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Synthetic Reference Epigenomics: Building a Secure Cloud Framework for Scalable Rare Disease Diagnostics

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Overview

Globally, 446 million people are affected by a rare genetic disorder (RGD). Standard-of-care genetic tests cannot deliver a diagnosis for 70% of these patients, limiting their access to specialized care and burdening healthcare systems.

Over the past decade, the EpiSign™ Research Program at LHSCRI has led the clinical application of DNA methylation patterns, called episignatures, establishing EpiSign™ as the world’s first and only clinically validated whole-genome epigenetic diagnostic test. The technology is deployed globally to diagnose unresolved RGDs and add functional context to variants of unknown significance.

EpiSign™ is entering the next stage of innovation with the release of EpiSign™ v6 to expand scope and capability in rare diseases. V6 will cover over 200 RGDs and nearly 500 canonical/non-canonical episignatures, including improved detection of mosaic, hypomorphic, and inverse patterns. These capabilities will strengthen diagnostic sensitivity, specificity, and interpretive power across the rare disease spectrum.

Complementing this, development is happening on EpiSign™ METRIC, a cloud-enabled analysis environment for processing DNA methylation microarray data with high throughput and accuracy. However, as 5-base sequencing technologies become integrated into routine clinical practice, there is a critical need for EpiSign™ to evolve beyond array-based data and peripheral blood.

This project will develop a synthetic reference framework that generates and validates high-fidelity methylation reference datasets across sequencing platforms and tissue sources. By creating privacy-preserving synthetic references, robust AI classifiers can be trained that maintain clinical performance without requiring the transfer or exposure of patient data. Deploying these new algorithms within a secure, distributed cloud infrastructure will enable scalable, privacy-preserving EpiSign™ testing within laboratories worldwide.

The outcome will be a unified, platform-agnostic epigenomic analysis system capable of integrating both sequence and methylation information, broadening EpiSign™’s clinical utility to hereditary and environmentally influenced conditions. This will lay the foundation for future applications in exposure-related and prenatal diagnostics, and position EpiSign™ as the cornerstone of next-generation clinical epigenomics-offering secure, cross-platform, and scalable diagnostic solutions that address one of medicine’s most persistent unmet needs.

Small Molecule Preventing and Reversing TDP-43 Protein Aggregation as Therapeutic for Amyotrophic Lateral Sclerosis

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Overview

Neurodegenerative diseases such as ALS, Alzheimer’s, and Parkinson’s affect more than 50 million people worldwide, robbing individuals of independence and placing a profound emotional and financial strain on families and healthcare systems. Despite decades of research, there are still no effective treatments that stop or reverse disease progression.

In ALS specifically, patients typically survive only two to five years after diagnosis, and current approved drugs only offer minimal benefit with about 6 months life extension. As such, there is an urgent need for new therapies that target the root cause of these diseases rather than just their symptoms.

Neuropeutics is addressing this unmet need by developing JRMS, a first-in-class small molecule that directly targets TDP-43 protein clumping, which is a key disease driver common across the wide range of neurodegenerative diseases. In 97% of ALS cases, toxic clumping of TDP-43 disrupts normal cell function and leads to neuron death. JRMS acts through a unique mechanism to prevent and reverse TDP-43 clumping, and that restores its normal localization, effectively addressing the root pathology rather than downstream effects.

Early studies in human cells and animal models have shown that JRMS reduces toxic TDP-43 protein clumps buildup and reverses clumps already formed at the time of treatment, offering strong proof of concept for disease modification. The program is now advancing through medicinal chemistry optimization and preclinical validation to select a lead development candidate for future clinical testing. This work is being advanced through a collaborative partnership between the Robertson Lab at the University of Toronto, Neuropeutics Inc, Toronto Innovation Acceleration Partners (TIAP) and AbbVie.

LifeArc contributes world-class medicinal chemistry and drug development expertise through Neuropeutics. AbbVie provides strategic guidance on industry insights and CMC development. Together, they are developing JRMS as therapeutic to extend patients’ lives and improve their quality of life, while also reducing the significant socioeconomic burden of ALS in Canada and worldwide.

