Major advances in genomics and informatics over the past several years have resulted in individual research projects producing enormous amounts of data. In particular, genomic data from large population and clinical cohorts, coupled with extensive health and lifestyle data, have the potential to generate critical biological insights into human health and novel determinants of disease. These technological developments have emerged as a new challenge for researchers because advances in genomics will be made (or limited) by bioinformatics analytical capacity and the ability to store and analyze data in new and more sophisticated ways.
The Canadian Data Integration Centre was established to help translate the biological research insights into tangible improvements for patients with cancer and chronic disease. Genome Canada recently renewed its commitment to the Canadian Data Integration Centre (CDIC), with a $6.4 million investment to establish a Genome Canada’s Genome Technology Platforms. Housed at the Ontario Institute for Cancer Research (OICR), the CDIC offers opportunities for cutting-edge pan-disease health research and big data analytical approaches.
As Canada’s first public site to offer third generation bioinformatics and genomics tools to support both functional and clinical genomics, the CDIC has emerged as a tried-and-tested solution for challenges faced in the application and management of advanced sequencing technologies, pathology and biospecimen handling, genomics, and data integration. This is evidenced by the platform supporting large-scale health and research initiatives such as the International Cancer Genome Consortium and Canada’s largest population cohort and precision health program, the Canadian Partnership for Tomorrow Project.
The CDIC is led by Dr. Philip Awadalla (Director of the CDIC and CPTP), and co-investigators Lincoln Stein, Jared Simpson, Vincent Ferretti and John Bartlett, bringing together a team of international experts on the collection, harmonization and publication of genomic and phenomic data. Together, they are able to provide the full breadth of support for projects ranging from the initial design, collection and analysis of complex data, through to the development of integrated data portals to facilitate data sharing and the translation of research findings into tangible health outcomes. The CDIC provides client-oriented access services that are customizable to diverse research areas, such as genomics, epigenetics and population level studies, in addition to supporting biopharmaceutical initiatives in biomarkers discovery, drug development and repurposing. Having supported some of the world’s largest programs in data analysis and hosting, including the NCI Cancer Genomic Data Commons and the Pan-Cancer Analysis of Whole Genomes Consortium, the platform has been established as an international leader in genomics, informatics, and translational research.
To date, the CDIC has attracted more than $87 million in grants and generated $14 million in service revenue through providing bespoke support for local and international projects. This has culminated in numerous high-impact publications in Nature, Science and Nature family journals, including a recent study featured in Nature Communications, and highlighted in the Globe and Mail, showing that environmental exposures are more determinant of respiratory health outcomes than inherited genetics.
The investment through Ontario Genomics will support the expansion of the CDIC’s services to include the genomic infrastructure supported by OICR’s Genome Technologies and Diagnostics teams. The informatics and bio-computing core at the CDIC is currently the largest academic cancer informatics program in Canada, offering real-time, long-read PromethION direct sequencing technology, Chromium 10X single cell library preparation and is proudly home to the first operational NovaSeq in Ontario. This allows the CDIC to equip researchers and industry clients alike with state-of-the-art software and analytical tools to interrogate the underlying causes of complex diseases. As CDIC researchers help to facilitate a new era of Canadian-led genomics and informatics research projects, they will develop novel technologies and methodologies for long-read sequencing, facilitate the development and clinical roll-out of therapeutic biomarkers and streamline the translation of research innovations to the clinical context. With this renewed commitment from Genome Canada, the CDIC looks forward to supporting national and international efforts to better combat cancer, chronic and infectious disease.
On the digital side of things, Bill Peck of Twist Bioscience described his company’s work with Microsoft in digital data storage using DNA and how this will help handle the deluge of data being generated. The AI panel moderated by Alison Paprica, VP of Health Strategy and Partnerships at Toronto’s Vector Institute alongside the speakers Brenda Andrews of the University of Toronto Donnelly Centre, Nathan Magarvey of McMaster University and Adapsyn, and Ratmir Derda of 48 Hour Discovery explored the intersection of AI and synthetic biology and the potential to solve fundamental biological problems as well as in discovering new therapeutics. A common barrier addressed by the panelists was the availability of quality, standardized data that is essential inputs to AI technologies.
Stephen Chambers, CEO of the UK organization SynbiCITE, a national synthetic biology accelerator, summed up synthetic biology succinctly: “Engineering biology to make useful stuff”, an apt description given the focus throughout the day on manufacturing of products. In his keynote, he described why the UK selected synthetic biology as one of eight great technologies to propel UK growth and the metrics he is judged on- jobs and wealth. He stated that the UK government didn’t aim to pick winners, but to bet on the right race and synthetic biology is one they think they can win. He described a level of coordination and collaboration that is enviable, making the UK an ideal model and partner for Canada.
