 7900HT Sequence Detection System

The Centre for the Analysis of Genome Evolution and Function (CAGEF)

University of Toronto’s CAGEF platform services include:

  • Next generation sequencing technologies using the Illumina/Solexa Genome Analyzer II, MiSeq
  • Bio-Array Resource (web based Arabidopsis resources)
  • Ettan sample prep station
  • Thermo Fisher Scientific LTQ OrbiTrap mass spectrophotometer equipped with a nano 2D-LC system.
  • Biacore 3000
  • Certified Affymetrix Core Facility
  • DNA Sequencing with Applied Biosystems 3730 DNA Analyzer
  • FACS-Aria flow cytometre for cell sorting and counting

StemCore Laboratories

Ottawa Hospital Research Institute (OHRI)’s StemCore Laboratories platform services include:

  • Next generation sequencing technologies using the Illumina/Solexa Genome Analyzer II
  • Flow Cytometry Facility
  • Certified Affymetrix Core Facility
  • DNA Sequencing with Applied Biosystems 3730 DNA Analyzer

Donnelly Sequencing Centre (DSC)

The Donnelly Sequencing Centre platform services include:

  • All aspects of library preparation and QC, including Caliper’s next generation separation solutions 1. genome-resequencing
  • Metagenomic sequencing
  • Chip-seq
  • RNA-seq (directional and non-directional)
  • Multiplexing samples (by PCR and PCR-free)
  • Tag sequencing
  • Full suite of Affymetrix instrumentation, hybridization ovens, fluidics stations and 7G scanner.

The McMaster Genomics Facility

The McMaster Genomics Facility platform services include:

  • Illumina Custom Genotyping
  • Illumina Pre-designed Genotyping-Infinium
  • Illumina Whole Genome Gene Expression
  • ABI TaqMan Genotyping
  • DNA extraction