Genomics-Driven Upcycling of Food Waste to Medium-Chain Fatty Acids Using Engineered Anaerobic Consortia

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Overview

This project will advance a novel anaerobic fermentation technology for upcycling food waste into high-value specialty chemicals called medium-chain fatty acids (MCFAs). MCFAs are carboxylic acids of 6 to 12 carbon atoms with diverse applications in animal feed, industrial chemicals, food and pharmaceuticals.

Current MCFA supply is heavily dependent on coconut and palm kernel oil, creating major vulnerabilities to the chemicals industry: reputational risks due to deforestation, greenhouse gas emissions, high and volatile pricing, and supply chain disruptions. Production is geographically concentrated in Southeast Asia, and regulatory pressure is mounting to reduce the environmental impact of palm oil. These factors create a clear market pull for secure, domestic, low-carbon MCFA production.

Bioproduction of MCFAs from food waste has significant shortcomings. Existing open-culture microbiomes primarily generate C6-C8 MCFAs, show poor selectivity for MCFAs over short-chain fatty acids, and suffer from low yields due to competing processes like methanogenesis. SymBL overcomes these gaps by developing engineered microbiomes from the bottom up. Using defined combinations of bacteria and metabolic engineering, these engineered microbiomes can redirect carbon and energy from food waste toward MCFAs with far greater control, yield, and selectivity compared to conventional open-culture fermentations.

SymBL constructs microbiomes from large in-house culture collections, leveraging automation tools, machine learning, and genetic engineering to assemble and test thousands of microbiomes towards optimal MCFA production. A microbiome with enhanced C6-C8 production from source-separated organic waste (SSO) has already been designed and benchmarked.

The proposed project will support the next development phase: expanding MCFA production up to C12. They have identified the enzyme that restricts MCFA production to C8. The project will deploy novel genetic tools to modify this enzyme in key bacteria, enabling production of C6 to C12 MCFAs via anaerobic fermentation for the first time. These enhanced strains will be integrated into optimized microbiomes, and performance will be validated using SSO in a 20-L continuous bioreactor system.

By achieving first-to-market C6-C12 MCFA bioproduction from food waste, this project significantly expands the market potential for waste-to-MCFA upcycling, while displacing palm-derived chemicals and reducing the economic.

Optimization of the Nanopore-Optimized Mobile Analysis for Diversity (NOMAD) System for Analysis of Dairy Product Quality

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Overview

Canada’s dairy industry faces a significant challenge ensuring the microbial safety and quality of dairy powders used in high-value products. Current lab-based microbial testing methods are too slow, often taking days to yield results, which delays critical quality control decisions and contributes to waste, recalls, and lost revenue.  

With the Canadian milk powder market valued at approximately $8.4 billion and losses from poor quality ranging from 2 to 10 percent annually, the opportunity for a faster, on-site solution is clear. To address this, Gay Lea Foods, in collaboration with the University of Guelph, Dairy Farmers of Ontario, and technology partners including Oxford Nanopore and NEB, will develop and deploy the Nanopore-Optimized Mobile Analysis for Diversity (NOMAD) system.  

NOMAD is a portable, genomics-based platform that uses full-length 16S rRNA gene sequencing on the Oxford Nanopore MinION device to deliver same-day, species-level microbial detection. This project will validate NOMAD for routine quality control, target a sample-to-result turnaround time of under 10 hours, and benchmark its performance against traditional lab testing.  

Field-ready protocols for DNA extraction, PCR, and sequencing, paired with a cloud-based taxonomy pipeline and intuitive dashboard, will enable real-time decision-making at the production site. The path to commercialization includes launching a dedicated service company to offer NOMAD as a mobile microbiome testing platform, starting with Gay Lea’s network of 1,300 producers and expanding to other dairy processors and adjacent sectors such as brewing.  

