June 26, 2020
OICR’s Genome Informatics team announces international release of the ICGC-ARGO Data Platform, the all-in-one data hub for the largest clinical-genomic data sharing initiative in the world
We’re in the midst of an era of big data that is changing the way we understand the world – including how we study, diagnose and treat cancers.
Improvements in sequencing technology and computational power have allowed us to collect massive amounts of information about cancer patients and their tumours. This information, however, is only powerful if it can be accessed by those who can transform big data into new discoveries.
Over the last decade, OICR’s Genome Informatics has built a reputation for developing robust big data portals that provide cancer data access to thousands of researchers around the world. Now, the Genome Informatics team has set out to do it again – this time with bigger data.Continue reading – Opening the virtual floodgates for cancer research and discovery
June 10, 2019
OICR-supported researcher Dr. Nicole Mittmann leads collaborative initiative to determine the value of new cancer solutions and the burden of cancer care on Canada’s healthcare system
Canada is well known for its publicly funded healthcare system, its universal health coverage, and in most recent news – for the Toronto Raptors.
What is less recognized, however, is that with its distinctive healthcare system, Canada has unique healthcare reimbursement processes and resource needs, especially for the delivery of cancer care. While Canada collects some of the most robust and comprehensive healthcare data, Canadian datasets are underutilized in research and policy decision making.
Dr. Nicole Mittmann has set out to close this gap and, in turn, transform our administrative health information into tangible healthcare improvements.
“As cancer-drug costs continue to rise, there is – now more than ever before – a need to understand the Canadian context with respect to costs and health system resource use,” she writes in Current Oncology.
Turning data into action
Mittmann, who was recently appointed as the Chief Scientist and Vice-President of Evidence Standards at the Canadian Agency for Drugs and Technologies in Health (CADTH), sees Canada’s rich data as a goldmine for improving the management of diseases and the delivery of care.
“This information can be used to help us make decisions, help us plan and help us understand the value of new technologies,” she says. “It could also show us areas where we need to improve, or problems that weren’t apparent through practice alone, but we needed to reduce the barriers to using these data for research.”Continue reading – It’s our health information: a goldmine for improving the quality of cancer care
October 23, 2018
The Global Alliance for Genomics and Health (GA4GH) held its 6th Plenary Meeting in Basel, Switzerland earlier this month. The meeting brought together more than 430 participants from 25 countries, making it the biggest GA4GH event yet. Attendees of the meeting learned about GA4GH Connect – a strategic phase focused on connecting GA4GH development work to the immediate data sharing needs of the community.
At the meeting, Peter Goodhand, Chief Executive Officer of GA4GH, announced a call for new real-world genomic data initiatives – Driver Projects – with a specific focus on global collaboration and scientific merit. The Steering Committee will announce the accepted Driver Projects in February 2019.
Also at the meeting, Dr. Marc Fiume, Chief Executive Officer of DNAstack and OICR Associate, presented on the recent progress of the Beacon Project – an international collaborative initiative that has developed a realtime discovery platform for genetic mutations. The Beacon Project has released Beacon API V1.0.0 on Friday – the first genomic data interoperability standard from the GA4GH 2018 Strategic Roadmap.
“It was a fantastic meeting and an eye-opening experience to learn about how the field of precision medicine is linking genomic tools with clinical databases and patient outcomes to drive a patient-centered, learning healthcare model,” says Dr. Laszlo Radvanyi, President and Scientific Director of OICR. “GA4GH continues to play a critical role in establishing standards for genomic data acquisition, quality, interpretation, integrity, security, and sharing that many national genomic health initiatives are beginning to embrace around the world.”
January 10, 2017
The Global Alliance for Genomics and Health’s (GA4GH) Beacon Project has partnered with ELIXIR, the body that organizes Europe’s infrastructure for life science data, to make genomic data in that continent more easily discoverable by researchers. The Beacon Project is a demonstration project that enables genomic data centres to make their data more easily discoverable to users by allowing them to use simple queries to explore a dataset’s contents.
May 2, 2016
On March 31, Intel Corporation and the Knight Cancer Institute at Oregon Health and Sciences University announced two new leading cancer centres have joined the Collaborative Cancer Cloud (CCC): Dana Farber Cancer Institute and OICR.
