Genomics

Faculty of Applied Science & Engineering

Chemical Engineering

Industry

Mining

Sustainability

Researchers from the University of Toronto – in collaboration with a group of mining firms – are using acid-loving bacteria to design new processes for recovering nickel, a critical mineral in growing demand around the world.

The research partnership with the Faculty of Applied Science & Engineering includes the following companies: Vale, Glencore, Metso-Outotec, BacTech, MIRARCO and Yakum Consulting. The insights gained could enable these companies to reduce their environmental footprint while at the same time gaining access to new sources of nickel, which is used in everything from stainless steel to next-generation batteries for electric vehicles.

Supported by $2 million in funding through Ontario Genomics from Genome Canada and another $2 million from the Government of Ontario, the industrial partners will also provide approximately $2 million in funding and in-kind contributions, bringing the total up to $6 million.

Radhakrishnan Mahadevan (photo by Sara Collaton)

“Tailings from nickel mining operations have been an environmental challenge for a very long time,” says Radhakrishnan Mahadevan, a professor in the department of chemical engineering and applied chemistry who is leading the new partnership.

“If exposed to oxygen, chemical reactions in the tailings generate acids that makes them toxic to most forms of life. But we know that there are some microbes that can thrive in these environments. The biochemical techniques they use to survive can offer us new pathways to meet our goals.”

In Canada, nickel is found in ores that are mostly composed of iron and sulphur. After most of the nickel is extracted, the iron and sulphur remain, along with trace amounts of nickel – typically less than 1 per cent by weight. Together, these substances are known as tailings, and they exit the extraction process in the form of a slurry, a suspension of tiny mineral particles in water.

If the slurry is exposed to oxygen, the sulphur remaining in the slurry can become oxidized to form sulphate, a key component of sulphuric acid. To slow this process, the tailings are typically stored under water in tailings ponds. However, over time, these ponds still become highly acidic, with a pH in the range of 1-2.

Mahadevan, University Professor Elizabeth Edwards and Professor Vladimiros Papangelakis – all in the department of chemical engineering and applied chemistry – have been studying the organisms that are able to survive in these tailings ponds.

Several years ago, the team obtained samples from a mine tailings site operated by one of their industrial partners. By analyzing DNA present in this sample, they were able to identify a new strain of an organism known as Acidithiobacillus ferridurans. In 2020, they published the full genome of this new strain, which they called Acidithiobacillus ferridurans JAGS.

Ever since, the researchers have been further enhancing the capabilities of this bacterium through a process known as adaptive evolution. Samples that grow well in the presence of low concentrations of mine tailings are gradually exposed to increasingly higher concentrations. The best of those cultures are exposed to even higher concentrations, creating new strains that are more effective at carrying out key chemical reactions.

“This bacterial strain can actually extract energy from the oxidation of both iron and sulphur in a process that we call bio-leaching,” Mahadevan says.

“In the process, they also liberate the remaining nickel, which would otherwise be very difficult to recover from a solution this dilute. What’s amazing about the bacterium is that it can carry out these reactions at ambient temperatures and low pressures. And even more exciting is the idea that, if we understand how they are doing it, we might be able to control and direct the process.”

For example, the sulphur in the tailings is in the form of sulphide. Mahadevan says that instead of oxidizing it all the way to sulphate, which forms the acid, it might be possible to alter the process to instead create elemental sulphur. In this case, the sulphur would precipitate out of solution and could be sold as a commodity chemical for other applications, such as the production of fertilizers.

Mahadevan says the team will continue enhancing the bacterium through adaptive evolution, but that they are also pursuing a genetic engineering approach by using the emerging gene editing technique known as CRISPR.

“One of the things we’ve learned from studying this strain is that it has made more copies of certain genes that are involved in the transport of metal ions within the cell.

“If we use gene editing to further enhance the expression of these kinds of genes, we might be able to help it to grow even better, or to be more effective at carrying out the kinds of chemical transformations we want it to do,” Mahadevan says.

“Partnerships between the researchers and industry are the cornerstone of Ontario’s thriving innovation community,” says Bettina Hamelin, president and CEO of Ontario Genomics.

“By supporting the development and uptake of new technologies that provide game-changing solutions to the world’s most pressing challenges, Ontario Genomics is helping to nurture healthy people, a healthy economy and a healthy planet for generations to come.”

Mahadevan estimates that it will take another three to five years before the research team has both a bacterial strain and an associated process that will be ready to be tested in the field.