Services will be offered through a subscription or per-test pricing model, with tiered offerings for routine surveillance, hygiene validation, and on-demand testing. The expected benefits to Canada include job creation, increased molecular diagnostic capacity, reduced waste, improved product safety, and enhanced competitiveness of the Canadian agri-food sector. With strong alignment between the receptor, academic researchers, and technology providers, this project is designed to deliver meaningful, scalable impact across Canada’s dairy industry and beyond.

Future-proofing the Canadian dairy herd: a new genomic breeding tool to enhance climate resiliency

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Overview

Dairy plays a critical role in Canada’s economy, generating $8.88 billion in net farm cash receipts and contributing $20 billion to GDP in 2024. As the sector strives to meet ambitious climate targets, producers face the challenge of balancing environmental goals with animal productivity, health and resilience.  

Recognizing this, Semex, Canada’s leading cattle genetics company, and Lactanet, Canada’s leading provider of dairy herd management solutions, are spearheading the development and implementation of a genomics-based tool to identify climate-resilient cattle. This initiative aims to create and implement the Future-Proof Index – a novel genomic selection tool designed to optimize both mitigation and adaptation potential in dairy cattle.  

The innovation addresses a critical gap in the industry: the need to reduce greenhouse gas emissions while managing the growing impact of heat stress on animal welfare and productivity. Unlike existing approaches, this index will incorporate broader genetic relationships among resilience, adaptability, and environmental traits, offering a more comprehensive solution.  

Lactanet, a farmer-led, not-for-profit organization, brings essential expertise and infrastructure to the project. Its genomic toolbox already includes three mitigation traits (feed and methane efficiency, and body maintenance requirements), while University of Guelph research has been used to develop methodologies for adaptation traits, such as the effects of heat stress on health and performance.  

By integrating mitigation, adaptation, and productivity traits, the Future-Proof Index will represent a world-first in breeding goals that simultaneously address climate resilience, as well as ensure social, economic and environmental sustainability. The index will be deployed through Semex’s Elevate platform, Canada’s largest and the world’s fastest-growing genomic testing system (expanding 15–20% annually), which currently serves 235,000 animals annually across 46 countries, including 45,000 in Canada.  

The domestic rollout will be accelerated by Lactanet’s commitment to offer the index free of charge for male animals nationwide and for female animals within its membership (over 60% of producers), covering approximately 10,000 farms and 1.4 million cows.  

Internationally, Semex will license the index at cost, positioning it as a premium climate-smart breeding solution. This dual-market strategy is projected to a) sustain Semex current growth trajectory of 15%/year ($14M this year) in exports of dairy genetics, b) deliver $778M to the Canadian dairy sector, c) cut 4.8Mt CO2e yearly, and d) position Canada as a global leader in climate-smart dairy genetics.  

By leveraging existing infrastructure and integrating cutting-edge genomic science, this project will empower the dairy industry to meet net-zero targets while improving animal health, productivity, and welfare, ensuring long-term sustainability and profitability.

A novel approach for petroleum pollution: in situ anaerobic biodegradation

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Overview

Federated Co-operatives Limited (FCL), based in Saskatoon, is Canada’s largest non-financial co-operative and one of the country’s top petroleum marketers. With over 780 fueling locations and 500+ contaminated sites, FCL faces major environmental and financial liabilities from petroleum hydrocarbon impacts.  

Many FCL-owned sites are anoxic and contain deep, mixed plumes that are impractical to remediate by excavation or soil vapour extraction. One such plume in Dryden, Ontario, has persisted for decades and could expose FCL to regulatory penalties, lawsuits, and reputational damage if not addressed.  

Bioremediation offers a lower-cost, sustainable treatment option by harnessing microorganisms that degrade hydrocarbons in situ, but reliable tools to assess anaerobic biodegradation are lacking. To address this gap, FCL is partnering with Prof. Elizabeth Edwards (a world expert in anaerobic bioremediation) and SiREM (an Ontario-based bioremediation service provider) to validate genomics-enabled tools at Dryden and other field sites by directly tracking hydrocarbon-degrading microorganisms and linking their abundance and activity to degradation rates.  