The panel on climate change and synthetic biology, chaired by Catalina Lopez-Correa, CSO and VP Sectors at Genome BC, stressed Canada’s bio-advantage from ample biomass and the critical role synthetic biology plays in converting that into valuable bio-chemicals at commercial scale. Speakers covered the innovation pipeline from academic research shared by Steven Hallam on mining microbes, to David Bressler and Murray McLaughlin of Bioindustrial Innovation Canada discussing scaling technology, to commercial successes shared by Rasmus Jensen of LanzaTech and Cathy Hass of BioAmber. BioAmber is a Canadian success with manufacturing operations in Sarnia, where they produce bio-succinic acid with more than a 100% reduction in greenhouse gases over the petroleum-derived counterpart.
Dr. Molly Shoichet, Ontario’s first Chief Scientist, moderated the panel on human health and synthetic biology. Exciting science was discussed, including a cross-Canada network to manufacture CAR-T cell therapies for cancer treatment presented by Rob Holt of UBC, genetic circuits used for stem cell treatments discussed by Peter Zandstra, and engineered probiotics for GI diseases presented by Krishna Mahadevan. Dr. Shoichet also emphasized the responsibility that rests on everyone in attendance to promote a culture of science in the general community, and especially to engage the public on topics like Engineering Biology to ensure benefits are realized.
While the conference focused on numerous areas of Engineering Biology, a recurring theme was the key underlying technology underpinning applications – DNA synthesis and assembly. Adam Clore shared Integrated DNA Technologies’ work in enabling applications including CRISPR and Francis Ouellette, VP Scientific Affairs at Genome Quebec chaired a panel on writing whole genomes. The panel included Leslie Mitchell of NYU and member of both the synthetic yeast project (Sc2.0) and GP-Write, Bogumil Karas of Western University, working on storing and moving large fragments of DNA, and Vardit Ravitsky who is building ethical and social perspectives (GE3LS) into large projects like GP-Write. The panel concluded with a call for a Canadian Genome Project-Write Consortium by Vincent Martin of Concordia University. To this end, a planning meeting is scheduled for August in Montreal with interested researchers invited to contact Vincent Martin and Bogumil Karas, the two leaders of the Canadian effort.
The topic of GE3LS continued into the agri-food panel, where Jun Axup of Indie Bio moderated a panel where Neal Carter and Dave Conley talked about the Arctic (non-browning) Apple and AquAdvantage Salmon as Canadian success stories, with Jennifer Kuzma of NC State and Ian Affleck of CropLife Canada emphasizing the need for public engagement and a robust regulatory system to ensure acceptance of innovative products.
The afternoon also focused on the robust startup scene of synthetic biology, with early stage companies raising over $1.7B in 2017 globally. The investor panel moderated by Joško Bobanović of Sofinnova Partners included the largest private investor in synthetic biology, Sean O’Sullivan, who has invested in 9 Canadian companies through his Indie Bio and Rebel Bio accelerators, as well as other leading investors Jenny Rooke from Genoa Ventures, Andreas Jurgeit of M (Merck) Ventures, and Canadian investors JF Pariseau of BDC Venture Capital and Ken Nickerson of OMERS Ventures. It was a real treat to have these industry leaders lend their time, with some visiting Canada for the first time, and provide their outlook on the field as well as tips to the audience on how to get their investment (hint: use Fedex, not email!).
The lightning talks panel moderated by Anita Ludwar of Genome Alberta showed the bright future Canada has in Engineering Biology, and was a chance for companies to pitch their platform technologies to the investors. We heard about variant libraries and strain development (Ranomics and Designer Microbes) and products from water sensors for mining wastewater (FREDsense), cannabinoids for the pharma industry (Hyasynth Bio), natural flavors and fragrances (Ardra Bio), and educational kits for students (Amino Labs). HJ Wieden from SynBridge in Alberta talked about the importance of space and equipment for these companies as well as the benefit of programs like iGem to get students excited about entrepreneurship.
The Day ended with Yung Wu, CEO of MaRS Discovery District and conference partner, underscoring the importance of the field and MaRS’ role in supporting the startup ecosystem. Dr. Bettina Hamelin, President and CEO of Ontario Genomics, closed the day, summing up the highlights and ended with a forward-looking question:
Her comments emphasized that the day wasn’t just about learning. It was about mobilizing the community to come together, create opportunities for collaboration and partnership, and to develop a strategy for Canada to capitalize on this emerging area. This was done informally over coffee and the networking reception held in the Autodesk Community Space, but it continued into March 7 in a more intentional way through a day long workshop.