“Our goal with this project is to eliminate the technical bottlenecks to the application – to de-risk sufficiently so that our partners can put in the resources it would take to fully deploy it in their operations,” he says.

“If they can do that, it could not only completely change the way they deal with mine tailings, but also provide access to new sources of nickel – which will only become more important in the years to come.”

��˾��ֱ��'s Leah Cowen on Canada’s opportunity to become a genomics 'powerhouse'

Christopher.Sorensen — Wed, 15 Mar 2023 13:16:45 +0000

��˾��ֱ��'s Leah Cowen on Canada’s opportunity to become a genomics 'powerhouse'

Christopher.Sorensen Wed, 03/15/2023 - 09:16

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Leah Cowen, centre, ��˾��ֱ��'s vice-president, research and innovation, and strategic initiatives, says Canada is an invaluable resource for genomics research in fields such as health, environment, food and agriculture (photo by Steve Southon)

Rupinder Bagha

Topic

Temerty Faculty of Medicine

Leah Cowen

Faculty of Arts & Science

To drive innovation in genomics through commercialization, create socioeconomic growth and cement Canada’s position as a world-leader in genomics research and innovation, the federal government is expected to announce the Pan-Canadian Genomics Strategy (PCGS) later this year – funded through an allocation of $400 million announced in the 2021 budget.

In March, the results of consultations toward the national strategy were released, with participants underlining the opportunity for Canada to establish a clear, long-term vision for genomics in this country. Other specific recommendations made by participants included:

Data standards, co-ordination and privacy regulations that enable broad access to and use of data across the genomics ecosystem
Increased funding, lab capacity and access to infrastructure and equipment to support research and development
De-risking commercialization through the Government of Canada adopting a first purchaser role
Specialized training in genomics, bioinformatics and private sector awareness and capacity to employ genomics trainees

While human health remains a primary focus of genomics research, other fields are benefitting from advances in the field. In agriculture, for example, scientists are using genomics as a tool to track biodiversity (biosurveillance) and to understand why some organisms are more resilient to environmental change. As knowledge advances, genomics can be applied to develop mitigation strategies such as using plants to decontaminate soil. The federal government, through Genome Canada, launched the Climate-Smart Agriculture and Food Systems initiative to capitalize on this potential.

Leah Cowen, vice-president, research and innovation, and strategic initiatives at the University of Toronto, is a recognized genomics leader, researcher and entrepreneur. She recently discussed how Canada is preparing to shape and lead the genomics sector.

The federal government’s consultation toward the launch of a national strategy identifies three key areas of opportunity: national competitiveness through regional strengths, co-ordination among stakeholders, and infrastructure. Where do you see Canada’s opportunities in the future of genomics?

Canada is a powerhouse in genomics. Its strength in genomics lies in its uniqueness as a jurisdiction with an incredible diversity among its ecosystems and human populations. These strengths position Canada at a global advantage and serve as an invaluable resource for genomics research across fields such as health, environment, food and agriculture.

On regional strengths, I would suggest that one of Canada’s assets in this sector is the ecosystem in the Greater Toronto Area (GTA). The GTA encompasses foundational assets like the Toronto Academic Health Science Network (TAHSN) – a network of 14 affiliated hospitals with ��˾��ֱ�� as the primary research and training hub – as well as more than 10 campus-linked accelerators across our three ��˾��ֱ�� campuses and catalysts like the MaRS Discovery District and the Centre for Commercialization of Regenerative Medicine.

We have remarkable talent and training programs, from fundamental to applied genomics, and a hub of diversity in Toronto. From a genomics point of view, diversity is essential for understanding population-level processes. One-of-a-kind training programs such as CANSSI STAGE offer skills and career development to graduate students and post-docs in high-demand areas of genomics like genetic epidemiology and statistical genetics. In addition, ��˾��ֱ��’s flagship masters of science in genetic counselling program provides students with the skills needed to apply their genomics knowledge to clinical settings.

The GTA is also home to diverse sets of minds that bring different perspectives to tackle biological challenges. Companies like Deep Genomics – Canada’s highest-valued biotech company – use AI and machine learning to develop treatments for genetic disease.

The expertise, relationships and skills leveraged in these areas are accelerating the pace of genomics discovery and creating significant impact for Canada’s bioeconomy. 

The recently released summary of stakeholder consultations identified data as an area of opportunity. What are your thoughts?

