Disruptive Innovations in Genomics (DIG) Competition

Genome Canada’s Disruptive Innovations in Genomics (DIG) competition seeks to support research projects that focus on disruptive innovations with the potential to advance the field of genomics and eventually lead to social and/or economic benefits to Canada. For the purposes of this competition, a disruptive innovation is defined as either a new genomics technology or the application of an existing technology from another field, applied to the field of genomics. These Innovations must be truly transformative in that they have the potential to either displace an existing technology, disrupt an existing market, or create a new market.

Launched on June 11, 2015, the DIG initiative exists to capture true disruptive innovation and translate it to improve human health, agriculture, and natural resources.

Funded Ontario DIG Projects

2015
On December 09, 2016, the Government of Canada announced the investment of $9.1 million in Disruptive Innovation in Genomics to improve human health, agriculture, natural resources. Ontario Genomics led twelve (12) of the awarded early-stage feasibility (Phase 1) projects:

Ontario Genomics led two (2) of the awarded prototype development (Phase 2) projects:


DIG Project Descriptions:

Phase 1 Projects

AbSyn Technology for identification of synergistic cancer therapeutics

Project Leaders: Charles Boone, Jason Moffat
Institution: University of Toronto
Total Project Funding: $249,389

Genome sequencing has revolutionized our understanding of the genetic changes that lead to cancer. Unfortunately, treatment still remains in the relative Dark Ages, with decades-old treatments that can be highly toxic and that don’t consider the subtle genetic differences among each patient’s disease. Dr. Charles Boone and his team at the University of Toronto are developing AbSyn, a new technology that will identify combination therapies tailored to individual cancers. AbSyn stands for the development of antibodies (Ab), whose promise for treating cancer has been hugely under-realized, and synergistic (Syn) therapies for cancer based on these antibodies. AbSyn will change the way we prioritize and discover new cancer drugs, building a new bridge between the gap of biological understanding and the commercial drug discovery process.
TOP

RNA-seq in patient derived ex-vivo models: Genetic diagnostics beyond whole exomes

Project Leaders: James Dowling, Michael Brudno
Institution: The Hospital for Sick Children
Total Project Funding: $250,000

There are more than 6,000 rare diseases caused by mutations in a single gene; together they affect more than 500,000 Canadian children. Exactly what gene is causing a disease is unknown in more than half the cases. RNAseq may provide a strategy for discovering novel genetic mutations that cause rare diseases – but can’t be used without obtaining the specific tissues in which the disease is present. Drs. James Dowling and Michael Brudno, of The Hospital for Sick Children will use ex vivo disease models created at Sick Kids in place of tissue biopsies to perform RNAseq for gene mutation discovery. By combining recent advances in cell biology, genomics and bioinformatics, the lab will develop a new diagnostic methodology, fundamentally transforming the clinical diagnostics process.
TOP

Massively parallel single molecule protein sequencing in-situ

Project Leader: Andrew Emili
Institution: University of Toronto
Total Project Funding: $250,000

Proteins in cells are responsible for virtually every biological process. When they don’t work properly, the result can be human diseases such as cancer, Alzheimer’s, diabetes and heart disease. Dr. Andrew Emili of the University of Toronto will develop a revolutionary new sub-microscopic imaging technology that will allow researchers to identify and quantify each and every one of the many millions of different protein molecules present in human cells and tissues at an unprecedented level of detail. The proprietary chemical probes and tool “kits” he and his team develop will be applicable to a wide diversity of biomedical specimens, displacing existing technologies and ultimately changing the study of human cell biology and medicine.
TOP

RapidAIM: A high-throughput assay of individual microbiome

Project Leaders: Daniel Figeys, Alain Stintzi
Institution: University of Ottawa
Total Project Funding: $250,000

The more than 1,000 different species of bacteria that colonize our gastrointestinal tract are collectively known as our microbiome. Dr. Daniel Figeys and Dr. Alain Stintzi of the University of Ottawa are developing RapidAIM to gain information on how drugs affect the microbiome and vice versa. The team will also develop a computational program that will combine and analyze these results, to better predict drug efficacy and clinical outcomes. RapidAIM could allow rapid screening of candidate or current drugs for potential adverse microbiome effects. The economic benefits will come in the form of a commercializable assay and computational platform for the screening of human microbiomes.
TOP

Development of advanced genetic toolbox for Sinorhizobium meliloti to enable genome scale engineering

Project Leader: Turlough Finan
Institution: McMaster University
Total Project Funding: $250,000

