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Our Services

The CGEn centres 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 15 HiSeq X 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 Vancouver, Toronto, and Montreal.  Over the last 15 years, these centres have continually kept state-of-the-art genomics research accessible to all Canadian researchers serving over 1300 users 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 centres' culture of innovation led to a number of globally impactful discoveries. Highlights include:           

  • SARS: In 2003, the Vancouver team was the first in the world to decode the genome of the SARS Coronavirus, providing vital information within one week to assist infectious disease control Marra et al., 2003.
  • Personalizing Cancer Treatment: In 2010 the Vancouver team published the first ever case of a patient whose treatment decision was based on genomics information derived from the patient's tumor. These results laid the foundation for BC's Personalized Onco-Genomics program (POG) Jones et al., 2010; Sheffield et al., 2015 .
  • Advancing autism research through genomics: The Toronto team is a leader in applying whole genome sequencing (WGS) to autism research. Results of the first large scale WGS project in autism conducted at the Toronto centre have been published Nature Medicine Yuen et al., 2015 and the American Journal of Human Genetics Jiang et al., 2013.
  • Mapping the structural variations in the human genome: The Toronto team's contributions enabled a large scale discovery and mapping of copy number variations and  structural variations in the human genome Redon et al., 2006Pinto et al., 2010Conrad et al., 2010.
  • Human genome variation: In 2007, the Montreal team catalogued the single nucleotide polymorphisms in the human genome as part of the International HapMap Project, providing the cornerstone reference markers for the study of genetic variation in diseases and responses to therapeutic drugs International HapMap Consortium, 2007
  • Type 2 Diabetes: The Montreal team has established itself as a world-renowned leader in deciphering the genetic complexities of type 2 diabetes Sladek et al., 2007; Saxena et al., 2010; Gaulton et al., 2015.


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 27,000 human genome equivalents per year. This unprecedented Canadian research infrastructure ranks amongst the top few sequencing platforms in the world. 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 nearly 19,000 compute cores, over 20 Petabytes of storage, and an equivalent amount of archive storage. CGEn's partnership with Compute Canada enables access to additional relevant computational resources.

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