Canada’s genomics-related data infrastructure is significantly limited in both size and scope relative to international counterparts, impeding the full potential of genomics within Canada. Maximizing the impact of the vast amounts of genomics data currently available requires a strategic and co-ordinated effort to support the development of cutting-edge genomic technologies and leading genomic infrastructure at scale. This involves limiting the existing fragmentation of valuable data assets across Canada, prioritizing open access to data for Canadian researchers and supporting the pipeline of next-generation technology development.

The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL -EBI) is one model for data storage, analysis and management. Canada does not need its own analogous system to the EMBL-EBI but should actively participate and contribute to these international initiatives so that they are available to our researchers.  

Canada is home to a number of deep data portals that are housed within provincial boundaries and some national portals, such as CIHI and CANUE, offer great data points for researchers. If we can integrate data repositories and standards, we can garner significant understanding and benefits.

Critical to the utility of genomics data infrastructure is the necessary representation of all individuals in genetic data. The Pan-Canadian Genomics Strategy should prioritize establishing a national approach to meaningfully engaging underrepresented populations in the collection, management and analysis of genomics data. 

How can the national strategy address diversity, equity and inclusion – another area stakeholders identified as significant?

Addressing the historic inequities and underrepresentation of marginalized groups in biomedical research and in genomics data will strengthen the value of Canada’s genomic enterprise.

There are also many ethical, social sciences and humanities components to genomics that Canada can inform the appropriate use and privacy of genetic and genomic information – just as it can with the inclusion of diverse populations in genetic research.

The Pan-Canadian Genomics Strategy should recognize universities as partners in supporting these actions. ��˾��ֱ��, for example, is committed to equity, diversity and inclusion in all its activities, including genomic innovation, addressing health disparities and fostering equity in genomics-related areas.

The Data Sciences Institute at ��˾��ֱ�� accelerates the impact of data sciences across fields like genomics to address pressing societal questions around inequity and the use of new statistical and algorithmic techniques to drive positive social change.

The Schwartz Reisman Institute for Technology and Society is also a resource that can convene and amplify conversations on ethics and access to genomics careers and applications. This is also one of our strengths of ��˾��ֱ�� – our phenomenal breadth of research expertise.

What specific elements are you looking to see in the Pan-Canadian Genomics Strategy?

The critical piece is ensuring that the strategy supports the full continuum of innovation.

This includes support for discovery-based science. Often the focus winds up being on terminal parts of the pipeline such as translation, commercialization or implementation without supporting the early-stage work. This is short-sighted as work at the discovery stage enables new ideas and the knowledge from which different applications are born.

CRISPR is a great example of how fundamental discovery science changed the world and created a technology that impacts how we think about disease treatment and virtually every aspect of modifying biology on the planet. CRISPR is a cost-effective genetic engineering tool that will continue to increase options for treating diseases among humans and all organisms.

Talent will also be a significant element in determining Canada’s genomics capacity to lead. Every country in the world is thinking about genomics. There is competition for great talent and great talent can go anywhere in the world – so investment is critical for Canada to retain a leadership position.

Are there approaches to training in your lab that you think would successfully scale to a national approach?

Training for genomics is interdisciplinary. This is where Canada has an advantage with strengths across fields that inform genomics science and applications.

I think about how to develop talent in my own lab a great deal to ensure that trainees are enabled to reach their potential. We ensure that students and post-doctoral fellows are trained at the intersection of fields such as functional genomics, structural genomics, chemical genomics, molecular genetics and computational biology to develop and work with the next generation of technologies. In our broader community, we also focus on training in related fields such as genetic epidemiology, statistics, computer science, AI and quantum computing to unleash the full potential of genomics research.

Universities are powerful players in providing specialized and interdisciplinary training for Canada’s genomic workforce.

For example, researchers at ��˾��ֱ��’s Institute for Biomedical Engineering and the Terrence Donnelly Centre for Cellular and Biomolecular Research are inventing and applying new technologies to target therapies for schizophrenia and other psychiatric conditions, testing the effects of human mutations in yeast to help clinicians diagnose patients more accurately and monitoring and managing sulfur compounds in mines to limit toxicity and contamination impacts.

How has your experience as an entrepreneur in this sector shaped the training offered in your lab?

