Canada's national platform for genome sequencing and analysis
Naveed's Note

Welcome back to the CGEn Sequence, and our last issue of 2021. It’s hard to believe that this year is nearly over. We are not out of the woods yet with this pandemic – unfortunately, COVID-19 is trailing into 2022. Over the past 18 months, the world has recognized the major role genomics is playing both in tracking and tracing this virus, and in developing vaccines to protect us from it. As you read this note, countries all over the world are sequencing virus genomes to detect new variants, including Omicron, while companies are working to develop new vaccine candidates to adapt to these variants. Genomics has been ‘taken out of the lab and into the public domain’: Ask people what is something new they have learned in this pandemic, and you will hear many of them say “Genomics”. There is a stronger recognition and appreciation for genome science than ever before. We know that genomic surveillance and data sharing have been absolutely vital to the global pandemic response. Thankfully, in Canada, the investments made in genomics infrastructure over the past few years laid the foundation for today’s capacity to rapidly sequence viral and human genomes across the country to respond to this pandemic. It is ever more apparent that biological research in Canada can and should be backed by genomics, and that the data generated can and should be shared so that all can benefit. These are big goals, but I believe they are achievable. As Canada’s engine for genomics-enabled research and discovery, we will continue to work together with our partners to realize these goals in the near future.

Wishing you and your loved ones safe, healthy, and happy holidays, and hope for a better 2022.


Dr. Naveed Aziz


CGEn hosted and participated in two panel discussions at this year’s CSPC (Canadian Science Policy Centre) virtual conference in November. The first pre-conference session organized by Genome Canada included Dr. Naveed Aziz, CGEn CEO, and Dr. Stephen Scherer, CGEn Toronto node Scientific Director, on a panel entitled: ‘Bringing the bio-revolution to Canada: Towards a Pan-Canadian Genomics Strategy’. The panelists discussed how to build an effective national strategy, the opportunities for Canada’s continued leadership in genomics, and the confluence of genomics with other transformational technologies.​​​​ Click below to watch the full session on YouTube.
‘Bringing the bio-revolution to Canada: Towards a Pan-Canadian Genomics Strategy’
CGEn and Genome Canada also organized a panel discussion entitled: ‘Role of Genomics and Big Data in informing Public Health Policy’, moderated by Naveed. Speakers included Dr. Catalina Lopez-Correa, Executive Director and Chief Scientific Officer, CanCOGeN; Professor Yann Joly, Research Director, McGill University, Faculty of Medicine, Department of Human Genetics; Dame Sue Hill, Chief Scientific Officer, England; and Genya V. Dana, Head of Healthcare, World Economic Forum. The panelists shared their views on how to foster a robust data ecosystem for the current pandemic and future public health emergencies, especially from a Canadian data strategy perspective. Click below to watch the full session on YouTube.
‘Role of Genomics and Big Data in informing Public Health Policy’

