McLaughlin Centre

U of T researchers help lead national effort to explore role of genes in COVID-19

Christopher.Sorensen — Wed, 20 May 2020 19:07:52 +0000

U of T researchers help lead national effort to explore role of genes in COVID-19

Christopher.Sorensen Wed, 05/20/2020 - 15:07

Cutline

Lisa Strug, the scientific lead of the CGEn sequencing project, says there appears to be a genetic component to the coronavirus, which could explain why some families report similar experiences with the illness (photo courtesy of SickKids)

Paul Fraumeni

Topic

Our Community

Coronavirus

Faculty of Arts & Science

Faculty of Medicine

Hospital for Sick Children

McLaughlin Centre

Molecular Genetics

Statistical Sciences

The global spread of COVID-19 has forced us to become familiar with terminology – from contact tracing to social distancing – most of us didn’t know a few months ago. Now, if the hunch of many scientists is correct, we are about to hear a lot about genome sequencing, too.

In search of a genetic explanation for why the novel coronavirus affects some people much more severely than others, the federal government has invested $20 million into a national project to sequence and analyze the genomes of 10,000 Canadians who have had COVID-19.

The project, part of a larger $40 million investment in the Canadian COVID Genomics Network, will be managed by CGEn, a federally funded national platform for genome sequencing, a complex process that, among other things, can help spot DNA mutations in individuals or groups that predispose them to certain illnesses.

“There seems to be a genetic component to this virus. You can see that in the individuals who have had the same level of exposure to the virus but respond very differently,” says Lisa Strug, associate director of The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children (SickKids) and an associate professor in the department of statistical sciences in the ��Ƶ’s Faculty of Arts & Science.

“That points to this idea that our genetics could impact our response to the virus and how some people can fight it off and some can’t. So, we need to know what are the genetic variations that are determining this variable response?”

Strug, who is scientific lead of the CGEn sequencing project, says published studies have already examined so-called “heritability.”

“Researchers have looked at whether some of the symptoms being seen with COVID-19 run in families,” she says. “Some families are experiencing the virus in the same way – they all have mild symptoms, or all have very severe experiences. So it appears that there is some hereditary component. And that’s another piece of evidence pointing to genetics.”

Strug will work with scientists at CGEn nodes at U of T and SickKids, McGill University and at the University of British Columbia. CGEn will collect blood samples from 10,000 patients from across the country, of all ages and genders, who have COVID-19. The researchers will then extract the DNA from the samples, sequence and analyze it with sophisticated computing and statistical techniques and put all the clinical and genetic information in a protected database so researchers around the world can use it in their COVID-19 projects. A similar project is being conducted in the United Kingdom, which will involve about 20,000 patients.

“The large sample size is essential because there are likely different factors that contribute to the response to COVID-19 infection in different individuals and at different ages, and the more data we have, the greater the ability researchers will have to identify these,” says Strug. “There is a huge benefit in not just looking at one patient at a time, but across the population and across all genes.”

How will this information benefit research into the novel coronavirus? Strug says the results will be useful in identifying who is the most susceptible to COVID-19 and in understanding which genes scientists should be targeting when developing drugs to treat the virus and, ideally, a vaccine that will help control it.

There is also another major benefit of starting this massive, two year-long project immediately: data that can be used to protect ourselves from future illnesses.

U of T’s Stephen Scherer, the lead principal investigator of CGEn, says the genetic information gleaned from the project can be used to help guard against future outbreaks (photo courtesy of SickKids)

“This is Canada’s first time doing a large-scale project like this,” says Stephen Scherer, TCAG’s director and a University Professor of molecular genetics at U of T. “When global society moves past the COVID-19 pandemic, there will be another one. All this genetic information will be extremely useful for that point in the future.

“We’re about to get an excellent genetic cross-section of the Canadian population. This virus has been destructive, but it is also forcing us to create new knowledge that we will be able to leverage for years to come.”

For example, knowledge gained from the SARS epidemic of the early 2000s has been useful during the current outbreak, according to Strug and Scherer. That’s because of the similarities between the two coronaviruses.

“That has helped the global research community be able to respond quickly to this new virus,” says Strug.

That said, genetic sequencing must deal with a huge amount of data. The numbers are staggering – the human genome contains three billion base chemical units that code for about 25,000 to 35,000 genes, and this project will sequence 10,000 genomes.

“This is very big data analysis,” Strug says.

Both scientists note that computing technology used for sequencing is far more advanced than even a decade ago. “The technology has become so sophisticated and affordable that we can propose to look at entire DNA sequences,” says Scherer. “In 2003, for SARS 1, we couldn’t do this.”

Scherer, who is the lead principal investigator of CGEn, a senior scientist at SickKids and director of U of T’s McLaughlin Centre, says he’s impressed with how the global research community has pivoted to focus on solving the COVID-19 puzzle.

“It’s amazing how scientists around the world have come together on this,” he says. “Just at U of T, there are researchers working on COVID-19 who I would have never predicted would be. I would say that 75 per cent of the people I’m talking with every day, now, are not the same people I was talking with eight weeks ago. But they have a specific technology or some useful knowledge that links in.

“That’s how scientific research needs to work to be effective: By bringing in a wide breadth of perspectives and specialists, cracking COVID-19 could become this generation’s moonshot.”

