CGEn’s Response to COVID-19

CGEn’s Response to COVID

Over the last few months CGEn through its nodes in Toronto, Montreal and Vancouver have joined the fight against COVID-19 by leveraging our best resources – our people, expertise and infrastructure.  As many research laboratories, companies and government agencies are laser focused on finding ways to stop the spread of COVID-19, CGEn is doing its part both collectively and individually. Here is a brief summary of CGEn’s ongoing response to COVID-19:

  1. CGEn will lead Canada’s COVID-19 host genome sequencing initiative as part of Genome Canada’s newly launched Canadian COVID Genomics Network (CanCOGeN). An investment of $20 million from the federal government will enable this initiative which includes sequencing 10,000 Canadians affected by COVID-19.
  2. CGEn is working with strategic partners to develop databases and tools to store and share COVID-19 related genomic data to researchers and public health agencies globally
  3. CGEn-Montreal is leading the set up and management of the province wide COVID-19 biobank
  4. CGEn-Toronto, through strategic partnerships with the McLaughlin Centre at University of Toronto, is assisting investigators access COVID-19 research funding to conduct critical studies
  5. CGEn-Vancouver is assisting the province of British Columbia Centre for Disease Control by developing and implementing automated high throughput viral nucleic acid extraction and investigating alternate sustainable reagent sources. They are also conducting naso-pharyngeal metagenome analysis for the presence of microbial species that may influence disease trajectory
  6. All three CGEn nodes have made safeguarding of staff a priority with strict social distancing measures in place, and non-essential staff working from home
  7. CGEn Toronto and CGEn-Vancouver continue to support important non COVID related research especially in cancer and paediatric development
  8. CGEn is supporting scientists across the country to apply for the many newly launched COVID-19 related grant funding programs.

COG-UK Partnership

The COVID-19 Genomics UK (COG-UK) consortium and the Canadian COVID Genomics Network (CanCOGeN) launch new partnership

COG-UK and CanCOGeN are working together to share knowledge and protocols

News announcement: 4 May 2020

The COVID-19 Genomics UK (COG-UK) consortium is collaborating with the newly formed Canadian COVID Genomics Network (CanCOGeN) as it launches a national sequencing network to monitor the pandemic’s development.  By sharing knowledge, lessons learned and protocols , the initiatives will each support national efforts to coordinate the work of healthcare, public, private and academic organisations to sequence and analyse the spread and evolution of the SARS-CoV-2 virus and how it affects patients. The partnership will also allow both groups to share insights and discoveries to drive understanding of the pandemic as it changes over time.

For further details, click here.

NR-April-23-2020

CGEn joins Canada’s fight against COVID-19 with the launch of Canada’s COVID-19 Host Genome Sequencing Initiative

CGEn will receive $20 million in Federal funding to sequence the genomes of thousands of Canadians, in order to better understand the variable clinical response to COVID-19.

April 23, 2020 – OTTAWA, Ontario – Following an announcement by Prime Minister Justin Trudeau, the Federal Government is committing $40 million to support Genome Canada’s launch of the newly formed Canadian COVID Genomics Network (CanCOGeN). This investment includes $20 million in funding to CGEn, Canada’s national facility for genome sequencing and analysis, to lead a nation-wide Host Genome Sequencing Initiative with the aim to sequence genomes of 10,000 Canadians affected by COVID-19.

As the national and global data on the infection and disease burden evolve, the risk factors for severe illness are still being established. Older patients and those with chronic medical conditions appear to have higher risk, although disease severity varies among individuals with similar levels of exposure. This implies an important role played by the human host genome in response to the virus.

“This investment will allow CGEn to harness the power of our Canadian genomics infrastructure to explore the genetic architecture of the human genome”. said Dr. Naveed Aziz, Chief Administrative & Chief Scientific Officer at CGEn. “Canada’s COVID-19 Host Genome Sequencing Initiative promises to generate new knowledge and provide much-needed data to support diagnosis, prognosis, and treatment of this devastating pandemic, and those that will surely follow”.

