Bringing RNA-seq to clinical diagnostics

December 11, 2016

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.

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Synthetizing cancer target inhibitors

December 11, 2016

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.

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Understanding metastatic cancers

December 11, 2016

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.

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Identifying cancer biomarkers

December 11, 2016

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.

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De novo whole genome assembly

December 11, 2016

“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.

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$110M invested in 13 Canadian research projects to deploy genomics

December 9, 2016

Today, the Honourable Kirsty Duncan, Minister of Science, announced $32 M in federal support for 13 large-scale applied research projects that will use genomics to solve long-standing challenges. These projects, representing a total investment of $110M, look to mitigate the effects of climate change on forestry and fisheries, protect the Arctic, and support wildlife.

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Enhancing naturally-occurring nutrition in soil

October 13, 2016

Boreal Agrominerals Inc. is collaborating with researchers from Wilfrid Laurier and Algoma University to identify soil that contains beneficial naturally-occurring microorganisms to enhance the benefits in amended soils. This academic-industry partnership will work to characterize the distribution of microorganisms naturally found at various mining sites from the SRC deposit near Sudbury, Ontario, and investigate the effects of mining and site characteristics on soil microbial communities based on nutrient solubilisation and plant nutrient availability.

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Improving paediatric cancer diagnostics using genomics

October 5, 2016

SickKids’ Drs. Cynthia Hawkins and John Racher and NanoString Technologies are merging their individual strengths to develop additional tools for diagnosing cancer in children. Funded through Round 6 of Genome Canada’s Genomic Applications Partnership Program, they are working to create tools that will deliver key information in a targeted, cost-effective and timely way. This initial work will focus on low-grade glioma (brain tumours), leukemia and soft-tissue sarcoma, for which no comprehensive tests currently exist. This tool will improve survival times and quality of life for children with cancer, reduce healthcare costs and generate licensing revenue, which will be shared between the partners.

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Standardization of molecular diagnostic testing for non-small cell lung cancer

October 5, 2016

Non-small cell lung cancer is the most common type of lung cancer. Specific genetic mutations in a patient’s tumour can determine which drug will work best for that patient. Dr. David Stewart, from The Ottawa Hospital and the University of Ottawa, is working with the Eastern Ontario Regional Laboratory Association (EORLA) to develop an assay that can accurately detect important genetic mutations in the very small biopsy samples from patients with advanced lung cancer. The assays will test for multiple genetic variations at once, for a more timely result than is possible with current sequential testing strategies.

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$1.45M for genomics big data research in Ontario

September 14, 2016

Parliamentary Secretary for International Development, Karina Gould, on behalf of the Honourable Kirsty Duncan, Minister of Science, announced the funding recipients from Genome Canada’s 2015 Bioinformatics and Computational Biology competition, a partnership with the Canadian Institutes of Health Research. The following eight projects were awarded to Ontario researchers – with two projects co-led with British…

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