Canada's national platform for genome sequencing and analysis
SPECIAL EDITION: International Day of Women in Science (Feb. 11)

CGEn is celebrating International Day of Women and Girls in STEM (science, technology, engineering, and mathematics) by highlighting the many women who are an integral part of CGEn’s success. Happy Women in Science Day!

Guest message from Professor Bartha Maria Knoppers

I never saw myself as a STEM scientist (still don’t). That may be strange as I have been working with scientists since my PhD research on the legal and ethical aspects of reproductive technologies (aka Louise Brown) in the late seventies, early eighties. Maybe my lack of “STEM-ness” arises from the fact that the social representations of science as a field bring to mind bench and IT researchers with white coats, the “geeks” that occupy the labs and hallways of the Genome Innovation Centre at McGill University where I now work. Maybe I have adopted them or vice versa.
What is important here is the fact that when recruited by McGill in 2009 from the Université de Montréal where I had been teaching law for 23 years, I did not want a law and bioethics space for my new Centre of Genomics and Policy but to be embedded with the “real” scientists.
I like the scientific mind (inquisitive). I like discovery science (without limits). I especially like infrastructure science (building the policies and tools to make responsible science happen via the creation of platforms for use by others). Since for me law was always about reform, especially in the dynamic and epigenetic environment of international genomic research and regenerative medicine to say nothing of sample/data collection and AI quandaries, I became a convert from being solely a social scientist/humanities researcher to participating in the scientific enterprise.
STEM-ness is not boring. It may take time and is subject to endless reconstruction and validation. But, the joy of being involved in imagining and creating a quality policy “product” is beyond description. Take building governance structures; struggling with gene editing dilemmas or with the lack of global approaches to data sharing (do I dare mention COVID and vaccines?), these challenges mean that women are perfect for the job! Imagining and prospectively addressing the needs of the future are what we are made for.
Word of warning….no one is born with STEM-ness (cloning is illegal!). I did comparative literature and surrealist poetry for quite a number of years at different universities but do not regret not having taken the straight and narrow….the point is to be interested in not only “knowing” but creating and transforming…or to be more scientific, should I say “engineering”?
– Bartha Maria Knoppers

Bartha Maria Knoppers, PhD, is a Professor, Canada Research Chair in Law and Medicine, and Director, Centre of Genomics and Policy, Faculty of Medicine, McGill University. She is also a valued member of CGEn's Board of Directors.

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.
PRecision Oncology For Young peopLE (PROFYLE) program
Program Director: Dr. David Malkin, professor in the Department of Paediatrics, University of Toronto, and oncologist, senior scientist and director of the Cancer Genetics Program at The Hospital for Sick Children (SickKids).

What is the goal of PROFYLE?

More than 30 paediatric cancer research and funding organizations have joined forces through PROFYLE, a pan-Canadian program to transform the care of children, adolescents and young adults (CAYA) with refractory, relapsed and metastatic ('hard-to-cure') cancer across Canada by using next-generation molecular tools and cancer model systems to identify disease- and patient-specific biomarkers that are tractable targets for therapy. The ultimate goal of the program is to positively impact the lives of CAYA patients across Canada (no matter where they live) with hard-to-cure cancer.

What is CGEn’s role? 

The PROFYLE Program involves the three sequencing centres that align with CGEn’s national platform nodes in Vancouver, Toronto and Montreal. The PROFYLE Program Executive Committee (PEC) is responsible for planning and managing all of PROFYLE program activities. Members include CGEn staff and leadership, including Dr. Steven Jones, Scientific Advisor, CGEn-Vancouver node.
Why is this work important – how will it impact Canada and Canadians?
Research centres and top scientists and clinicians across Canada are working together to molecularly profile the tumours of young cancer patients. PROFYLE seeks to take advantage of the genomic revolution to look at the molecular composition of these cancers. Molecular profiling is a set of emerging biological tests that looks at an individual's cancer tumour, studying its genetic characteristics and any unique biomarkers. The information gathered will be used to identify and create therapies that are designed to target a specific cancer tumour profile so patients can enjoy a better quality of life and live longer.
In the past, if a child battling cancer lived in a region without a molecular profiling site, accessing this was not an option. PROFYLE has broken down barriers, giving young people who need it the most access to the best cancer care in Canada.
Learn more about the program on the PROFYLE website.