CGEn’s team of renowned researchers from across Canada will work together to decode the genomes of thousands of Canadians across the country, who have been infected with the virus causing COVID-19, or are still at risk of infection. CGEn will develop and bring access to an information-rich, national database which will serve as a resource to catalyze national and international research to help determine why people experience vastly different health outcomes.

“The emergence of COVID-19 at the footsteps of SARS and MERS highlights a significant issue –   that there will be similar outbreaks of severe infectious disease in the future. This investment from the Government of Canada addresses the current COVID-19 outbreak, prepares Canada for a possible re-emergence, and lays the foundation to handle future pandemics”, says Dr. Stephen Scherer, CGEn Principal Investigator and Professor of Genome Sciences at the Hospital for Sick Children and University of Toronto.

Canada’s COVID-19 Host Genome Sequencing Initiative will be led by CGEn, a national platform for genome sequencing and analysis, developed to be response-ready to large-scale Canadian scientific challenges. CGEn has already developed regional, national, and international linkages to ensure that this project will have maximal impact for the health of Canadians.

“CGEn brings to the CanCOGeN partnership table the ability to undertake host genome sequencing on an unprecedented scale. Understanding the disease burden – why in some cases people get very sick and others do not – is essential in helping us identify individuals at highest risk and take proactive measures to protect them and the frontline workers treating them. These measures could include more targeted, patient-specific therapies as well as better public health policies in preparation for secondary waves or future pandemics,” said Dr. Rob Annan, President and CEO, Genome Canada.

CGEn scientists were the first to sequence the SARS genome in 2003 and determine it to be a coronavirus. This funding will further Canada’s salient contributions to our understanding of the genetic interactions and genomics of coronavirus infection” said Dr. Steven Jones, Principal Investigator CGEn-Vancouver node and Co-Director & Head, Bioinformatics, Genome Sciences Centre, while Mark Lathrop, Principal Investigator CGEn-Montreal node and Professor, Human Genetics, McGill University added “This initiative highlights the importance of the government’s investments in national research infrastructures such as CGEn which are necessary to assure that Canada can respond to globally important challenges including health dangers such as COVID-19”.

About CGEn

CGEn, funded primarily by the Canada Foundation for Innovation (CFI) and Genome Canada, and leveraging investments from other stakeholders, is a genome sequencing and analysis network operating as an integrated national platform with nodes in Toronto (The Centre for Applied Genomics at The Hospital for Sick Children), Montréal, (McGill Genome Centre at McGill University) and Vancouver (Canada’s Michael Smith Genome Sciences Centre). CGEn’s mission is to enable Canadian science in basic and clinical research through the characterization of genome sequences, the promotion of genome research in Canada, and by building and operating an unprecedented infrastructure that enhances our national capacity for sequencing and informatics analysis.

CGEn Year in Review: Highlights of 2019

CGEn Year in Review: Highlights of 2019

Enabling Canadian leadership in genomics research by supporting world-class research or technology development

  • In 2019, using the infrastructure funded by the Canadian Foundation for Innovation (CFI), CGEn completed the delivery of over 18,000 whole genome, 39,500 transcriptome, 5,359 exome, and 110,611 other genome-wide experiments on biosamples from Canadian research projects, including human and non-human studies.
  • CGEn’s flagship  CanSeq150 program, committed to de novo sequencing of 150 novel Canadian species, has now selected over 90 species as individual projects. Data delivery is complete for some and sequencing is now well underway for many other projects. See full list of projects here.

CGEn scientific leaders acknowledged for their contributions through prestigious awards and recognitions.

  • Dr. Stephen Scherer, (Scientific Director, CGEn-Toronto) was awarded the Killam prize in health sciences. Dr. Steven Jones (Scientific Director, CGEn-Vancouver) was awarded the first Tier 1 Canada Research Chair in Computational Genomics and Dr. Marco Marra was awarded the Don Rix Award for Lifetime achievement by Life Sciences BC.
  • CGEn investigators Dr Steven Jones and Dr Marco Marra were named on the highly cited list in 2019

CGEn researchers made significant scientific contributions to genomics research and precision medicine

  • The Autism MSSNG project reached its initial goal of sequencing more than 10,000 whole genomes of individuals with autism and their family members, creating the world’s largest open-source precision medicine database specific to understanding autism.
  •  Exciting high-impact research findings from all three nodes have been disseminated through peer-reviewed publications. A few examples of such findings are the development of single-cell sequencing approaches to detect changes in Cancer, identification of predictive markers for early diagnosis of Autism, and single-cell transcriptomics to define developmental mechanisms in Childhood Brain Tumors.

