Canada's national platform for genome sequencing and analysis
CGEn Sequence Newsletter: Vol. 1, Issue 1, November 2021
Naveed's Note

I am pleased to welcome you to CGEn’s inaugural newsletter, the CGEn Sequence!
CGEn is Canada’s national platform for genome sequencing and analysis. CGEn provides the leading genomic infrastructure for Canada’s research and innovation communities. Today, thousands of scientists and researchers across Canada are capitalizing on the opportunities presented by our cutting-edge technology and large-scale data-generation platforms. Since its inception, CGEn has facilitated the sequencing of thousands of genomes in humans and other species, catalyzing ground-breaking new research in Canada.
This newsletter will serve as a connector between 2,000+ principal investigators and research groups across the country, whose programs are supported by CGEn’s national facility. We aim to profile and promote the wide range of genomics work taking place in Canada and internationally, and celebrate the talented individuals working in genomics and bioinformatics across multidisciplinary teams. In these CGEn Sequence newsletters, we will share stories about advances in genome research and technology, and the current applications that are improving the lives of Canadians and others around the world through international collaborations. I encourage you to reach out and share your stories with us.
I am proud of the collaborative partnerships that we have built over the last several years since CGEn’s inception. I look forward to continued engagement with each of you and discussions on how we can continue to make strides in the health and wellbeing of people and the planet through genomics-enabled research and discovery. If you have any questions or suggestions for this newsletter, please feel free to get in touch.

Dr. Naveed Aziz

Sequence Showcase

In each CGEn Sequence newsletter, we aim to provide a lens into the important work being undertaken by Canadian scientists and researchers from coast to coast. Each month we will showcase a project enabled by our national platform.

Project: HostSeq 

What is the goal of HostSeq?
COVID-19 displays significant interindividual clinical variability, ranging from asymptomatic infection to causing lethal disease. It is important to understand and characterize the role of human genetics in determining clinical response. HostSeq aims to provide insights into the role human genetics play in the manifestation of disease severity, deliver new biomarkers that predict people at highest risk, and implement appropriate healthcare strategies, including potential precision therapies.
What is CGEn’s role?
CGEn is leading HostSeq as Canada’s national facility for genome sequencing and analysis. Working with partners across the country, CGEn is mandated to develop regional, national, and international linkages to ensure that this investment has maximal impact for the health of all Canadians.
Why is this work important – how will it impact Canada and Canadians?
HostSeq aims to sequence the genomes of 10,000 Canadians affected by COVID-19 and deposit the sequence and the associated clinical data in the CGEn databank, providing access to data that will support the research of all investigators. To do so, CGEn is collaborating with investigators across Canada who are engaged in COVID-19 research.
Learn more about HostSeq on the CGEn website, including:

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: Janick St-Cyr
Tell us a bit about yourself. I have a Master of Science in Molecular Biology. I am currently enrolled in a microprogram in Management at HEC Montreal to acquire more technical knowledge in personnel management, business development and strategy. I have worked as a Lab and Research technician at Genome Quebec, prior to joining McGill in January 2017 as a Research Assistant. In March 2020, I started a new position as a Sequencing Laboratory Manager at the McGill Genome Centre in Montreal. I supervise the production/sequencing platform team. I assist Project Managers and Principal Investigators (collaborators) by recommending how large-scale experiments should be carried out on the NGS platforms and recommend which sequencing technology could be used to meet the client needs.
What are you are currently working on? Our primary focus is on applying and developing a variety of molecular biology methods for next generation sequencing based transcriptomic and genomic studies. Our pipeline includes RNAseq, Exome-seq, WGS, WGBS, and other epigenomic protocols. I coordinate all sequencing projects from sample receipt, library preparation, sequencing and run validation. As well as the Sequencing platform for both Illumina and MGI. We are currently working on projects related to COVID, cancer, and other diseases important for the health of Canadians.
How is CGEn an integral part of genomics in Canada? CGEn is an integral part of genomics in Canada as we host cutting-edge technology in the field. As a CGEn Platform we also join efforts and collaborate with different centres when it comes to large scale sequencing. We regularly collaborate to jointly advance projects.
How do you hope to make an impact with your work? I hope to make an impact as a female leader in the scientific community and more specifically in genomics. I lead by example by guiding others through my behavior and work ethic. Three of my intrinsic values are: passion, rigor and team spirit. I hope my contribution will lead to better understanding different viruses and diseases and to finding proper solutions and treatment. Also, I hope that my role as a female scientist will attract more girls and women to the field of science and genomics.
Why is genomics important for the health and wellbeing of Canada/Canadians? We have experienced the importance of genomics sequencing and the major role they played in the fight against the recent COVID-19 pandemic. Sequencing allows us to have a better understanding of the host genomics and therefore explain the positive and negative reactions of our bodies in front of a threat. These recent events confirmed that Genomics play an integral part in identifying at-risk individuals, protecting them, and improving treatment of this viral disease.
CGEn Trainee: Kate Glennon
Tell us a bit about yourself. I am a 4th year PhD Candidate studying in the Department of Human Genetics at McGill University. I grew up in Ottawa, and spent my undergrad in Halifax studying Biochemistry and Molecular Biology at Dalhousie University where my interest in genetics started. I moved to Montreal in 2018 to pursue my PhD at McGill and develop my skills in genomics and bioinformatics. While most of my time is spent on research or as a teaching assistant for undergraduate biology, when I’m not in the lab I love to go out for hikes and to weekly trivia.
What are you are currently working on? I am currently researching in the lab of Dr. Yasser Riazalhosseini, where we are investigating the genomics of renal cell carcinoma, the most common type of kidney cancer. I have been working on developing a kidney cancer focused NGS assay to capture genomic biomarkers in tissue and liquid biopsies. We are using this assay to investigate the link between genetic signatures of RCC tumors and disease progression with the goal of developing robust biomarkers for personalized risk-assessment.
Which scientist inspires you? Mary-Claire King has been an inspiration not only in the world of cancer genomics (with the discovery of the BRCA1 gene), but also in applying her expertise in genomics to helping victims of human rights violations. She is a fantastic example of how to make an impact in the world through scientific research.
How do you hope to make a difference with your work? I have the privilege to be working in a field that can advance and improve both risk stratification and care-delivery to patients with cancer. I hope to continue to conduct research in the field of oncology, developing solutions for personalized medicine in cancer.
Why is genomics important for the health and wellbeing of Canada/Canadians? Healthcare in Canada is continuously evolving, and genomics plays an integral role in bringing personalized medicine to Canadians. Genomic medicine is already making an impact in oncology and the treatment of rare diseases, but widespread access to genomic based healthcare solutions will greatly improve the health of Canadians.