I was able to use my academic genomics research on fungal pathogens to enable the translation of fundamental discoveries for treating invasive fungal reactions – a growing public health crisis. Participating in the University of Toronto Early-Stage Technology (UTEST) program helped our team launch Bright Angel Therapeutics, a biotechnology company focused on developing novel antifungal drugs that has attracted interest and investment from around the world. We talk about the opportunities to build on the critical skills taught in the lab to become entrepreneurs.

Read the original article at ��˾��ֱ��’s Office of Government Relations

Software tool built by ��˾��ֱ�� startup shares genetic data with COVID-19 researchers around the world

Christopher.Sorensen — Mon, 04 May 2020 16:08:33 +0000

Software tool built by ��˾��ֱ�� startup shares genetic data with COVID-19 researchers around the world

Christopher.Sorensen Mon, 05/04/2020 - 12:08

Cutline

Co-founded by ��˾��ֱ�� alumnus Marc Fiume, DNAstack launched a search engine aimed at the global research community that scans and indexes genomic information about the novel coronavirus (photo by Jeff Beardall)

Topic

Dalla Lana School of Public Health

Startups

One of the most puzzling things about the novel coronavirus is how it affects people in such different ways.

Among a single group of very similar people of the same age, some who contract COVID-19 will be asymptomatic, others mildly ill, while still others will be seriously sick and some will die.

Marc Fiume doesn’t know why this is the case. The University of Toronto alumnus is a computer scientist, not a medical researcher. But he does know what the scientists studying the virus and developing treatments need: a near-constant flow of information.

So he and his colleagues at DNAstack are adapting their health-oriented search engine technology to a new tool that offers shared genetic data about COVID-19.

“What we know about the virus is changing hourly as researchers and clinicians accumulate and analyze data,” says Fiume, who earned his PhD, master’s and bachelor’s degrees from ��˾��ֱ��. “So we are deploying our technologies at DNAstack to support researchers investigating the virus.”

Dubbed COVID-19 Beacon, DNAstack launched their new tool in late March. It’s a search engine that scans and indexes genomic information about the virus shared by scientists from around the world, making it possible for users to share and discover knowledge about the genetics of the virus in real time.

Researchers can then use the information – a mix of the virus’s genome (a complete set of genes) and other biological data – to see how the virus is changing as it moves through the global population.

“By sharing this genomic information over a cloud-based global network, there is the potential to improve knowledge of COVID-19 at a speed and scale that isn’t otherwise possible,” Fiume says.

“That will contribute to new ways to fight the virus, such as the development of a vaccine.”

Fiume launched DNAstack with partner Ryan Cook in 2014. The startup received support and guidance from ��˾��ֱ�� Entrepreneurship. As Fiume told MaRS Magazine two years ago, the inspiration to start the company came from his best friend, Dan, who has cystic fibrosis. Genetic disease is “…actually a very common problem. If you talk to anyone, within one or two degrees of separation they have someone in their family, or someone close to them, who’s affected by a genetic disease.” But given the complexity of individuals’ genetic make-up, Fiume said he quickly realized that his field – computer science – would play an important role in the search for treatments for genetic ailments.

Since then, the startup has built software to facilitate collaborative biomedical research and has partnered with leaders in cloud computing, sequencing, software and security to form the Canadian Genomics Cloud to further research discovery. DNAstack has also embarked on a partnership with Autism Speaks to enhance the agency’s research portal. Through the collaboration, DNAstack organized one of the largest collections of autism genomes in the world and made them more easily accessible and able to be analyzed by researchers.

“DNAstack has demonstrated remarkable leadership in its innovative and collaborative approach towards finding a solution for COVID-19,” says Sue Paish, CEO of Canada’s Digital Technology Supercluster, a cross-industry collaboration of diverse organizations, including DNAstack, that aims to position Canada as a global leader in digital technologies.

“The global opportunity to aggregate, track and share real-time data across medical communities has enormous potential to unlock a cure for the virus.”

DNAstack is getting noticed – and supported, too. Prime Minister Justin Trudeau recently mentioned the company in his April 21 announcement about the bold ideas being put forth by groups working with Canada’s Digital Technology Supercluster. And the company’s COVID-19 tool was one of the winning submissions in Roche Canada’s Open Innovation Challenge, which called for solutions to the challenges of the pandemic.

COVID-19 Beacon is a first step in DNAstack’s efforts to support the research community with cloud-based tools for conducting research on the novel coronavirus.

“This service is intended to help share data on COVID-19 as broadly as possible and connect a global ecosystem of data generators and researchers,” says Fiume. “We’re urging researchers who are interested in making data available through this service, or using it for analysis, to get in touch with us.”

