What We Do

Our Services

CGEn nodes have combined their expertise to continue the adoption and integration of new technologies, the development of innovative protocols, the creation of new databases, and the pioneering of new bioinformatics tools to provide state-of-the-art genomics support to world leading research projects addressing important biological questions.

Our platform of sequencing instruments is accessible to Canadian and international researchers from all disciplines in academic, private, and government sectors alike for complete high-throughput, low-cost, and high quality sequence generation and analysis services to decode whole genomes from humans and other species. CGEn also provides additional services supporting a wide range of genomic applications.

Our Expertise

CGEn builds on the combined knowledge and expertise of the three regional centres in Toronto, Montreal and Vancouver.  Over the last 15 years, these centres have continually kept state-of-the-art genomics research accessible to all Canadian researchers serving over 2000 Principal Investigator laboratories per year from academic, private, and government sectors alike.  Disciplines extend far beyond biomedical and health research, such as environment, infectious disease, agriculture, forestry, fisheries, zoology, botany, ecology, metagenomics, biofuels, bioremediation, disease surveillance, evolutionary biology, and others.

The CGEn team also has a strong track record in method and technology development generating some of the earliest publications for RNA sequencing Morin et al., 2008, and for analyzing histone modifications Robertson et al., 2007.

A number of bioinformatics tools developed by the CGEn centres have been adopted by researchers across the globe, examples include the CIRCOS viewer, which provides a graphical synopsis of genomic changes and alterations Krzywinski et al, 2009, and the ABySS assembler, which was the first short read assembler capable of assembling mammalian sized genomes Simpson et al, 2009.

Our Infrastructure

In March 2016, CGEn completed the installation of 15 HiSeq X instruments with a combined sequencing capacity of over 35,000 human genome equivalents per year.  To stream line efficiencies in sample preparation, robotic liquid handling systems are integrated into the HiSeq X workflows and linked to laboratory information systems (LIMS). QA and QC programs for laboratory and bioinformatics processes ensure the highest quality of our services.

To enable the data processing and storage of this deluge of genomic information, the CGEn platform is supported by an equally impressive computational and data storage infrastructure, which currently includes over 50,000 compute cores, over 26 Petabytes of storage, and an equivalent amount of archive storage. CGEn’s partnership with the Digital Research Alliance of Canada enables access to additional relevant computational resources.

Our Technologies

Sequencing Technologies

  • Illumina HiSeq X
  • Illumina HiSeq 2500
  • Illumina HiSeq 4000
  • Illumina NovaSeq 6000
  • Illumina NextSeq 500
  • Illumina MiSeq
  • PacBio RS II
  • PacBio Sequel
  • Oxford nanopore MinION
  • ABI 3730XL

High Performance Computing

  • 50,000+ hyper-threaded cores
  • 25+ PB online disk storage capacity
  • 800+ desktop computer

Additional Technologies

  • 10X Genomics
  • Affymetrix Microarrays (GeneChip & GeneTitan)
  • Illumina Microarrays (HiScan & iScan)
  • Cytogenomics (FISH, karyotyping)
  • Agena MassArray System (formerly Sequenom)
  • Real-time qPCR and droplet PCR
  • TaqMan and Short Tandem Repeat (STR) profiling
  • DNA Extraction robotics
  • Cell culture/immortalization facilities
  • ThermoFisher Orbitrap Fusion MS
  • AB Sciex 5600+ TripleTOF
  • AB Sciex 6500 Q-Trap
  • ABI 4000 Q-Trap