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.
Our first conversation is with Dr. David Malkin, Senior Staff Oncologist, Division of Haematology/Oncology, and Senior Scientist, Genetics and Genome Biology Program, The Hospital for Sick Children (SickKids) in Toronto. You can watch the full interview on YouTube.
Tell us about your recent study published in JAMA Oncology.
“Li-Fraumeni syndrome (LFS) is a cancer predisposition syndrome that is caused by inherited mutations in a tumour suppressor gene called TP53.  LFS presents as a constellation of cancers, which can occur at any age – some people get one tumor, some people get multiple tumors, some first when they're a baby, for others their first tumor might be when they're 40-years-old. Now, in analyzing an international database of the TP53 mutation spectrum of over 3,000 people from over 1,200 LFS families, looking at where the mutations occur in the gene and whether you can correlate them with the phenotypes, we are actually redefining the syndrome as a spectrum. So, in other words, an individual lies somewhere along the spectrum depending on how penetrant the gene defect is and what the phenotype looks like, from a very classical constellation of cancers to a much more limited presentation. This gives us a much better handle on being able to predict based on a genetic alteration what cancer phenotype an individual may have. If you know that from a clinical perspective, you can think of ways to try to predict more accurately what tumors may develop and at what age they'll develop. With that information, we can design more precise approaches to detect them early and to manage them accordingly. This leads to this idea that there are a whole bunch of other cancer syndromes that really aren't syndromes–they're really a spectrum of disease that is dependent on more than just a single gene alteration.”
How has genome sequencing evolved and how is it being used today in your work?
The traditional approach for mutation identification was generally single gene or small gene panels, and in the cancer world that's been the case for some time. In a sense, cancer genetics has been a little bit ahead of the game just because there are genes that we know to look for and we know what they do. So, we, as with many others, would basically do single gene P53 sequencing on these families, identify a mutation, and then take it from there. Now we’ve taken it to the next level; we're doing whole genome sequencing, RNA sequencing on tumors, and methylome sequencing. With that, we're much better able to refine the genetic landscape of both the tumors that occur in these patients, as well as the germline ‘normal’, to get a better understanding of, in addition to the driver mutation and TP53, what other genetic alterations are occurring that are modifying the phenotype. So now, when a family or a patient presents with clinical features of the syndrome, a cancer history of some sort, rather than just doing TP53 sequencing, they actually get a large panel sequencing or whole exome. We're doing that now through the SickKids Cancer Sequencing Program (KiCS for short), which is also supported through CGEn. That's a huge advantage because we're not just finding a mutation in TP53, we're now able to find what else is going on in their genome.”
How does this impact patient care?
“This ability to sequence the genomes of tumors has very rapidly led to an ability to translate that information, identify molecular changes in a very precise way to then match those to the development of drugs that target those particular molecular alterations. In the old days, not so long ago, you'd have to sequence one gene at a time, and you'd have to have an idea of what genes you wanted to sequence because you can only do so many, so you're very limited. Now we can go in agnostic, meaning we're not expecting anything – we don't know what we're going to find because we can sequence everything. From that, we are able to glean information that's most relevant and then new drugs are being designed and can be used to target against those genetic alterations.”
Learn more about the SickKids ‘KiCS’ Cancer Sequencing Program: Integration of Next Generation Sequencing into Clinical Oncology Care, led by Drs. David Malkin, Anita Villani and Adam Shlien.
Dr. David Malkin, Senior Staff Oncologist, Division of Haematology/Oncology, SickKids, 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
CGen is pleased to announce the appointment of Dr. ​​Bartha Maria Knoppers as a member of our Board of Directors.
CGEn and Genome Canada are co-hosting a panel session on the
Role of genomics and Big Data in informing Public Health Policy at the virtual Canadian Science Policy Conference on Nov. 24 from 10:30 a.m. to noon. Learn more about the conference.
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. 10, 2021.

Sequencing the Crisis: How genomics morphed from a COVID-19 research tool to a critical part of the pandemic response – Public Policy Forum
Genome sequencing as a diagnostic test – CMAJ
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