Staff Spotlight

Our greatest resource is our people. To shine a light on the CGEn community, we will spotlight a staff member and trainee in each issue. Want to nominate your team member or yourself to be in the spotlight? Please email us!
CGEn Staff: Richard Wintle
Tell us a bit about yourself. I have a PhD in Molecular and Medical Genetics from the University of Toronto, and did my postdoctoral training in C. elegans neurobiology at the Centre for Addiction and Mental Health. I am currently the Assistant Director of The Centre for Applied Genomics (TCAG), the Toronto CGEn node, located at The Hospital for Sick Children. I joined TCAG in 2006, initially as interim facility manager, and transitioned into the Assistant Director role early in 2007. Before joining TCAG, I spent six years in startup companies in Toronto. I grew up in Kingston, and now live in the suburbs just north of Toronto.
What are you currently working on? We’ve recently finished writing the renewal grant, applying for the next six years of CGEn funding from the Canada Foundation for Innovation’s Major Science Initiatives fund. This took up almost all of my time in September and October of 2021. Now, I have a little more time to focus on our whole genome sequencing study in cerebral palsy, and my involvement with the International Cerebral Palsy Genomics Consortium. I’ve also very recently taken on the role of Executive Director of HPC4Health, a high-performance computing architecture that is designed with privacy of healthcare and personally identifiable data in mind. Getting up to speed on this is a new and exciting challenge.
How is CGEn an integral part of genomics in Canada? CGEn was founded with the vision that the three largest, individual genome centres across Canada should form an integrated, national facility. The immediate, operational benefits are obvious: coordination of large projects, a national platform for sharing of data and expertise, and maximized economies of scale. Building on these large-scale approaches, CGEn provides the opportunity for dialogue and collaboration between genome scientists operating in many disciplines, across Canada’s diverse geographical regions. CGEn’s roles in enabling Canadian science, and in conducting large projects at home in Canada, are critical to the future of Canadian genome science.
How do you hope to make an impact with your work? Thinking again about our work on the genomics of cerebral palsy, we hope to better understand not only how genomic changes can contribute to risks and outcomes in this very common neuromotor disorder, but also basic knowledge of how the central nervous system and neuromuscular systems function. In collaboration with colleagues both locally and around the world, the CP genomics project also has roles to play in informing policy, clinical practice, and diagnostic guidelines, potentially identifying new treatment options, and advancing knowledge of this condition both within the community of CP patients and their families and in the general public. All of this is enabled by the core genome sequencing and analysis capabilities of CGEn.
Why is genomics important for the health and wellbeing of Canada/Canadians? Personalized, or precision, medicine is a reality, and its widespread adoption is coming quickly. In order to maximize the impact of these approaches, we need to fully understand the genome, the information it encodes, how it varies between individuals, and how alterations within it impact our health or wellness. Fully understanding the genome is a gateway to understanding susceptibility to infectious disease, the differing presentations of common diseases and disorders such as diabetes, autism, or cancer, the characteristics of rare diseases, how newly arising (de novo) changes occur and impact health, and so much more. Add to this the genomics of agriculture, of species and populations with environmental importance, the microbiome, and many other areas where genomics can be applied, and there really is an almost limitless amount yet to discover.
CGEn Trainee: Annabel Rutherford
Tell us a bit about yourself. I am a Boston native who moved to Kingston, Ontario to complete my undergraduate degree in Biopsychology at Queen’s University. During my time at Queen’s, I held a summer research position in Dr. Christ Dulla’s lab at Tufts University, studying epilepsy. I then conducted my fourth-year thesis in Dr. Susan Crocker’s lab at Kingston General Hospital, researching copy number variation in Alzheimer’s disease. Currently, I am in the second year of my Master’s degree in Molecular Genetics at UofT, doing research in Dr. Stephen Scherer’s lab, at SickKids. Outside the lab, I enjoy exercising and playing with my kitten!
What are you are currently working on? My current Master’s research focuses on discovering the function of a novel Autism (ASD) risk gene. While the Scherer lab has discovered many ASD risk genes, the one I am studying is unique in that it encodes a long noncoding RNA (lncRNA) instead of a protein. Studying the effects of lncRNAs is an exciting new area in genetics as these molecules appear to have roles in many conditions, ranging from cancer to schizophrenia. Using a variety of wet lab techniques on both mouse brain and human cell derived models, I have been working to understand how this particular ASD associated lncRNA plays a role in the ASD phenotype. Our goal is to be able to apply this understanding to improve early intervention strategies and treatment of ASD.
Which scientist inspires you? A scientist who greatly inspires me is Siddhartha Mukherjee, the author of notable books such as ‘The Emperor of Maladies’ and ‘The Gene’. He is able to eloquently illustrate the connection between genetics and disease, using personal stories, to explore the importance of both the historical and current aspects of the field.
How do you hope to make a difference with your work? I hope to improve the patient and family experience of those impacted by neurological disorders. Neurodevelopment is an extremely complex process, meaning individuals will likely have unique experiences even from those affected by the same disorder. It is vital to address these differences to provide optimal care to both patients and their families, and I believe this will be achieved using personalized genetic medicine. ASD is a prime example of a complex polygenic disorder, as there are over 100 ASD risk genes and many different presentations of symptoms. By working on one of these genes I aim to contribute to a deeper understanding of ASD and enable personalized treatment for patients affected by these variants.
Why is genomics important for the health and wellbeing of Canada/Canadians? Personalized genetic medicine is the future of healthcare, and understanding genomics is an integral part of it. ASD is a great example of how complex disorders can have many genes that contribute to the phenotype, but it is by no means the only one. Many conditions are polygenic, which highlights the importance of being able to interpret a person’s whole genome in order to adequately give individual risk assessments and health advice.

In Conversation With…

Each month, we’re speaking with principal investigators working in diverse fields of genomics with the aim to gather ideas and insights, and share them with you! In doing so, we will also shed light on the many advances being made through genomics.