Fiume notes that scientists developing drugs and vaccines for COVID-19 are in a much stronger position today because of the increasing sophistication of technology.

“The technology is so much better than it was even five years ago. We now have better tools for cloud computing, more mature standards for data sharing and better frameworks for machine learning – and the technology keeps improving. We also have a better ability to understand genetics and translate that into precision medicines.”

While the world waits for a vaccine to be developed, Fiume says DNAstack will do what it can to help researchers in their quest. “We’re trying to do our part to minimize the impact of COVID-19,” he says.

“There is so much that scientists don’t understand about this virus. Our job is to get people the information they need, so we can find solutions and get people back to normal.”

��˾��ֱ�� and Sunnybrook virologists work on tools to combat coronavirus outbreak

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

��˾��ֱ�� 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

Faculty of Medicine

Laboratory Medicine and Pathobiology

McLaughlin Centre

Mount Sinai Hospital

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 University of Toronto’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 ��˾��ֱ��’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 ��˾��ֱ��’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, ��˾��ֱ��’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 ��˾��ֱ��-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 ��˾��ֱ�� 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 ��˾��ֱ�� 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 ��˾��ֱ�� 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.”

��˾��ֱ�� experts and Friesen Prize winner debate gene editing, AI and other disruptive medical technologies

geoff.vendeville — Mon, 21 Oct 2019 15:50:23 +0000

��˾��ֱ�� experts and Friesen Prize winner debate gene editing, AI and other disruptive medical technologies

geoff.vendeville Mon, 10/21/2019 - 11:50

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McGill University's Bartha Knoppers, winner of the 2019 Henry G. Friesen International Prize in Health Research, delivers a lecture at an event co-sponsored by ��˾��ֱ��'s Schwartz Reisman Institute for Technology and Society (photo by Johnny Guatto)

Geoffrey Vendeville

Topic

Schwartz Reisman Institute for Technology and Society

Artificial Intelligence

Awards

CIFAR

David Naylor

Faculty of Arts & Science

Faculty of Law

Faculty of Medicine

Hospital for Sick Children

Joint Centre for Bioethics

Massey College

Women's College Hospital

Gene editing represents a promising new pathway to treat disease-causing mutations and other medical conditions. But as with other powerful emerging technologies, it also raises many ethical and legal concerns.

On Thursday, a panel of distinguished University of Toronto experts and McGill University’s Bartha Knoppers, a world-leading expert on the issues surrounding biomedical research in genetics and genomics, grappled with the ethical dilemmas posed by gene editing and other disruptive new technologies, as well as their potential to revolutionize medicine.

Knoppers said gene editing raises difficult questions involving the rights of children and future generations – questions that erupted into public consciousness last year after a Chinese scientist claimed to have used the powerful gene-editing tool, Crispr, to alter human embryos, which were then implanted in the womb of a woman who gave birth to twin girls.

News of the experiment, intended to protect the girls – whose father is HIV-positive – from the virus, was greeted with outrage and even calls for a moratorium on gene editing research.

But Knoppers said a ban would be the wrong approach since it would “silence debate” and wouldn’t cover “outlier” scientists. Instead, she argued for emphasizing the rights of children and patients, while taking into account existing laws and international obligations.

“Let’s see whether there’s some sort of road map for translation as we move to perhaps one day having germline editing under certain conditions,” she said.

Knoppers, the winner of the 2019 Henry G. Friesen International Prize in Health Research, made the remarks during a Friesen Prize lecture at Women’s College Hospital that was co-sponsored by ��˾��ֱ��’s Schwartz Reisman Institute for Technology and Society, a new interdisciplinary home for scholars studying the impact of technology and innovation on society. Other sponsors included ��˾��ֱ��’s Joint Centre for Bioethics, Massey College and Friends of the Canadian Institutes of Health Research.

In the panel discussion that followed experts, including ��˾��ֱ�� President Emeritus David Naylor, picked up on the theme of disruptive technologies and their impact on medicine, focusing on big data and artificial intelligence.

Panelist Gillian Hadfield, i naugural director of the Schwartz Reisman Institute for Technology and Society , as well as a ��˾��ֱ�� professor of economics and law, remarked on the role of universities in developing governance systems for introducing algorithmic decision-making in all kinds of fields, including health care.