Genetic engineering seeks to improve agricultural outcomes by enhancing traits such as disease resistance, drought tolerance or superior levels of production. Conducting this engineering, however, requires a host where genes can be implanted and researchers perform genetic manipulations – a process known as synthetic biology. Drs. Turlough Finan, Bogumil Karas and Trevor Charles are developing a bacterial surrogate host system (Sinorhizobium meliloti) that allows replication and engineering of large DNA fragments before reintroducing them back to the original organism. In addition to its general application for genome engineering, the S. meliloti surrogate host-system technology can be used in short-term technology developments, including the generation of large DNA libraries for bioprospecting.
TOP

Cell biosensors for rapid screening of insect attractants

Project Leaders: Peter J. Krell, Daniel Doucet
Institution: University of Guelph, Natural Resources Canada
Total Project Funding: $233,901

Forestry and agriculture together contribute close to eight per cent of GDP in Canada, but insect pests pose a continual threat. Functional genomics has long promised to bring new solutions to recurrent and new pest problems. Dr. Peter J. Krell of the University of Guelph, in collaboration with Drs. Daniel Doucet and Jeremy Allison (NRCan), is creating highly sensitive surveillance and mitigation systems targeting insects, using a family of insect genes known as odorant receptors (ORs). This innovation should not only disrupt the discipline of functional genomics, but also the field of insect pest management, making surveillance and mitigation more feasible and faster, while helping preserve Canada’s position as a leading exporter of forest and agricultural products.
TOP

Economical high throughput de novo whole genome assembly

Project Leaders: Stephen Scherer, Si Lok
Institution: The Hospital for Sick Children
Total Project Funding: $241,467

“De novo” sequencing, or constructing an individual’s genome from his or her own data alone (as opposed to comparing it to a reference genome), is a formidable task, akin to assembling a jigsaw puzzle comprising hundreds of millions of small blank pieces. Drs. Si Lok, Stephen Scherer, and their colleagues from The Hospital for Sick Children are developing a new “mate-pair” technology that would overcome the financial and logistical barriers to de novo sequencing by linking sequences to one or more other reads in precisely known orientations and distances. Mate-pair technology would create a high-resolution backbone to enable de novo sequencing to be carried out in a single simple step. This new adaptation of mate-pair sequencing is a disruptive technology that could supersede all current methods of de novo sequencing, thereby representing a leap forward in many areas of research and, ultimately, in healthcare.
TOP

Development of SIMPL, a novel protein-protein interaction assay based on split intein for biomedical research

Project Leader: Igor Stagljar
Institution: University of Toronto
Total Project Funding: $250,000

Proteins control every function of every cell in our body. Proteins, however, never act alone; rather, they interact with many other proteins in what are called protein-protein interactions (PPIs). Gain or loss of PPIs can be the driving force behind disease development. Dr. Igor Stagljar of the University of Toronto is leading a team to develop and implement a novel disruptive genomics technology that can detect and monitor PPIs in human cells. This technology can be used to identify novel proteins as components of many essential cellular processes, leading to greater understanding of the role of specific proteins in our cells. Furthermore, the technology also has the potential to identify drugs that disrupt a defined set of PPIs when the PPIs cause disease.
TOP

Solid-state nanopore-based quantification of low-abundance biomarkers

Project Leader: Vincent Tabard-Cossa
Institution: University of Ottawa
Total Project Funding: $250,000

Many illnesses, such as cancer or cardiovascular disease, leave physical evidence in our bodies, called biomarkers. Spotting these biomarkers early would make it possible to begin treatment with personalized, targeted therapy, or even prevent disease entirely. Solid-state nanopore-based devices can do this, but are too expensive for widespread use. Dr. Tabard-Cossa’s laboratory has pioneered a technique to fabricate nanopore devices more rapidly and at substantially lower cost than present-day technology. They are integrating the devices into a disposable cartridge within compact platforms offering comprehensive sample-in, answer-out capability. The lab is positioned to develop a point-of-care prototype that can be used in the lab and the clinic, resulting in significant economic and health benefits for Canada.
TOP

Functional genomics in human cells for drivers of lethal metastatic human cancers

Project Leaders: Michael Taylor, Rama Khokha
Institutions: The Hospital for Sick Children, Princess Margaret Cancer Centre
Total Project Funding: $250,000