U of T to support high-impact coronavirus research projects through Toronto COVID-19 Action Fund

rahul.kalvapalle — Mon, 20 Apr 2020 20:34:01 +0000

U of T to support high-impact coronavirus research projects through Toronto COVID-19 Action Fund

rahul.kalvapalle Mon, 04/20/2020 - 16:34

Cutline

(photos by Steve Russell/Toronto Star via Getty Images, Christopher Morris/Corbis/Getty Images, Nick Iwanyshyn)

Topic

Donnelly Centre for Cellular & Biomolecular Research

Institute of Health Policy Management and Evaluation

Biochemistry

Chemistry

Dalla Lana School of Public Health

Faculty of Applied Science & Engineering

Faculty of Arts & Science

Faculty of Information

Faculty of Medicine

Global

Hospital for Sick Children

Institute of Biomaterials and Biomedical Engineering

Laboratory Medicine and Pathobiology

Lawrence S. Bloomberg Faculty of Nursing

Research & Innovation

Sociology

St. Michael's Hospital

Sunnybrook Hospital

U of T Mississauga

U of T Scarborough

University Health Network

Vivek Goel

The ��Ƶ will support more than 30 research projects through the nearly $9-million Toronto COVID-19 Action Fund – set up less than a month ago to support high-impact research by U of T and its hospital partners that contributes to the global fight against the novel coronavirus.

The projects, which range from medical interventions to measures aimed at supporting the economy and vulnerable populations, were chosen on the basis of their potential to have a positive impact on individuals, communities and public health systems within a timeframe of a year or less.

They were selected from among 338 applicants via a fast-tracked, peer-reviewed competition. Less than 30 days elapsed between the creation of the fund and the winning projects being announced.

“The Toronto COVID-19 Action Fund is a testament to the ��Ƶ’s unique ability to quickly mobilize its resources, engage the creativity and ingenuity of its researchers and draw on the strength of its partnerships with partner hospitals to respond to the most urgent public health, economic and societal challenge of our time,” said Vivek Goel, U of T’s vice-president, research and innovation, and strategic initiatives.

“COVID-19 presents an array of unprecedented global problems that require urgent attention and expertise from experts in a wide variety of disciplines – from medical specialists and public health researchers to economists, social scientists and mathematicians.

“We are confident these projects will each, in their own way, make important contributions to the global fight against this pandemic.”

The projects include an initiative to research the effects of the COVID-19 pandemic response on marginalized people, led by Ahmed Bayoumi, a professor in the department of medicine in the Faculty of Medicine and a scientist at the Li Ka Shing Knowledge Institute of St. Michael’s Hospital, part of Unity Health Toronto.

In the realm of medical interventions, Jordan Feld, associate professor in U of T’s department of medicine in the Faculty of Medicine and a senior scientist at the Toronto General Hospital Research Institute at the University Health Network, plans to carry out a phase two drug trial for the treatment of COVID-19.

Also funded were research projects by Sunnybrook Health Sciences Centre's Samira Mubareka and Robert Kozak, both of the department of laboratory medicine and pathobiology at U of T’s Faculty of Medicine, that could pave the way to better understanding and treatment of the novel coronavirus, also known as SARS-CoV-2.

The role of genetics in the pandemic response will be explored by Aled Edwards, professor at the Donnelly Centre for Molecular and Biomolecular Research and director of the Structural Genomics Consortium. He will lead work on the Toronto Open Access COVID-19 Protein Manufacturing Centre.

Other research projects will address social, economic and public policy issues.

Janet Smylie is a professor at the Dalla Lana School of Public Health, director of Well Living House at St. Michael’s Hospital and an expert in public health in the context of Indigenous populations. She will use an action fund grant to support the rapid implementation of a shared COVID-19 tracking and response platform for First Nations, Inuit and Métis populations.

U of T Mississauga anthropologist and lecturer Madeleine Mant will receive support for her project titled, “Going viral: COVID-19 and risk in young adult health behaviour models.”

The impact of COVID-19 on the economy is another area of significant concern, with Professor Scott Schieman, chair of the department of sociology in the Faculty of Arts & Science, leading a project to explore the impacts of COVID-19 on the quality of work and economic life in Canada.

The funding for these and other projects was drawn from U of T and other university sources, including the McLaughlin Centre, Medicine by Design, partner hospitals and philanthropic donors. Successful applicants are also eligible for additional support for a trainee through a generous agreement with MITACS.

“We would like to extend our thanks to all the scholars who submitted proposals to the Toronto COVID-19 Action Fund, and we will continue to work hard to find ways to support our researchers in their efforts to devise solutions to this crisis,” said Goel. “I would also like to thank the reviewers that provided assessment in a short period of time and our staff that worked diligently and around the clock to complete this record-setting peer review process.”

“U of T takes very seriously its public responsibility to make key contributions to the response to COVID-19, and I would like to congratulate everybody involved in the rapid creation and execution of the action fund for their tireless efforts.”

Goel noted that additional projects may be funded through the action fund as funds continue to be raised and additional partners contribute. All those that were not selected are being directed to other funding sources, including those listed on the Centre for Research and Innovation Support’s COVID-19 research website.

Here are the researchers being supported by the Toronto COVID-19 Action Fund:

Note: this list was updated with additional projects on May 8, 2020

Upton Allen of the department of paediatrics in the Faculty of Medicine, Institute of Health Policy, Management and Evaluation and the Hospital for Sick Children – Immune responses to COVID-19: Correlates across the age spectrum

Robert Batey of the department of chemistry in the Faculty of Arts & Science – Synthetic chemistry as a core technology platform for the response to the COVID-19 pandemic: chemistry COVID-19 core facility

Ahmed Bayoumi of the department of medicine in the Faculty of Medicine and Unity Health Toronto –The effects of the COVID-19 pandemic response for people who are marginalized

Laurent Brochard of the department of medicine in the Faculty of Medicine and Unity Health Toronto – Careful ventilation in patients with ARDS induced by COVID-19

Jeannie Callum of the department of laboratory medicine and pathobiology in the Faculty of Medicine and Sunnybrook Health Sciences Centre – Convalescent plasma for COVID-19 research trial

Warren Chan of the Institute of Biomaterials and Biomedical Engineering in the Faculty of Applied Science & Engineering – A quantum dot portable diagnostic device for COVID-19

Angela Cheung of the department of medicine in the Faculty of Medicine and Institute of Health Policy, Management and Evaluation and the University Health Network – The Ontario COVID-19 prospective cohort study

