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 Innovation Network (GIN), the following three technology platforms provide researchers with access to cutting-edge genomics technologies to advance genomics research.

The Centre for Applied Genomics

Stephen Scherer, Lisa Strug

The Centre for Applied Genomics (TCAG) is dedicated to conducting and promoting groundbreaking research in genomics including service and training support for academic, government, and private sector scientists worldwide. Its development of new algorithms and methods for the analysis of whole genome sequence data underpin many major international research collaborations and embedded projects. Established in 1998, TCAG has served as a Science and Technology Innovation Centre since the inception of Genome Canada in 2001.

TCAG focuses largely on projects concerned with whole genome sequencing data, and maintains core facilities for: DNA sequencing and synthesis; cytogenomics and genome resources; microarray analysis and gene expression; genetic and statistical analysis; and biobanking and databases.

The technologies available at TCAG are supported by conventional DNA sequencing, targeted analysis of specific genes, synthesis of custom DNA fragments for specific assays and biobanking of blood, cell lines and DNA samples. TCAG hosts internationally-used databases like the Database of Genomic Variants, and has developed the Ontario Population Genomics Platform repository of control DNA samples.

In addition to providing these services, TCAG is actively involved in researching and developing innovative new methods for genome analysis, particularly as it relates to examining variation in the genome between individual humans, and how genes act together in networks and pathways to cause disease. TCAG’s activities and impact are acknowledged in hundreds of peer-reviewed scientific publications each year.

Ontario Genomics is currently funding The Centre for Applied Genomics (TCAG) as part of Genome Canada’s Platform Technology program.

The Centre for Phenogenomics

Colin McKerlie

The Centre for Phenogenomics (TCP, formerly “Toronto Centre for Phenogenomics”) is a state-of-the-art facility that enables groundbreaking research and discovery with the goal of advancing human health. Using mouse models, the TCP seeks cures and treatments in areas such as diabetes, cancer, musculoskeletal disease, neurodegenerative disorders, cardiovascular and renal disease, and stem cell and regenerative medicine. Jointly owned and operated by Mount Sinai Hospital and The Hospital for Sick Children, TCP serves local, national and international users.

Human diseases are characterized by complex interactions between genes (genotypes) and physical traits (phenotypes). Because of the similarity between mouse and human genomes, scientists can study this interaction in mice to learn how genes function and which mutations cause disease and to develop improved treatments for these diseases. TCP helps researchers analyze custom-designed mouse models with the same kinds of tests used on humans such as vision tests and medical imaging. It also provides support services to companies that are developing new drugs.

The TCP designs, generates, analyzes, archives, and distributes more than 250 genetically modified mouse models each year, providing scientists with the expertise and services they need to create mice with specific mutations and study their phenotypes – thereby supporting researchers in the quest to learn more about the causes of disease and develop improved treatments.

TCPs broad range of services include:

  • expert consultation and assistance to enable scientists to effectively execute their research projects; mutant model design and production to meet specific scientific needs;
  • analysis of mouse models including the identification of abnormalities and study of how mutations affect tissue structure and cause disease;
  • cryopreservation and distribution services using state-of-the-art and stringent quality-controlled technologies; and
  • informatics to provide online access to clients to assist them in project design, quality control and data analysis.

TCP supports excellent research, industry innovation, and a highly skilled workforce, all in the interest of improving human health.

The Network Biology Collaborative Centre

Jeff Wrana, Anne-Claude Gingras

The Network Biology Collaborative Centre (NBCC) provides Canadian scientists with a functional understanding of the role of genes and gene products in human health, and the impact of their alteration on the initiation and progression of disease.

Formed in 2014 from the amalgamation of two flagship Lunenfeld-Tanenbaum Research Institute facilities, the NBCC is composed of integrated, state-of-the-art facilities.

The Proteomics Facility uses mass spectrometers to precisely measure the “fingerprints” of protein fragments in order to identify which proteins assemble together into complexes to form cellular substructures, and/or propagate signaling cues within a cell. This type of analysis helps scientists to understand how these protein complexes assemble into signaling networks and how these networks become deregulated in diseases such as cancer.

The SMART High-Throughput and High-Content Screening Laboratory was one of the first high-throughput screening centres established in Canada. It uses robotic platforms and automated cell imagers to characterize and/or manipulate genes (or the proteins they encode) through genetic or chemical means to identify those of particular importance for disease initiation and progression.

The NBCC’s mandate is to assist Canadian and International scientists in their investigation of complex biological networks related to human health and disease by providing access to advanced instrumentation, proven workflows, and world-class expertise in functional proteomics and genomics.

The NBCC provides extensive expertise in the design and application of sophisticated screening strategies, as well as the ability to integrate these screens to drive biological insights. It works closely with its customers at every step to guide study design and implementation, ensure proper sample preparation and provide robust data review and analysis. The NBCC is poised to be a major Canadian resource for functional studies of genes and gene products relevant to human development and disease.

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