The CCC is a distributed precision medicine analytics platform that allows institutions to securely share and analyze large amounts of data while also preserving patient privacy and security. The CCC will make it easier, faster and more affordable to determine how genes interact to cause disease in individual patients.
March 1, 2016
TORONTO, March 1, 2016 /CNW/ – The International Cancer Genome Consortium (ICGC) announced today that its Data Access Compliance Office (DACO) authorized its 1,000th user, giving them access to the Consortium’s Controlled Access datasets. This means that more authorized researchers than ever before are accessing ICGC’s Controlled Access data for their research and using these datasets as the foundation for the next generation of cancer diagnostics and treatments.
ICGC datasets that catalogue tumour-specific mutations are unrestricted and freely available to the scientific community. However, the ICGC developed an authorization process to distribute clinical and inherited genetic data associated with unique individuals in order to minimize the risk of identification of donors based on computer analyses of demographic, clinical or genetic data.
February 19, 2016
The International Cancer Genome Consortium (ICGC) took another major step into the cloud last month, joining forces with Amazon Web Services (AWS) to bring 1,200 encrypted whole genome sequences to more researchers worldwide.
This means that one of the world’s largest collections of cancer genome data is now more easily accessible to qualified researchers, potentially accelerating the development of new treatments for cancer patients.
December 3, 2015
The amount of genomics data produced today is enormous and challenges in accessing that vast amount of data are increasingly blocking the ability for scientists to perform their research. There is a growing consensus that cloud storage for genomic data makes research far more accessible than traditional methods of storing it locally. In a major shift earlier this year, the National Institutes of Health (NIH) removed its nearly decade-long ban on storing genomic data in the cloud, which was seen by many as a major step forward in the shift toward cloud computing in genomics.
November 20, 2015
On October 6, at the 2015 Annual Meeting of the American Society of Human Genetics, Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research, assumed the role of Chair of the Global Alliance for Genomics and Health (GA4GH) Steering Committee, succeeding Dr. David Altshuler. Altshuler has served as Chair since GA4GH was established in 2013, and will remain as a member of the Steering Committee.
“Just over two years ago, a group of leaders from around the globe came together to enable the responsible sharing of genomic and clinical data. Tom was a key contributor from the start, and with his help, GA4GH has made substantial progress,” Altshuler said. “I cannot think of a better person to lead the Steering Committee.”
The role of the Steering Committee is to make high-level decisions about the direction, values, and working products from the GA4GH. GA4GH is a community of individuals and world-leading organizations working together to create interoperable tools and approaches to enable genomic and clinical data sharing. More information about GA4GH can be found at www.genomicsandhealth.org.
July 9, 2015
World-leading Big Data researchers call for support for more accessible and more effective storage of data in the cloud to facilitate genomics research
Improved support of cloud infrastructure is essential to the delivery of the next generation of treatments for major diseases like cancer
TORONTO, ON (July 9, 2015) Today in the journal Nature prominent researchers from Canada, Europe and the U.S. have made a powerful call to major funding agencies, asking them to commit to establishing a global genomic data commons in the cloud that could be easily accessed by authorized researchers worldwide.
This would increase access to the data for researchers, reduce the time and cost associated with transferring and storing data on local servers and accelerate genomics research worldwide. Storing data in the cloud has been shown to be as secure, if not more secure, than storing it locally.
With a typical university connection it can take months to download datasets from major international projects like the International Cancer Genome Consortium (ICGC) and the hardware costs associated with storing and processing those data can also prove quite expensive.
With cloud computing a data set from a big genome project can be executed in days, at a fraction of the price.
The authors propose that funding agencies request that major data sets be uploaded into the cloud and that they pay for its long-term storage. Data would then only need to be copied once and researchers would only have to pay for temporary storage while the analysis was in progress. Access would only be provided to authorized researchers.