Leo Chou of the Institute of Biomaterials & Biomedical Engineering in the Faculty of Applied Science & Engineering – Enzyme-free, one-step nucleic-acid detection for point-of-care COVID-19 diagnostic screening

Gerald Chaim Cupchik of the department of psychology at U of T Scarborough – Managing coping strategies and avoiding anxiety during the COVID-19 pandemic: A multilevel analysis from epidemiology to psychology and education

Paul Dorian of the department of medicine in the Faculty of Medicine and Unity Health Toronto – Evaluation of a small gas-powered and patient-responsive automated resuscitation/ventilation

Aled Edwards of the Donnelly Centre for Molecular and Biomolecular Research – Toronto Open Access COVID-19 Protein Manufacturing Centre

Jordan Feld of the department of medicine in the Faculty of Medicine and the University Health Network – Interferon lambda for immediate antiviral therapy at diagnosis: a phase II randomized, open-label, multicentre trial to evaluate the effect of peginterferon lambda for the treatment of COVID-19

Jessica Fields of the Interdisciplinary Centre for Health & Society at U of T Scarborough – Impact of COVID-19 on the mental health and vulnerability of sexual and gender minorities living in Toronto

Benjamin Fine of the department of medical imaging in the Faculty of Medicine and Trillium Health Partners – Building a real-time health system COVID collaborative data and analytics hub in Ontario

Joseph Hermer of the department of sociology at U of T Scarborough – Pandemic policing of the homeless: from crime control to public health strategy

Shana Kelley of the Leslie Dan Faculty of Pharmacy – Accelerated, centralized development of diagnostics and therapeutics to combat the COVID-19 pandemic

Robert Kozak of the department of laboratory medicine and pathobiology in the Faculty of Medicine and Sunnybrook Health Sciences Centre – Development of models of pathogenesis and vaccines for SARS-CoV-2

Madeleine Mant of the department of anthropology of U of T Mississauga – Going viral: COVID-19 and risk in young adult health behaviour models.

Rhonda McEwen of the Institute of Communication, Culture, Information and Technology at U of T Mississauga – Digital technologies and Chinese interpersonal communication on the mainland and in the diaspora: the case of COVID-19

Allison McGeer of the department of laboratory medicine and pathobiology in the Faculty of Medicine, Dalla Lana School of Public Health and Mount Sinai Hospital – Working on control of COVID-19 outbreaks in long-term care

Andrew Miles of the department of sociology at U of T Mississauga – Using pro-social behaviour to safeguard mental health and foster emotional well-being

Jason Moffat of the Donnelly Centre for Molecular and Biomolecular Research – Identification of host dependency factors for SARS-CoV-2 infection and replication to accelerate drug repurposing efforts

Samira Mubareka of the department of laboratory medicine and pathobiology in the Faculty of Medicine and Sunnybrook Health Sciences Centre – Just-in-time pathogenomics for SARS-CoV-2, data for immediate action

Elizabeth Peter of the Lawrence S. Bloomberg Faculty of Nursing – Reducing the moral distress of nurses during the COVID-19 pandemic

Blake Poland of the Dalla Lana School of Public Health – Connected communities in a time of physical distancing: community-led responses to the COVID-19 pandemic in City of Toronto

Mohammad Qadura of the department of surgery in the Faculty of Medicine and Unity Health Toronto – Keeping everyone safe: Using contactless transdermal optical imaging to obtain patient vitals and symptom report in the time of COVID-19

Matt Ratto of the Faculty of Information – Toronto Emergency Device Accelerator

Scott Schieman of the department of sociology in the Faculty of Arts & Science – COVID-19 impacts on the quality of work and economic life in Canada

Michelle Science of the department of paediatrics in the Faculty of Medicine and the Hospital for Sick Children – Health-care worker seroprevalence of anti-SARS-CoV-2 antibodies

James Scott of the Dalla Lana School of Public Health – Improving and evaluating aerosol PPE and containment devices for the COVID-19 virus

Jayeeta Sharma of the department of historical and cultural studies at U of T Scarborough – Feeding our city, pandemic and beyond: documenting food system experiences, community challenges and local resilience, lessons for sustainable food solutions

Janet Smylie of the Dalla Lana School of Public Health and Unity Health Toronto – Rapid implementation of a shared COVID-19 tracking and response platform for First Nations, Inuit and Metis populations in Canada

Igor Stagljar of the department of biochemistry in the Faculty of Medicine – Immunotyping of COVID-19 Patient Sera Using Novel Protein Complementation-Based Assays

Rima Styra of the department of psychiatry in the Faculty of Medicine and the University Health Network – Mental health outcomes in health-care workers during COVID-19

Jeff Wrana of the department of molecular genetics in the Faculty of Medicine and Mount Sinai Hospital – A massively parallel, ultra-high throughput next-generation sequencing platform for widespread screening of COVID-19 and associated risk factors

William Yun Yu of the department of computer and mathematical sciences at U of T Scarborough – Privacy-preserving contact tracing app

U of T and Sunnybrook virologists work on tools to combat coronavirus outbreak

geoff.vendeville — Wed, 19 Feb 2020 14:48:54 +0000

U of T and Sunnybrook virologists work on tools to combat coronavirus outbreak

geoff.vendeville Wed, 02/19/2020 - 09:48

Cutline

Robert Kozak and Samira Mubareka are part of a local working group of scientists researching the COVID-19 coronavirus outbreak and developing a suite of tools to control it (photo by Nick Iwanyshyn)

Geoffrey Vendeville

Topic

Breaking Research

Coronavirus

Dalla Lana School of Public Health

Faculty of Medicine

Genomics

Laboratory Medicine and Pathobiology

McLaughlin Centre

Mount Sinai Hospital

Research & Innovation

Sunnybrook Hospital

In order to contain a virus, it’s important to know exactly what you’re dealing with – and the COVID-19 coronavirus is no different.