Staff Spotlight

Our greatest resource is our people. To shine a light on the CGEn community, we will spotlight a staff member or trainee in each issue. Want to nominate your team member or yourself to be in the spotlight? Please email us!
CGEn Staff: Yuka Takemon

Tell us a bit about yourself.

I am a fourth-year PhD candidate in the Genome Science and Technology Program at the University of British Columbia, and my thesis work is conducted with Dr. Marco Marra’s mentorship at Canada’s Michael Smith Genome Sciences Centre, BC Cancer. I am originally from Japan and grew up moving around a lot between different cities in Japan, China, and Hong Kong. Eventually, I moved to Maine, USA, to pursue a Bachelors of Human Ecology at the College of the Atlantic (COA), where I was first introduced to genetics through internships at the Mount Desert Island Biological Laboratory and at the Jackson Laboratory (JAX). After graduating from COA, I worked at JAX as a research assistant at Dr. Ron Korstanje’s group for several years, while also completing a masters degree in bioinformatics at the Graduate School of Biomedical Engineering at the University of Maine. Outside of my main passion as a researcher, I am an instructor and a lesson maintainer at The Carpenties, a non-profit organisation that teaches programming skills; an organiser of RLadies Vancouver; and serve as a board member of a local 2SLGBTQIA+ organisation. 

What are you currently working on?

My doctoral research sets out to characterise genetic interactions (GIs) of cancer-associated genes using in silico techniques. Two genes are said to have genetic interaction, when the perturbation of the two genes, simultaneously in a cell, leads to an increase in lethal or an advantageous fitness effect compared to a cell with a single gene alteration. Understanding GI networks of cancer-associated genes are important, because many cancers harbour mutations that render them not amenable to targeted therapeutics, due to the mutation leading to reduced or absence of the encoded protein to bind drugs. However, identifying lethal GIs (also known as synthetic lethal interactors) of the mutated gene would provide an alternative target for therapeutic intervention. Current in vitro techniques to screen GIs in patient samples are not feasible to perform at scale, so our goal is to understand whether computationally predicted GIs using a patient’s genomic and transcriptomic sequencing data collected at BC Cancer’s Personalized OncoGenomics (POG) program would be informative for personalised genomic cancer medicine. ​

How do you hope to make a difference or impact with your work?

Personalised cancer genomic medicine has become accessible to some cancer patients; however, not all eligible patients benefit from having their cancer genome sequenced, based on the mutations identified in their tumours. If we are able computationally predict lethal GIs and that these are targetable using therapeutics, then our work may be able to provide clinicians with evidence to consider for alternative treatment options for those patients who would have otherwise not benefited from current practices.

Why is genomics important for the health and wellbeing of Canada/Canadians?

Providing access to personalised cancer genomic medicine is important for Canadian cancer patients, because we know that cancer cells in one patient may not be identical to another patient’s cancer cell even though the two patients may be given the same disease diagnosis and that some cancer patients respond better to standard of care treatments compared to others depending on their genomics. Information gained from sequencing tumour genomes provide researchers and clinicians with the ability to understand differences within cancer types, and to identify and target vulnerabilities that are specific to a patient and their cancer cells. Unfortunately, not all cancer patients in Canada/Canadians are able to access programs like POG at BC Cancer, which is why initiatives such as the Marathon of Hope Cancer Centres Network is necessary to accelerate the access of personalised cancer genomics to more cancer patients across Canada.

On International Day of Women and Girls in STEM (science, technology, engineering, and mathematics), what message would you like to share?

When I started my journey into the STEM field, I did not see scientists like me (female, queer, and visible minority) represented in leadership positions or highlighted as keynote speakers at large conferences. This made me question whether someone like me would be able to be successful and welcomed in this field. However, I think the tides are turning and folks in our field are beginning to realise the importance of including women (and women who have multiple intersecting identities) as decision makers in STEM fields. I think that by including diverse perspectives within leadership positions, beneficial outcomes gained from research will improve quality of health and research for more Canadians. For example, through decision makers' interests in understanding diseases that are prevalent in minority groups, and being able to understand the importance of practicing cultural sensitivity. Given this increase in awareness, there has never been a better time to encourage girls and empower women to pursue a career and climb to leadership positions in STEM fields. 