Dr. Holly Longstaff

This month, we spoke with Dr. Holly Longstaff, Director, Privacy and Access, Provincial Health Services Authority (PHSA) Research and New Initiatives, and an Adjunct Professor with the Faculty of Health Sciences at Simon Fraser University. You can watch the full interview on YouTube.
How has big data changed the notion of consent with regards to participation in research and sharing data?
The bioethics community has long called for a movement towards consent to good governance. It’s no longer individualistic notions of consent, which don’t work with big data or big biobanks; instead, it’s consenting to a model of good governance, which has to be very well thought out in terms of uses of those data and biospecimens, and how they are governed. Patients should be involved in those decisions, but it’s not about every single little use of the data because a lot of it is hypothesis-generating. This is a very different model and it’s important to acknowledge and accept that we cannot do everything with consent. It’s actually unethical because if you depend solely on consent, we cannot get whole populations to participate in research and that is absolutely essential if we are going to move research forward. The pandemic is a good example of this. Health systems are not consenting for every use; they are collecting everyone’s data for the betterment of everybody. But that has to be carefully regulated and governed to ensure that it is appropriate and that the public good is always what you are marching towards.
How has the COVID-19 pandemic affected how data is shared, particularly with genomic surveillance?
HostSeq, part of the Canadian COVID Genomics Network (CanCOGeN), is an incredible example of what is possible when everyone works hard together, and with the most precious data that there is: whole genomes. Patients have been involved throughout the whole process, we’re already reviewing and approving studies, and we have a great multidisciplinary team on our data access committee, including patients, and we’re working with great scientists. We’re able to review these data in ways that are efficient and high quality, within a couple of days. CanCOGeN is an example of what is possible when everyone works together and when it is properly funded.
What else should people know about data sharing and privacy?
With data sharing, there are all sorts of mythology out there around privacy and ethics, and a lot is blamed on privacy, ethics, and legal, but I say do not drink the Kool-Aid! There is so much flexibility and permissibility in Canada. Yes, there are different privacy laws regulated by jurisdiction as opposed to our national ethics guidance, but despite that, there are a lot more similarities between jurisdictions than there are differences. I think we put up barriers in privacy and ethics that are imaginary as a way of avoiding the hard work that we need to do. Once we accept that these things are all possible, then you have to do the hard work of figuring out what those governance mechanisms look like to support it: How do you set up a data access committee with people represented from across the country, how to engage patients, and set up a group to ensure all of the data is provided in a safe manner. That’s a lot of hard work and a lot harder than just saying no. But saying no has consequences, and inaction is not value-neutral. Sometimes in privacy and ethics, we think if we say no then we will be able to protect this very precious, sensitive data. But if we say no there are of course consequences to that. We just have to roll up our sleeves and all work together and figure out that hard work. And we know we can because we’re doing that right now with CanCOGeN.
You can have incredible innovation and data sharing and still preserve privacy and do good and ethical work. You can have it all. And these projects like CanCOGeN show how to do that and you can take these lessons learned and apply them broadly. I hope that we will and I hope that we won’t just make it about COVID-19, that we’re going to continue and broaden these lessons.
What is your take-home message?
It is unethical not to share data. It is unethical not to include everybody in research. It is unethical not to learn from our data, not to share it, and not to ensure that we are always working towards the public good, and that includes everyone in the public, not just a narrow public.
CGEn is the essential ingredient and the thing that is going to carry this all forward. It shows what can happen when you have something central and well-funded and supported. The resources we put into it now will have all sorts of benefits for everyone in the future.

Learn more about HostSeq, part of the CanCOGeN initiative, and the HostSeq Data Access Compliance Office (DACO) chaired by Dr. Longstaff.
Dr. Holly Longstaff, Director, Privacy and Access, Provincial Health Services Authority (PHSA) Research and New Initiatives, Simon Fraser University, in conversation with Hillete Warner, CGEn's Communications Manager.
Click above to watch the full interview on CGEn's YouTube channel.

Genomics News & Events

We're pleased to share news, publications, events and other items of interest to the genomics community in our monthly newsletter. Please share your news and items of interest with us. We accept submissions at any time to:
CGEn News
CANSSI Ontario STAGE (STAGE), in partnership with the CGEn Host Genome Sequencing Initiative, invites trainees from across Canada to apply to become a CANSSI Ontario STAGE HostSeq Fellow. Deadline to apply: Dec. 15, 2021.

Giant’s Dot Lichen: from newly discovered species to complete genome sequence in one year – Canada’s Michael Smith Genome Science Centre

It’s time to transition to an era of genomic medicine – Healthy Debate
Whole Genome Sequencing data on 200,000 UK Biobank participants are made widely available for research – UK Biobank
Whole-genome sequencing can improve childhood cancer outcomes – The Guardian
Covid-19 ‘neanderthal’ gene variants explained – Genomics Education
Overlooked DNA may be what separates humans from other primates – Jerusalem Post
Share your news with us!

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