“One of the key tools to try to contain or limit transmission of infectious diseases is case identification,” says Samira Mubareka, a virologist in the ��Ƶ’s Faculty of Medicine and at Sunnybrook Health Sciences Centre.

“If you identify cases, then you can contain them. If you miss them, then you don’t.”

Mubareka and her colleague Robert Kozak, both in U of T’s department of laboratory medicine and pathobiology, are part of a local working group of scientists who are researching the novel coronavirus outbreak and are developing a suite of tools to control it.

One of their current projects involves using the latest in whole-genome sequencing technology to help hospitals characterize the virus more quickly. Their work may help to track the virus’s evolution and trace its spread.

“If the virus’s genome was a book, we’re going to figure out its entire story,” Kozak says.

Mubareka and Kozak collected specimens of the coronavirus from the first confirmed case in Canada, an adult male who was treated and eventually discharged from Sunnybrook after returning from Wuhan, China – the epicentre of the outbreak. Two more cases in Ontario have since been confirmed: the original patient’s wife, who accompanied him to China, and a woman in her 20s in London, Ont. who had also traveled to Wuhan.

Worldwide, there are more than 73,300 confirmed cases of COVID-19 as of Feb. 18. More than 1,800 have died.

Robert Kozak, pictured here in the lab, and Samira Mubareka say their team’s work will enable front-line hospital staff to run a test on-site, helping to identify and triage patients more efficiently (photo by Nick Iwanyshyn)

In Canada, where there are so far seven confirmed cases, health authorities say the risk remains low. But Mubareka and Kozak are preparing for any possible scenario.

“You put a smoke alarm in your house even if you hope there’s no fire,” says Kozak, who previously worked at the National Microbiology Laboratory in Winnipeg on Ebola and Zika.

Part of the team’s work involves developing a test that will speed up the characterization of the virus. Currently, patient samples in Ontario are sent from local hospitals by courier to the Public Health Ontario lab in downtown Toronto for testing, and to the national lab in Winnipeg for confirmation.

The process can take a few days, depending on the hospital’s distance from the labs and test volumes.

Mubareka and Kozak say their team’s work – in collaboration with McMaster University and infectious disease expert Allison McGeer of U of T’s Dalla Lana School of Public Health, Faculty of Medicine and Mount Sinai Hospital – will enable front-line hospital staff to run a test on-site, helping to identify and triage patients more efficiently. The test involves using swabs from a patient’s nose and throat to do genomic testing to sequence the virus.

“If they’re negative, you can take them [the patients] out of precautions and maybe even send them home,” Kozak says. “If they’re positive, then you can again take the appropriate precautions to isolate them and do everything else that needs to be done.”

The researchers hope they can adapt the approach for mini-sequencers the size of a cell phone, so it can be used more widely.

Vivek Goel, U of T’s vice-president, research and innovation, and strategic initiatives, says the university worked quickly to mobilize support for the project.

“With its cross-disciplinary expertise and close relationships with area hospitals, the university recognizes that it’s uniquely positioned to play a leadership role when it comes to these sorts of global health issues,” Goel says.

“We also have the benefit of having experienced the SARS outbreak in Toronto in 2003, so we know first-hand how important this sort of research can be.”

The genomic testing being performed by the U of T-led group could also help researchers get a fuller picture of the mysterious illness.

Although genomic sequences of the virus were published and shared in public databases, many were deposited soon after the first cases were identified in China’s Hubei province, according to Mubareka.

“The problem is that was early on before it started going from person to person-to-person,” she says, noting that viruses mutate.

There are only about 50 sequenced genomes of the virus, adds Kozak – for about 48,000 confirmed cases.

“You’re not getting a great snapshot,” he says. “It’s tough to really understand a lot about the virus.”

Among the nagging questions about COVID-19 that U of T and Sunnybrook researchers hope to answer are how long patients remain contagious and if the amount of the virus present in respiratory secretions is proportional to its severity.

Their work may help others understand how the virus spreads from point A to point B, and if it’s changing in ways that make it more dangerous.

The research team includes U of T students like Natalie Bell, a second-year master’s student in laboratory medicine and pathobiology who is also working with Mubareka on a project related to influenza from swine.

“It’s really interesting to see science happen in real time, especially being part of Sam’s lab [and] to see her involvement and the movement from lab to policy work, and how it impacts public health,” Bell says.

Mubareka and Kozak plan to upload the sequencing data to public servers and share it with the world to help with epidemiological studies and vaccine design.

“We will build global capacity any way that we can,” Kozak says.

Mubareka and Kozak say their work was made possible thanks in part to the McLaughlin Centre, which provided emergency funding for the project. “We have no shortage of ideas of things we can do to hopefully make a difference,” Kozak says, “but you always need someone to provide the resources to do it.”

Stephen Scherer, the director of the McLaughlin Centre at U of T and a University Professor in the department of molecular genetics, says the centre wanted to make sure the researchers had the necessary funds to do their work in time.

“Nobody is busier right now than this group, so we wanted to make the process as easy as possible for them,” Scherer says. “We also wanted these researchers to know the rest of us value their efforts to keep us safe.”

U of T researchers awarded Killam Prizes for contributions to humanities, health sciences

perry.king — Thu, 25 Apr 2019 13:20:11 +0000

U of T researchers awarded Killam Prizes for contributions to humanities, health sciences

perry.king Thu, 04/25/2019 - 09:20

Cutline

University Professors Stephen Scherer and Lynne Viola are recipients of 2019 Killam Prizes (photo by Perry King and Diana Tyszko)

Topic

Faculty of Arts & Science

Faculty of Medicine

History

Hospital for Sick Children

Humanities

McLaughlin Centre

Molecular Genetics

Research & Innovation

She has revealed knowledge about Stalinist Russia that was previously kept hidden. He has mapped our genes and given us a better understanding of autism.