Alan Bernstein, president and CEO of CIFAR (the Canadian Institute for Advanced Research) spoke about AI’s untapped potential to provide new diagnostic tools and treatments.

Meanwhile, Ronald Cohn, the president and CEO of the Hospital for Sick Children and chair of ��˾��ֱ��’s department of paediatrics in the Faculty of Medicine, described how AI and data are already being used in the hospital’s intensive care unit to save young lives. The unit gathers millions of data points every second – “the amount of data we collect per patient, per second, is the same amount that falls down, in terms of water, Niagara Falls,” Cohn said.

The wealth of data has helped the hospital create an algorithm predicting with 75 per cent accuracy whether a child will have a cardiac arrest, according to Cohn. “If you have an algorithm in place that tells you five minutes ahead of time the worst case scenario, you’re at least all assembled around the bed and you can act when it happens … or maybe you can actually prevent it from happening.”

��˾��ֱ�� President Emeritus David Naylor, an expert in health-care policy, said the university has the “firepower” to lead multidisciplinary debates “about where science and society are going, and how health care will evolve” (photo by Johnny Guatto)

For his part, Naylor, an expert in health-care policy who served as ��˾��ֱ��’s president from 2005 to 2013, said we now “live in a very different era” – one in which ethical, regulatory and governance issues will cause people to rethink how they do science.

Just over a year ago, he teamed up with ��˾��ֱ��’s Geoffrey Hinton, a pioneer of the sub-field of AI known as deep learning, to write companion pieces for the world’s most widely circulated medical journal about how AI can be harnessed to improve health care.

Naylor, who received the Friesen Prize last year, said Thursday’s panel discussion is exactly the kind of conversation that needs to continue to generate ideas and policy recommendations.

“We have the firepower – between the Joint Centre for Bioethics and the [Schwartz Reisman] Institute and all of the people who are interested in these issues in the city – to begin to have these important multidisciplinary debates about where science and society are going, and how health care will evolve,” he said.

Leong Centre for Healthy Children will help improve child health through new precision prevention

noreen.rasbach — Fri, 08 Mar 2019 17:07:06 +0000

Leong Centre for Healthy Children will help improve child health through new precision prevention

noreen.rasbach Fri, 03/08/2019 - 12:07

Cutline

(photo by Shutterstock)

Topic

Global Lens

Pediatrics

��˾��ֱ��

Artificial Intelligence

Subheadline

By applying innovative tools and targeted strategies, researchers can better predict and enhance health outcomes for children around the world

Thanks to a $25-million gift, the University of Toronto is creating the Edwin S.H. Leong Centre for Healthy Children, which will develop innovative approaches to improving child health.

The gift from alumnus Dr. Edwin S.H. Leong and the Tai Hung Fai Charitable Foundation will help researchers at U of T and The Hospital for Sick Children (SickKids) to harness the latest advances in the science of child health, and pair them with developments in artificial intelligence and machine learning technologies.

Leong Centre experts in genomics, pediatrics and public health will use this approach to develop powerful predictive models based on ��˾��ֱ��’s distinctive access to child health and demographic data sets.

As the first project of its kind in the world, the Leong Centre will address a global rise in chronic disease among children – with a particular focus on those who are underprivileged and at risk. It will do this by developing effective evidence-based practices, interventions and policies to prevent disease before it starts, while also improving outcomes for those with disabilities and chronic conditions. Ultimately, this will lead to solutions that help children to set a trajectory of health throughout their life.

“The Edwin S.H. Leong Centre for Healthy Children will enable both groundbreaking scientific discoveries and scalable policy solutions that have the potential to benefit all children,” says U of T President Meric Gertler.

“It will draw on the University of Toronto’s expertise in childhood health and development, and its position at the centre of one of the world’s strongest biomedical clusters. The Leong Centre is truly a game-changing initiative with potential to improve the lives of young people around the world.”

Leong’s benefaction, together with matching funds from the University of Toronto and SickKids Hospital, will support the centre’s work over an 11-year period.

A champion of the most vulnerable

This gift from Leong is the largest benefaction that ��˾��ֱ�� has ever received from outside of Canada; one that builds on the connection between Hong Kong and the University of Toronto.

“Raising children requires a holistic approach,” says Leong. “We cannot even begin broad conversations about prosperity, education or innovation without building from a healthy populace – which begins in childhood. I am proud to be able to give back to the institution that helped enable my own success, and improve health outcomes among society’s most vulnerable people. This centre is a chance to fulfill the promise of health for children everywhere.”