“Currently a great deal of valuable time and money is spent by researchers transferring data from a repository to their own preferred server, instead of easily and cheaply tapping into a global data commons whenever they need to,” said Dr. Lincoln Stein, Director of the Informatics and Bio-computing Program at the Ontario Institute for Cancer Research, leader of the ICGC’s Data Coordination Center in Toronto and a lead author on the paper. “We encourage a larger investment in the cloud in order to use public funds more effectively and to help accelerate the pace of genomics research.”
“Having authorized access procedures in place ensures respect for the wishes of data donors, including that their data be used safely and securely,” said Dr. Bartha Knoppers, Director of the Centre of Genomics and Policy, McGill University. “Applying the Framework for Responsible Sharing of Genomic and Health-Related Data (www.genomicsandhealth.org) is a first step in enacting the human right of citizens to benefit from scientific advances and of scientists to be recognized for their work.”
“The complexity of cancer biology means that we need huge data sets – basically, the bigger the better,” said Dr. Peter Campbell, Head of Cancer Genomics at the Wellcome Trust Sanger Institute. “We have now reached a stage where these data sets are too large to move around – cloud computing offers us the flexibility to hold the data in one virtual location and unleash the world’s researchers on it all together.”
“The amount of genomic data is growing at an amazing rate. Moving data and analysis tools to the cloud will democratize access to data and to the computational resources required to analyze that data,” said Dr. Gad Getz, Director of the Cancer Genome Computational Analysis Group at the Broad Institute of MIT and Harvard. “The expanded access will accelerate tool development, grow the population of researchers analyzing these rich data sets and ultimately increase the pace of scientific discovery. These cloud-based analysis platforms will also enable the testing of new distributed computing paradigms which expand both the scale of the analyses and the sophistication of the computational algorithms. We are now building a pilot of such a cloud platform.”
“The establishment of novel powerful cloud computing frameworks enabling us to store, share and analyze data across borders will open new perspectives in cancer research,” said Dr. Jan Korbel, group leader at the European Molecular Biology Laboratory (EMBL). “These will take into consideration developments in science and policies for the distribution and sharing of data sets as sensitive as patient genetic data ensuring a safe environment to serve the interests of both sample donors and researchers.”
Cloud computing is most widely associated with consumer products, such as storing music, photos or editing documents in real time. But in fact a great deal of research is already conducted in the cloud, safely and securely. Cloud computing is shared resource, giving researchers access to storage and computing power as needed, instead of making a long term investment in computer infrastructure. This also maximizes the use of the infrastructure as it can be used by many researchers instead of just one.
June 10, 2015
Over 250 Leaders Convene at Third Plenary Today to Build on Efforts and Drive Results
LEIDEN, the Netherlands (June 10, 2015) – The Global Alliance for Genomics and Health (GA4GH), an international coalition dedicated to improving human health by maximizing the potential of genomic medicine, marked its second anniversary this month. Today, more than 250 GA4GH Members are coming together in the Netherlands to collaborate on the development of innovative, integrated solutions that promote genomic and clinical data sharing, and the creation of a global learning system in genomic medicine.
Since its inception in June 2013, GA4GH has grown to include over 320 organizations across 32 countries and made important progress to unite and guide the field. Members include world leaders in healthcare, research, patient and disease advocacy, life science, and information technology. More than 700 individuals around the globe are actively developing dozens of tools, methods, and approaches to facilitate effective, responsible data sharing.
“Two years ago, we set out to engage a diverse set of leaders around the need to enable responsible sharing of genomic and clinical data. This has developed into a vibrant international effort beyond what we could have imagined when we first came together,” said David Altshuler, MD, PhD, Chair of the GA4GH Steering Committee. “In 2015 our mission is more critical than ever, as we increasingly see genomic information having positive impact on diagnosis, targeting, and development of new medicines.”
At today’s third Plenary Meeting, GA4GH Members are sharing progress on priority tools and projects and discussing ways to promote the use of these interoperable methods to encourage data sharing. Members are focusing on work being done to link existing solutions, emerging areas of interest like e-Health, and issues such as big data challenges and how best to align with major national and institutional efforts arising in genomic medicine.
“The future of medicine requires a collective commitment to developing scalable and interoperable approaches to sharing data,” said Francis S. Collins, MD, PhD, Director of the National Institutes of Health. “GA4GH has made important early progress by uniting critical communities, identifying challenge areas, and collaborating on efforts to help the world realize the benefits of genomic data sharing.”