Historian Lynne Viola and geneticist Stephen Scherer have not only made profound discoveries – their research has changed the entire landscape of their respective fields. The Canada Council for the Arts, the country’s public arts funder, is recognizing their lifetime contributions with Killam Prizes, the organization’s top annual award.

Viola, one of the world’s leading scholars on Stalinist Russia, is being awarded the prize in the humanities. Scherer, a leading genomic researcher, is being awarded one in health sciences.

“The scholarship of Professors Viola and Scherer are changing our understandings of their fields, leading to a healthier and safer world,” said Vivek Goel, U of T’s vice-president of research and innovation.

“The ��Ƶ congratulates them for this significant award, recognizing their outstanding careers.”

The council awards $100,000 Killam Prizes in five categories each year, including engineering, natural sciences and social sciences. The Killam Trust, which administers the award, also names researchers to a two-year Killam Fellowship that supports outstanding scholars on groundbreaking projects.

Since 2010, U of T faculty have won 13 Killam Prizes, accounting for more than a quarter of those awarded to Canadian researchers. In the past five years, U of T has had winners in all five Killam Prize categories – including double wins in each of engineering, health sciences and humanities.

“U of T’s researchers and their findings are resonating widely, inside and outside of the classroom,” Goel said.

Read about the U of T researchers awarded 2019 Killam Research Fellowships

Lynne Viola

University Professor Lynne Viola has worked for decades to shed light on Josef Stalin's Great Terror in the 1930s (photo by Diana Tyszko)

Lynne Viola sees Stalinist Russia, and its oppressive violence, “as a cube.”

Viola, a professor in the department of history, organized her extensive study of the period from a variety of different perspectives, or sides – each one helping to inform our overall understanding of the brutal regime.

“I wanted to look at violence from different angles to get a sense of the spectrum of responses and policy on terror through the '30s, and turning it around in different ways,” said Viola, who has published four definitive books on the topic.

Viola's first book, 1987's The Best Sons of the Fatherland, focused on the supporters of Stalin’s regime. Her second book, 1996's Peasant Rebels Under Stalin, looked at state government resisters. Her third book, The Unknown Gulag, published in 2007, looked at Stalin’s victims and their fates. Finally, her most recent work – 2017’s Stalinist Perpetrators on Trial – looked at those who implemented Stalin’s Great Terror, a campaign of political repression from 1936 to 1938.

Rich in detail and filled with primary sources, including from the KGB archives, Viola's research seeks to contextualize a period the Soviet government sought to hide from the public. She called the work “painstaking.”

“My last three books have been about using the voices of these people,” said Viola, who won the Molson Prize in 2018. “I tried to use their voices to tell the story, particularly in terms of that second book, Peasant Rebels.

“I wanted these peasants to have a say. I wanted them to present their side of the story.”

Since her days as a graduate student, Viola has worked to create a richer, more nuanced understanding of Soviet history – and push it in a more scholarly direction. When the Soviet archives became available in the 1990s, Viola was among the first researchers to seize the moment.

Viola’s most recent book about Stalinist perpetrators was based on Ukraine’s former KGB archives, which became available following a 2014 revolution that saw the country’s incumbent president ousted. Viola sees the work as completing the full circle of perspectives from that period.

“I certainly feel like we have a really good sense of the early 1930s and a better sense of the late 1930s,” she said.

She added that she views the archives as a “kind of a back door into the Great Terror, so that we can literally accompany these perpetrators into the execution room, the interrogation room and find out the mechanisms of how the Great Terror worked.”

Viola hopes her scholarship has opened the door for others – especially in the Kiev archives, where researchers will likely be sifting through documents for years to come.

“It’s really a great recognition of the humanities,” she said of winning the Killam Prize. “It was an absolute honour.”

Stephen Scherer

University Professor Stephen Scherer is the director and co-founder of the Centre for Applied Genomics at the Hospital for Sick Children (photo by Perry King)

Stephen Scherer will never forget what a fourth-year professor told him when he was applying to graduate school.

“Word for word, he said, ‘You’re terrible, you’re a loser. You’ll never do anything with your life,’” he recalled. A native of Windsor, Ont., Scherer wondered if the professor was trying to motivate him or was simply being a jerk.

Whatever the message, Scherer, now in U of T's department of molecular genetics, has gone on to become one of the top genetic researchers in the world. He is the co-founder and director of the Centre for Applied Genomics at the Hospital for Sick Children and the director of U of T’s McLaughlin Centre, which seeks to advance genomic medicine through research and education. In 2004, he founded the Database of Genomic Variants, the world’s most-used database for gene copy number variation (CNV) – repeated or deleted copies of entire genes that vary by individual – that helps facilitate thousands of clinical diagnoses around the world every day.

In the early 2000s, Scherer’s team identified the CNV of specific genes involved in brain development that contribute to autism.

Scherer’s initial breakthrough came while mapping chromosome 7 – the location of the cystic fibrosis gene – as a PhD student in the 1990s as part of the Human Genome Project. His findings, published in 2003, contributed to groundbreaking insights in the field of genetics.

“It gave me the ability to look at the genome in a way others hadn’t been able to do before,” said Scherer, whose work has been documented by 500 scientific papers and cited more than 50,000 times.

Scherer equated the discovery of CNV to recent news that researchers photographed a black hole for the first time – namely that he and his team were peering into the unknown.

“These things called copy number variations were basically parts of the genome hidden from us,” he said.

Yet, for years, his findings were met with resistance.

“It was about convincing the scientific community that something so prevalent was actually there,” Scherer said. “As you can imagine, there were a lot of scientists who were working in the same field who should have also made the discovery, or who had the data but didn’t make the connection.”