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 our community. In doing so, we will also highlight the many advances being made through genomics.

Dr. Nada Jabado

This month, we spoke with Dr. Nada Jabado, Professor of Pediatrics and Human Genetics at McGill University and a staff physician in the Division of Hematology and Oncology at the Montreal Children’s Hospital. You can watch the full interview on YouTube
Tell us about your work and how genomics plays a role.
I was lucky in that I started using next generation sequencing almost from inception. I am not the first one, but one of the first in Canada I would say. People thought that it would not work in cancer because cancer is a complicated disease but when we used sequencing on high-grade gliomas, a form of very deadly brain tumor in children, we found out new genetic alterations in genes that were never thought to be altered in human disease. What we identified were mutations affecting the epigenome, more specifically mutations in histone 3 genes. Histone 3 are proteins that help package our genetic information but also dictate how it is expressed. It makes the fact that while we have the same DNA sequence in every single cell that we have, we can produce so many different cell types with the same initial genetic information. It is how we express this genetic information that makes a cell your heart, your fetus, or whatever, and the way to do it is the epigenome and those histones. They allow opening and closing of the areas around the DNA that need to be transcribed.
In our work, identifying a mutation that makes this process messed up was the first step, and then using single cell transcriptome, and other technologies, we showed that the mutation we identified was making the cell stuck in time during development. More than that, it allowed us to pinpoint a very early developmental time point during brain development, during the fetal brain development, where potentially those mutations would arise, and create what I call in my jargon “Peter Pan”. Peter Pan doesn’t want to age further, and this mutation stops brain development or the cells that they arise in at a given time point, and the rest of the brain develops, but those cells are eternal progenitors that continue cycling, and this is a new way of creating cancer. This discovery was made possible by the next generation technologies that we have.
Those mutations that we identified not only are giving us a means to better understand and hopefully soon to better treat those children with deadly cancer, but they are amazing tools to tease apart the developmental stages because you could use them as another model system to ask what this gene and protein are doing at a certain time point in development; when is it needed and when it is not needed. So, it’s beyond just those cancers that we study, it really is a tool that helps us understand the wider picture of how our genetic information is being regulated.

What advice would you like to share for International Day of Women and Girls in Science?
I am a woman in science, I have a family of three, and I am very much involved with their daily life. People say that I am potentially a “super woman” and I hate that term because it’s not true. I think we put up our own obstacles. If we are lucky to be healthy, our children are healthy, we should go as far as our dreams and our wishes. It’s not because someone is telling you to do that, it’s because you want to do it and then you give yourself the means. There are times when you are going to be investing more in personal problems, other times when it’s going to be on your career. If you want to do something, just do it. Again, failure is not the problem. You learn from that and you adapt, and if you really want to try it again, you do it again. No success is guaranteed, but if you don’t try you never know, and I think we don’t try enough. We’re our own worst enemy and we put up obstacles before we go ahead and do the things. Don’t over think it. That is my message.
Watch the full interview with Dr. Jabado on YouTube.
Learn more about Dr. Jabado’s Lab.
Dr. Nada Jabado 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:
Bringing the Benefits of Genome Sequencing to the World – Public Policy Projects

Unprecedented exploration generates most comprehensive map of cancer genomes charted to date – OICR News

The Open Science Dialogues: Summary of stakeholders round tables – Government of Canada

Upcoming Events

Can-Gard, Genetics & Genome Biology Program and Clinical & Metabolic Genetics at SickKids invite you to join them on February 28 for Rare Disease Day. This year's theme: The role of Translational Genomics in Precision Health. Register now.

Yann Joly, Research Director, Centre of Genomics and Policy, McGill University, will present 'Addressing Key Challenges in Genomic and Health Data Sharing' on February 18 at noon ET/9 am PT. Tune in on YouTube.
Share your news with us!

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