Both Leong and the Tai Hung Fai Charitable Foundation that he chairs have an impressive record of international philanthropy. Among many different initiatives around the world, Leong funded the Henry G. Leong Program for Enhanced Training and Research on Holistic Care of the Elderly at Hong Kong University, as well as the Henry G. Leong Mobile Integrative Health Centre Program at Hong Kong Polytechnic University. Both of these programs were named in honour of Leong’s father.

Alongside these are five other endowed professorships, also named for Leong’s father: at Chinese University of Hong Kong, a professorship in gerontology and geriatrics; two professorships at Hong Kong University, one in social work and administration and one in neurology; and at Hong Kong Polytechnic University, a professorship in elderly vision health and another in in biomedical engineering.

In 2018, Leong made a remarkable gift of $24 million to the University of British Columbia to establish the Leong Healthy Aging Program at the Faculty of Medicine – the largest individual gift in that faculty’s history.

At the University of Toronto, in 2016 Leong created the Edwin S.H. Leong Scholarship, which recognizes academic excellence and leadership for international students in financial need, helping them to fulfil their goals in higher education.

Innovative solutions to child health outcomes

The Leong Centre will be centred at ��˾��ֱ��, but its researchers will collaborate with peers at sister institutions in Canada and around the world, including in Hong Kong, British Columbia and the United Kingdom. Through these collaborations, the Leong Centre will draw on world-class resources to develop targeted, effective and affordable child health interventions, resulting in improved health outcomes for everyone, and especially those with few health-care resources.

“We are profoundly grateful to Dr. Leong for this visionary support that will have a global impact in raising healthy, flourishing children in Canada and internationally,” says Professor Trevor Young, dean of the Faculty of Medicine. “The Leong Centre for Healthy Children will further develop our understanding of the social and environmental influences on child health. It will, ultimately, have a transformative impact across the lifespan since thriving children are more likely to become healthy, productive adults.”

Important research partnerships

SickKids is a central partner with the Leong Centre. It is one of the world’s foremost pediatric health-care institutions and a leader in advanced pediatric research that has generated innovative discoveries in children’s health care with global impact. Pediatric research performed at SickKids spans the applied health science range from detection, to solution, to prevention. Its researchers and resources will be a key component of the Leong Centre’s long-term success.

An international expert will lead the Leong Centre and report to ��˾��ֱ��'s chair of the department of paediatrics, currently held by Dr. Ronald Cohn, who is the incoming president and CEO of SickKids.

“We are at an unprecedented time in scientific discovery and computational technology,” says Cohn. “And we have a unique opportunity to improve human health by focusing on our most vulnerable time – childhood. The Leong Centre is taking a truly innovative approach to enhancing child health through precision prevention that will have local, national and global impact.”

As well, through its partnership with the Institute for Clinical Evaluative Studies, ��˾��ֱ�� benefits from access to a robust dataset of health information across the lifespan, giving it a competitive global advantage in demographic health research. The Leong Centre’s approach will build from this data, derived from the world’s most multicultural urban region, allowing it to create scalable programs and policies with global application.

Researchers at the Leong Centre aim to work in both theory and practice to lead exciting breakthroughs: from finding new and better ways to help low-income families effectively support children with long-term disabilities, to preventing the onset of cardiovascular disease in at-risk children, to helping immigrant families avoid chronic illnesses through better integration.

“The Leong Centre represents a paradigm shift in how we approach child health,” says David Palmer, vice-president advancement. “Dr. Leong has long been a champion of society’s most vulnerable and this new centre will carry on his global legacy. We are honoured and grateful to have his support in this far-sighted undertaking that will have positive implications for children around the world.”

Two ��˾��ֱ��-led projects receive $2.8 million to develop disease-resistant vegetables, surveillance tool for viruses

noreen.rasbach — Fri, 17 Aug 2018 19:53:55 +0000

Two ��˾��ֱ��-led projects receive $2.8 million to develop disease-resistant vegetables, surveillance tool for viruses

noreen.rasbach Fri, 08/17/2018 - 15:53

Cutline

Tomatoes grown in a greenhouse: ��˾��ֱ�� researchers are looking to find genes in tomatoes, cucumbers and sweet peppers that give the plants broader resistance to disease (photo by John Thys/AFP/Getty Images)

Don Campbell

Topic

Cell and Systems Biology

Faculty of Medicine

Global