Scherer’s 2004 report made waves and set the tone for an American Society of Human Genetics conference the same year in Toronto. Scherer recalled one conversation with a student that still stands out: “He said, ’I memorized every piece of data in that table in your paper. It was so critical for the interpretation of my experiments.’”

Scherer sees the Killam Prize as a way to rally resources around the discovery and expand its application. “We applied it in autism but we’ve seen it in every single disease,” he said.

Ideally, he hopes to be in attendance one day when one of his students wins a prize like the Killam.

“My strategy is to plant a thousand seeds,” he said. “We have a million things going on here all the time – and my job is to watch, listen and learn.”

Meet U of T's five newest University Professors

perry.king — Tue, 12 Feb 2019 19:56:08 +0000

Meet U of T's five newest University Professors

perry.king Tue, 02/12/2019 - 14:56

Cutline

From left to right: Susan McCahan, vice-provost, academic programs, Chancellor Rose Patten, newly named University Professor Shana Kelley of the Leslie Dan Faculty of Pharmacy and U of T President Meric Gertler (all photos by Nick Iwanyshyn)

Topic

Department of Chemistry

Faculty of Arts & Science

Faculty of Medicine

Hospital for Sick Children

Humanities

Leslie Dan Faculty of Pharmacy

Five ��Ƶ professors were recognized this week as the university's newest University Professors, an elite designation bestowed on a small number of faculty members.

Shana Kelley, John Kloppenborg, Tania Li, Douglas Stephan and Stephen Scherer were honoured at a reception on Monday for their productive and influential academic careers. University Professors are chosen for their unusual scholarly achievement and pre-eminence in a particular field of knowledge.

“Our five honorees are global leaders who each have had a profound impact in their respective fields and on society more generally,” said U of T President Meric Gertler.

“They’ve advanced influential new ideas, new methodologies and new technologies. They’ve challenged paradigms and defined entirely new areas of study.”

The five faculty members were presented plaques by President Gertler, Chancellor Rose Patten and Susan McCahan, U of T’s vice-provost of academic programs.

Between them, the five new University Professors have garnered five honorary degrees, four Royal Society of Canada fellowships, three Canada Research Chairs and two Steacie Prizes – which recognize a person under 40 who has made notable contributions to scientific research in Canada.

“For as long as I have been closely associated with the ��Ƶ, I have had such a keen interest, and inspiration really, about the great talent that is here,” said Chancellor Patten. “It’s uplifting and very humbling, to hear all you’ve done, to see all that you’re doing, to hear your fine words.

“The university is such a pool of talent, and you just raise it higher.”

Meet U of T's five new University Professors:

Shana Kelley

Shana Kelley, from the Leslie Dan Faculty of Pharmacy, is a trailblazing chemist who has pioneered nanotechnologies for new clinical diagnostic approaches to combat cancer and infectious diseases. Her research, which has been published in dozens of prestigious journals, was behind two molecular diagnostic companies she co-founded – GeneOhm Sciences and Xagenic.

“When I told my parents, they said, ‘You’re a university professor? Haven’t you been doing that for a while?’” joked Kelley prior to the ceremony. “The thing that is very special about it is that it’s your own colleagues who have decided that you’ve achieved this rank.

“That’s a very special kind of recognition. It’s one thing for the outside world, they don’t have to honour your accomplishments, but when your colleagues do it, it’s extra special.”

John Kloppenborg

John Kloppenborg, from the department for the study of religion, is considered one of the leading academics on the origins of Christianity and the New Testament. A 13-time winner of the Dean’s Special Merit Award, he has supervised 28 doctoral students and was an associate editor for a number of major journals in his field.

Kloppenborg used one word to describe his appointment: “daunting.”

“When you look at the list of people who are University Professors at the ��Ƶ, 50 of them right now, those are astonishing people who have done amazing things.

“It a real honour and humbling experience to receive this.”

Tania Li

A globally recognized anthropologist, Tania Li has investigated land tenure, forest politics, food security and global development. With a particular focus on Indigenous highland communities in Indonesia, Li's three award-winning books have been used in classrooms worldwide.

She was honoured last year with the 2018 Insight Award from the Social Sciences and Humanities Research Council of Canada (SSHRC) – the first U of T researcher to receive this award.

Li, who has worked abroad and been recognized globally for her scholarship, is pleased about being honoured by U of T.

“This particular [award] is like the home team, right? This is the institution where I’m based,” said Li. “I found a rich community of scholars here, and it’s really wonderful to be among that group, to be recognized.”

Stephen Scherer

Stephen Scherer is one of the top genetic researchers in the world, co-founding and leading the Centre for Applied Genomics at the Hospital for Sick Children, which recently defined genetic factors identifying autism – 300 scientific papers have documented this work, with about 20,000 citations.

He is internationally known for his work studying the structure and function of the human genome, especially his contributions sequencing the first genome of an individual and the human chromosome 7.

Scherer is the director of U of T’s McLaughlin Centre, which seeks to advance genomic medicine through research and education.

But it's the role of teacher that gives him the most satisfaction, he said.

“I contribute through the research I perform but the way I give back is through the teaching and mentoring of students,” said Scherer, who teaches two courses each year. "Now I'm the one providing the environment, the nurturing – whereas, in the past, I was the student.

“To become a University Professor is surreal.”

Douglas Stephan

Douglas Stephan is a celebrated chemist who is a pioneer in the field of organometallic and inorganic chemistry. His first major breakthrough was the discovery of a new class of catalysts for the polymerization of ethylene – basically affecting how plastics are made worldwide. A winner of the Steacie Prize, Stephan has authored nearly 500 scholarly articles, which have been cited more than 40,000 times.

He has garnered nearly every prize possible in chemistry, but says he is humbled by this appointment.

“There’s a number of University Professors in my department, in chemistry, and to be lumped into the same group as those guys is certainly an honour and humbling for sure,” he said.

“These are people I really admire and respect. It’s great.”