GA4GH Working Groups have already developed products that lay a technical and regulatory foundation for data sharing, including:
- A regulatory Framework to guide the responsible sharing of genomic and health-related data;
- A GA4GH Genomics API to enable the interoperable exchange of data in DNA sequence reads; and
- A Security Infrastructure that recommends policy and technology options for the ecosystem.
“The world is on the verge of an explosion in genomic data. If we fail to effectively navigate this rocky terrain, we will miss a tremendous opportunity to enable a new era of medical discovery and delivery,” said Tom Hudson, newly announced Chair-Elect of the GA4GH Steering Committee and President and Scientific Director of the Ontario Institute for Cancer Research. “GA4GH has not only brought critical communities to the table, but is showing the results of what happens when these diverse leaders combine their experiences and work together.”
“Health systems around the world must turn into learning systems that responsibly share information—we owe it to every citizen in the world to do this right,” said Eric Lander, Founding Director of the Broad Institute of MIT and Harvard. “GA4GH has taken critical steps to ensure that we unlock the transformational power of genomic medicine.”
GA4GH Members are now building off early foundational products. New Consent and Privacy and Security Policies released this week follow the guidelines and principles of the regulatory Framework. GA4GH recently developed a catalogue of current activities in eHealth and in April, a beta Reference Implementation for the Genomics API was released. Finally, a “data sharing start-up kit” is underway which will include downloadable APIs and reference implementations, as well as polices and standards necessary to implement them responsibly.
“GA4GH tools facilitate interoperability and allow researchers and clinicians to tap the power of genomic data on a global scale, while ensuring participants feel secure that their interests are protected,” explained David Haussler, Chair of the GA4GH Data Working Group and Scientific Director of the Genomics Institute at UC Santa Cruz. “No one of our Member organizations is in the position to provide every tool that is needed, but together we can really move the needle.”
“We started the Global Alliance two years ago to address current barriers to genomic and clinical data sharing before they became entrenched,” said Bartha Knoppers, Chair of the GA4GH Regulatory and Ethics Working Group and Director of the Centre of Genomics and Policy at McGill University. “We are working to guide the responsible sharing of genomic and health-related data around the world based on a human rights approach.”
Several projects advanced by GA4GH act as testing grounds and demonstrate immediate, real-world value:
- A global BRCA Challenge to merge and accelerate efforts to interpret BRCA 1 and 2 variants, holding its inaugural meeting June 12-13 at UNESCO in Paris co-organised by the Human Variome Project;
- Matchmaker Exchange, a project designed to help patients and doctors grappling with rare genotypes and phenotypes to find one another through a federated network of databases; and
- The Beacon Project, which tests the willingness of institutions to share data internationally and now includes over 250 datasets across 15 institutions, including the GA4GH Beacon Network.
“Right now consortia around the world are collecting genomic sequence data, but many efforts are happening in parallel, not in concert,” said Michael Stratton, Director of the Wellcome Trust Sanger Institute. “The Global Alliance is providing packaged, workable solutions and engaging with large-scale data collection and sharing programs around the world.”
“If we don’t ensure data interoperability now, within a few years it’s going to be too late,” said Kathryn North, Vice-Chair of the GA4GH Steering Committee and Director of the Murdoch Childrens Research Institute. “We must all work together to realize the potential of genomic research, reveal the underlying causes of genetic disorders, and transform the way individuals are treated and diagnosed.”
A Road Map produced in early 2015 lays out specific near-term goals for GA4GH. These goals align with the Global Alliance’s vital initial mission and will guide today’s Plenary Meeting.
The Global Alliance for Genomics and Health is an international, non-profit alliance formed to help accelerate the potential of genomic medicine to advance human health. Bringing together over 300 leading organizations working in healthcare, research, disease and patient advocacy, life science, and information technology, GA4GH Members are working together to create a common framework of tools, methods, and harmonized approaches and supporting demonstration projects to enable the responsible, voluntary, and secure sharing of genomic and clinical data. Learn more at: http://genomicsandhealth.org.