Often in cancer it’s the spread of the cancer to other areas of the body, a process called metastasis, that kills. This is particularly the case with two highly lethal types of cancer, medulloblastoma (MB), the most common malignant brain tumour in children, and pancreatic adenocarcinoma, the fourth leading cause of cancer deaths in Canadians. Recent results from the lab of Dr. Michael Taylor of The Hospital for Sick Children have shown that the biology of the metastases is extremely different from the primary tumour, making it unlikely that treatments developed to treat the primary tumour will work on the metastases. Dr. Taylor has teamed with Dr. Rama Khokha (Princess Margaret Cancer Centre) to develop and deploy unique tools to discover the drivers of metastasis, helping to improve survival rates of Canadians with these deadly human cancers.
TOP

Development of a digital microfluidic platform to identify and target single cells from a heterogeneous cell population for lyses in an ultra-low volume

Project Leaders: Aaron Wheeler, Elena Kolomietz
Institutions: University of Toronto, Mount Sinai Hospital
Total Project Funding: $250,000

Genetic abnormalities are a leading cause of death among Canadian newborns and infants. Less invasive, less expensive prenatal diagnostic techniques that are able to provide relevant information at earlier stages of pregnancy are needed. Scientists and physicians at Toronto’s Mount Sinai Hospital have developed a method to collect and isolate fetal cells non-invasively, using a technique similar to a PAP smear. Now Dr. Aaron Wheeler’s research group at the University of Toronto is developing techniques to isolate and analyze these cells for prenatal diagnosis of genetic abnormalities. If successful, these techniques could transform the way prenatal diagnosis is delivered, resulting in higher coverage of the population, reduced patient anxiety, increased medical options for at-risk pregnancies and significant reductions in healthcare costs.
TOP

SANGRE-seq (systematic analysis of blood gene regulation by sequencing): Bringing RNA-seq to clinical diagnostics

Project Leaders: Michael Wilson, Adam Shlien
Institution: The Hospital for Sick Children
Total Project Funding: $249,934

Diagnostic tests based on blood samples are mainstays of the healthcare system. Adding RNA sequencing (RNA-seq) can extract more information from blood samples, including a snapshot of all the genes active in a patient’s blood cells. Such a snapshot can tell us about the current condition of the patient’s immune system, whether there are cancer cells in the blood and/or whether blood cells are fighting an infection. Drs. Michael Wilson and Adam Shlien of The Hospital for Sick Children are developing an RNA-based clinical test called SANGRE (systematic analysis of blood gene regulation in blood) that will provide unprecedented power to use RNA expression as a routine and affordable test that can better diagnose disease, disrupting clinical practice and improving the health of Canadians.
TOP

Phase 2 Projects

Synthetic inhibitors of ubiquitin-binding cancer targets

Project Leader: Sachdev Sidhu
Institution: University of Toronto
Total Project Funding: $3,009,018

Our cells remove damaged or nonfunctional proteins through a small protein called ubiquitin, which attaches to target proteins and signals their destruction. In many diseases, ubiquitin does not work as it should. Dr. Sachdev Sidhu of the University of Toronto is using an innovative high-throughput molecular genetics engineering platform, which is unique in the world and has attracted intense interest from industry and academia, to enable the rapid and cost-effective development of highly specific and potent ubiquitin-like molecules. These molecules attach to key, cancer-associated enzymes of the ubiquitin system, to block or enhance their function. The project will enable the discovery of new drug targets, speed up drug development and generate effective anti-cancer drugs with fewer side effects, all of which should be of great socio-economic benefit to Canadians.
TOP

The Mammalian Membrane Two-Hybrid (MaMTH) assay: Advanced proteomics technology for biomedical research

Project Leader: Igor Stagljar
Institution: University of Toronto
Total Project Funding: $3,000,000

Integral membrane proteins have roles in many human diseases, but are notoriously difficult to study due to their unique biochemical features. Dr. Igor Stagljar and his team at the University of Toronto recently developed a powerful new technology, the Mammalian Membrane Two-Hybrid (MaMTH) assay, which can map protein-to-protein interactions (PPIs) of integral membrane proteins directly in the natural context of the cell. They now propose to further develop MaMTH technology by converting it into a platform that can map these PPIs on an extremely large scale. This work will allow researchers to develop better-targeted therapies for human disease more rapidly. The technology will be the foundation for an Ontario-based company called Protein Network Sciences that will offer easy access to this novel disruptive MaMTH technology, advancing biomedical research and therapeutic discovery while benefiting Canadian social and economic infrastructure.
TOP