See a list of all of U of T's University Professors

Gene genies: How Toronto became a global hub for genetic research

noreen.rasbach — Fri, 21 Sep 2018 20:38:56 +0000

Gene genies: How Toronto became a global hub for genetic research

noreen.rasbach Fri, 09/21/2018 - 16:38

Cutline

“It’s mind-boggling how fast the technology has improved,” says Stephen Scherer about sequencing a person's genetic information

Chris Sorensen

Topic

Global Lens

Artificial Intelligence

Faculty of Applied Science & Engineering

Research & Innovation

Startups

Stephen Scherer has had a finger on the pulse of genomic research for over 20 years. But that didn’t prepare him for what happened while he was vacationing at his Ontario cottage last summer.

“I had four consecutive days where people came and asked, on behalf of their relatives, about a genetic test – asking what does this mean?” says Scherer, a University Professor at the ��Ƶ who is a director at U of T’s McLaughlin Centre and the Hospital for Sick Children’s Centre for Applied Genomics.

The sudden rise in dockside queries is a result of the increasing ease of reading one’s genetic information. In a lab at SickKids’ Peter Gilgan Centre for Research and Learning, for example, it now costs about $1,000 to sequence an individual’s entire genome – a process that takes about a week. By contrast, it took researchers about $3 billion and 15 years to create a reference genome for the Human Genome Project, published in 2003.

“I couldn’t imagine, even a few years ago, we would be doing this,” Scherer says. “It’s mind-boggling how fast the technology has improved.”

Yet, what hasn’t improved quite so rapidly is our understanding of all that data. Recent research has shown our genomes are far more complex than previously thought. That, in turn, means much more work is necessary to decode our genomic “blueprints” so we know when mutations are something to worry about, and how prevent them from becoming full-blown illnesses.

Getting there will require tapping the expertise – and, critically, data – of researchers and clinicians who work in a wide swath of medical fields.

It’s an interdiscipinary challenge U of T and its partner hospitals are in a unique position to tackle.

“We think U of T is the right place to do this,” Scherer says. “The breadth of research here is so vast and the university has a single medical school, which is a huge advantage since people who are doing cancer research or autism research are actually meeting around the same tables.

“We really see this concept of precision medicine driven by the engine of genome sequencing.”

Toronto has another reason to be optimistic about its chances to be a leader in genomic medicine: The city already has a long history of research excellence when it comes to understanding our genes and genomes.

In the mid-1980s, for example, U of T University Professor Tak Mak discovered the T-Cell receptor, beating labs around the world and establishing a cornerstone of modern immunology. And he did it despite being turned down for a grant related to the work.

“It was a sunny Sunday afternoon in the summer of 1983,” Mak, who is also a senior scientist at the Princess Margaret Cancer Centre, recalled in a 2011 article published by the Proceedings of the National Academy of Sciences of the United States of America. “I walked into the lab, and there was a stack about two feet high of computer sheets comparing the sequences of our T cell-specific genes to everything in the gene bank.

“After scanning through hundreds of pages, I held up one sheet, looked at it from an angle, and there it was … I stared at it for a long time and finally said to myself, ‘I can't believe it. This could be the human TCR.’”

Other local success stories in the field were equally as momentous: In 1989, U of T University Professor Emeritus Lap-Chee Tsui, who was previously the geneticist-in-chief at the Hospital for Sick Children, discovered the mutation in the gene responsible for cystic fibrosis, a genetic disease that affects about one out of every 2,000 Canadians – mostly children; in the mid-1990s, U of T University Professor Peter St George Hyslop discovered the genes responsible for early-onset Alzheimer’s.

Scherer, too, has made several key contributions. In 2004, he co-authored a landmark study about copy-number variations, or repeated or deleted copies of entire genes that vary by individual. Then, earlier this year, Scherer and fellow researchers released a first-ever study as part of the Personal Genome Project (PGP) Canada. The paper, published in the Canadian Medical Association Journal, found all of the project’s 56 participants – all reasonably healthy – possessed “clinically relevant” genomic information.

While the PGP study noted there remains much ambiguity – some variants in the genome can lead directly to disease or genetic disorders, others appear to merely raise risks, still others seem to have no effect at all – it nevertheless concluded “these findings suggest that whole genome sequencing can benefit routine health care in Canada’s future.”

Scherer, for one, envisions a day when every child will have their genome sequenced upon being born – a sort of genetic instruction booklet. “That’s what we’re preparing for here at SickKids – essentially every child would have their genome done as a framework so they can use it in decision-making throughout their lifetime,” he says.

Beyond the hospital, there are also a growing number of private companies who offer direct-to-consumer genetic testing. The Silicon Valley startup 23andMe, for example, built an international business with five million users straddling nearly 50 countries in just over a decade. It has even attracted the interest of drug giant GlaxoSmithKline, which wants to use the company’s genetic database to find new drug targets.

No wonder, then, genetic counsellors – U of T offers a two-year master’s program – occupy one of the fastest growing job categories in the United States, according to numbers compiled by the U.S. Bureau of Labor Statistics.

From a research perspective, meantime, there’s hardly a facet of medicine, from autism to heart disease, that hasn’t been informed by the growing ocean of genetic data.

Michael Sefton is a member of the department of chemical engineering and applied chemistry and executive director of Medicine by Design (photo by Neil Ta)

University Professor Michael Sefton, the executive director of U of T’s Medicine by Design initiative, says genomic information is core to everything researchers do in the cutting-edge field of regenerative medicine, which aims to regrow, repair or replace damaged or diseased cells, organs and tissues.

“Some of the projects don’t worry so much about what the genes are up to, but will instead have a protein-centred perspective or are looking at how the cells interact,” says Sefton, who also holds appointments in the Institute of Biomaterials & Biomedical Engineering and the department of chemical engineering and applied chemistry.

“But if you scratch the surface, they are unwittingly using the genome information to understand what’s going on.”