Mark Caulfield

Mark Caulfield, Genomics England interim CEO & CGEn’s Board of Directors member awarded knighthood in the Queen’s birthday honours.

Professor Mark Caulfield, the interim Chief Executive at Genomics England and Professor of Clinical Pharmacology at Queen Mary University of London, has been awarded a knighthood in the Queen’s Birthday Honours List.

Since 2013 Professor Caulfield has been instrumental in delivering the world-leading 100,000 Genomes Project, which hit its target of sequencing 100,000 whole genomes in 2018 and has already delivered life-changing results for patients.

This NHS transformation programme used whole genome sequencing to bring new diagnoses to people with rare diseases and to help choose cancer therapies.

To increase the value for participants in the project, Professor Caulfield established a coalition of 3,000 researchers worldwide and assisted the NHS in the creation of the National Genomic Test Directory. This will offer equitable access for 55 million people, depending on clinical need, to the appropriate genomic tests via a new National Genomic Medicine Service.

For further details, click here.

GrizzlyBear

Canseq150 helps Canadian scientists map the Grizzly genome.

Among the largest predators in country, the Grizzly bear now has another claim to fame: the most complete genetic map for its species. Within 37 pairs of chromosomes composed of about 2.3 billion nucleotide base pairs, scientists have now revealed the location of 19,848 coding genes, 7,061 non-coding genes, 3,671 pseudo-genes, and more, within the Grizzly genome.

The Grizzly bear DNA was sequenced from a 20-year old male named Samson. He was found as an orphan in Alaska in 1998, when he was less than a year old, rescued and then raised at the Alaska Children’s Zoo. He now lives at the Toronto Zoo. The blood sample donated to the GSC was collected during a routine physical exam.

Published in the journal, Genes, the sequencing effort was performed at Canada’s Michael Smith Genome Sciences Centre at BC Cancer, a leading international centre for genomics and bioinformatics research. Dr. Steve Jones, GSC Co-Director and Head of Bioinformatics, was the Principal Investigator.

CanSeq150

Canada’s Genomics Enterprise launches CanSeq150 to lay the foundation for Canada’s next 150 years of science.

To commemorate the 150th Birthday of Canada in 2017 and to lay the foundation of Canadian excellence in research for the next 150 years, Canada’s Genomics Enterprise (CGEn) and its partners are embarking upon the Canada 150 Sequencing Initiative (CanSeq150). The aim is to sequence 150 new genomes to support sequence-based genomics research in Canada by enabling future research in biodiversity and conservation, applications in breeding and biomedicine, as well as technology development, across Canada.

For further details, please click here.

Naveed Aziz  joines SickKids as the Chief Administrative and Scientific Officer

Naveed Aziz  joins SickKids as the Chief Administrative and Scientific Officer for Canada’s Genomics Enterprise (CGEn).

Naveed comes from Genome Canada, where he has been serving as its Director of Technology programs since 2011. In this role, he led Genome Canada’s portfolio of technology programs, with the primary goal of helping to create opportunities to promote innovation and develop new capacity in genomics, big data and related sciences. He completed his Ph.D. in Gene Targeting at the University of Dundee, Scotland, and an executive MBA at the Bradford School of Management, England. His previous roles include serving as the Head of Genomics at University of York, UK, and as a Research Fellow at the S.R. Noble Foundation in Oklahoma, USA.

Naveed has a keen interest in the role of genomic-based technologies in providing solutions to pressing global challenges. His experience of working within the field of Genomics over the past 15 years has led him to strongly believe in the notion of convergence – especially when it originates from divergent fields.