As for the idea of Toronto becoming a leader in genomic-inspired medical research, Sefton says the interdisciplinary approach taken by Medicine by Design, made possible by a $114-million grant from the federal government, the largest in U of T’s history, proves Toronto is indeed a place where it’s possible for researchers to successfully work together across institutional boundaries.

Says Sefton, “We talk to each other, we collaborate – we’re Canadian.”

Toronto may also have a technological advantage in the race to develop genomic medicine. In recent years, the city has become an important hub for artificial intelligence, or AI, research in fields like deep learning, which was pioneered by people like U of T University Professor Emeritus ��Ƶ. The technology, which mimics the way the human brain learns, is capable of recognizing patterns in extremely large data sets – like the human genome.

Deep Genomics, for example, is a startup spun out of research by U of T Professor Brendan Frey that uses deep learning to search for clues about genetic diseases and potential treatments. It’s so far raised more than US$10 million in financing.

“Right now we look for bazooka wounds in the genes,” Scherer says. “But to find the subtle variations, we need to use machine learning.

“This is an area where Toronto could be a world leader.”

This story first appeared in the Faculty of Medicine's 2018 Dean's Report. Read the report.

Personal Genome Project shows whole genome sequencing may transform how Canadians manage their own health care

noreen.rasbach — Mon, 05 Feb 2018 15:57:20 +0000

Personal Genome Project shows whole genome sequencing may transform how Canadians manage their own health care

noreen.rasbach Mon, 02/05/2018 - 10:57

Cutline

“Though we’ve identified clinically relevant genomic information for all participants, each of their genomes has even more information that we can’t interpret yet,” says Stephen Scherer, director of U of T's McLaughlin Centre (photo by J.P. Moczulski)

Topic

Research & Innovation

Stephen Scherer

Researchers from the ��Ƶ and the Hospital for Sick Children (SickKids) behind the Personal Genome Project Canada are predicting that whole genome sequencing will likely become part of mainstream health care in the foreseeable future.

In the first-ever study from the Personal Genome Project Canada (PGP-C), the researchers found 25 per cent of participants to date had genomic information indicating they could be at risk for future disease and even more were found to have genetic variants that would be relevant for family planning or newborn screening. All participants had genomic information associated with risks for adverse drug reactions or altered drug effectiveness, with 23 per cent of participants identified as being at risk for severe, potentially life-threatening adverse drug reactions.

The study was published Feb. 3 online in CMAJ (the Canadian Medical Association Journal).

PGP-C is a comprehensive public data resource that integrates participants’ whole genome sequencing data with their health information to advance scientific understanding of genetic and environmental contributions to human health and disease. All of the project’s inaugural 56 participants have clinically relevant information in their genomes, highlighting the potential of using whole genome sequencing data proactively for precision medicine and to reduce the risk of therapeutic failure.

“Though we’ve identified clinically relevant genomic information for all participants, each of their genomes has even more information that we can’t interpret yet,” says Stephen Scherer, director of U of T's McLaughlin Centre and senior scientist and director of The Centre for Applied Genomics (TCAG) at SickKids.

Read an article in the Globe and Mail about the study and Personal Genome Project Canada

“As we analyze more samples, we continuously learn more about the human genome which will allow us to eventually take full advantage of the wealth of information it contains. That’s why the goal of the project is to sequence thousands of genomes each year.”

PGP-C is the Canadian arm of the global Personal Genome Project, a collaborative academic research effort that started with Harvard Medical School’s Personal Genome Project in 2005. A priority of the Personal Genome Project is to share information collected from the localized projects with researchers around the world to drive new knowledge about human biology.

Participants were required to undergo an extensive consent process as all data, including results from their whole genome sequencing, combined with personal and family history, is available online. Each participant had access to genetic counselling to appropriately contextualize the results of their genetic testing.

“Genetic counsellors play an important role in communicating and interpreting these results appropriately,” said Professor Trevor Young, dean of U of T's Faculty of Medicine, which runs Ontario’s only academic training program for genetic counselling. “The demand for these specialized skills is only going to rise given the massive increase in the number of genome-wide tests now being used in hospitals.”

Interested in publicly funded research in Canada? Learn more at U of T’s #supportthereport advocacy campaign

The cost of whole genome sequencing has fallen dramatically since PGP-C began recruiting and analyzing samples in 2012 and further still from when the project was conceptualized in 2007. Signs indicate the technology will continue to become more affordable and accessible, which the authors expect will transform whole genome sequencing into more of a mainstream practice for the general population. As a result, frontline health-care providers may become involved in interpreting and delivering resulting genomic information in the near future.

The work was funded by the ��Ƶ’s McLaughlin Centre, the Canada Foundation for Innovation, Genome Canada-Ontario Genomics, the Government of Ontario, the Canadian Institutes of Health Research (CIHR), Medcan Health Management Inc. and SickKids Foundation.

McLaughlin Centre

U of T researchers help lead national effort to explore role of genes in COVID-19

U of T to support high-impact coronavirus research projects through Toronto COVID-19 Action Fund

U of T and Sunnybrook virologists work on tools to combat coronavirus outbreak

U of T researchers awarded Killam Prizes for contributions to humanities, health sciences

Read about the U of T researchers awarded 2019 Killam Research Fellowships

Read more about previous Killam Prize winners

Lynne Viola

Stephen Scherer

Meet U of T's five newest University Professors

Shana Kelley

John Kloppenborg

Tania Li

Stephen Scherer

Douglas Stephan

Read more on the five newest University Professors

See a list of all of U of T's University Professors

Gene genies: How Toronto became a global hub for genetic research

Personal Genome Project shows whole genome sequencing may transform how Canadians manage their own health care

Read an article in the Globe and Mail about the study and Personal Genome Project Canada

Interested in publicly funded research in Canada? Learn more at U of T’s #supportthereport advocacy campaign

Read the full study in CMAJ