This project will deliver the first validated genomic framework to quantify and monitor anaerobic hydrocarbon biodegradation. The innovation integrates: (1) deep multi-omics sequencing to identify active anaerobic degraders; (2) quantitative PCR biomarker assays for widespread degraders and functional genes; and (3) predictive models to estimate site-specific biodegradation rates and guide remediation decisions.  

By advancing genomic tools and sharing results with Canadian stakeholders and regulators, FCL will reduce uncertainty and costs at its own sites while supporting a new industry standard for anaerobic bioremediation. The benefits to FCL are immediate and substantial. Validated genomic tools will reduce long-term monitoring costs (often $20–60K per site annually), accelerate closure of challenging sites, and lower liabilities across FCL’s portfolio, with potential savings in the millions.  

The Canadian remediation market is valued at over $2B, and site owners of the tens of thousands of BTEX-contaminated sites across the country also stand to benefit through significant cost savings. Regulators will gain transparent, evidence-based data that strengthen compliance and reduce uncertainty in remediation planning.  

Nationally, the project will expand markets for advanced molecular bioremediation technologies, including biomarker assays and bioaugmentation cultures offered by SiREM. Broader benefits include cleaner groundwater, reduced health risks, and employment growth in Canada’s environmental sector. By leading this innovation, FCL – in partnership with Prof. Edwards and SiREM – will set a national precedent for sustainable remediation while continuing to invest in the health and resilience of the communities it serves.

ONTARIAN: bespOke TevCas9 geNe ediTors enAbled by diRected evolutIon and mAchine learning

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Overview

Specific Biologics Inc. (SBI) is developing Dualase®, a two-site genome editing platform designed to precisely remove, repair, or insert DNA sequences as therapeutic for serious genetic diseases. Unlike other genome editing systems like CRISPR-Cas, base editing or prime editing, Dualase enables accurate, programmable outcomes at diverse therapeutic targets unlocking the market for genome editing that is rapidly growing (+15.7% per year) and expected to reach over $40 billion/year by 2034.

The key objective of this project is to build a machine-learning (ML)-enabled prediction tool to design bespoke Dualase editors that maximize on-target activity and minimize off-target risk and identify highly active Dualase editors for therapeutic targets. It draws on the expertise of Dr. David Edgell at Western University, whose lab discovered Dualase editors, and SBI whose have developed therapeutics based in Dualase genome editors to 10+ therapeutic targets to date.

The ML tool will rapidly generate and identify bespoke Dualase editors in silico, reducing design-build-test cycles that require considerable wet lab empirical evaluation. This increases the probability of successfully identifying potent editors and enables SBI to advance more therapeutic programs in parallel internally, and together with partners.

The key aims of the project include generation of novel variants of Dualase directed to therapeutically relevant sequences using directed evolution, developing and validating the predictive ML model, and piloting new editors across multiple high-value disease targets.

Commercialization will follow a staged pathway. Internally, the tool will accelerate Specific Biologics’ own pipeline toward the clinic. Externally, it will accelerate partnerships by allowing design of Dualase constructs, creating new licensing and co-development revenues.

The expected benefits to Canada include high-skilled job creation in AI/ML, computational biology, and advanced therapeutics; expansion of Canada’s leadership in genome editing and machine learning; and enhance SBI commercialization capacity through new intellectual property and licensable therapeutics positioning SBI as an end-to-end therapeutic anchor company in Canada.

The project will also deliver a powerful capability to accelerate research timeline in the Canadian research community through non-commercial licensing, saving months of wet lab experimentation and reduce R&D costs. Importantly, the tool will bring innovative treatments to patients sooner, and strengthen SBI’s asset value and partnership potential, all while contributing to improved health outcomes for patients in Ontario, Canada and globally.

A Peptide-Directed siRNA Delivery Platform for Glioblastoma Multiforme: Targeting Genes Driving Treatment Resistance

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Overview

ProteinQure is a revenue-generating (over $20M CAD total), clinical-stage biotech company developing peptides for precision therapeutic delivery. They combine machine learning and generative AI to design best-in-class therapeutics, both through fee-for-service partnerships with large pharmaceutical companies and via an internal drug discovery pipeline.

PQ203, is a peptide-drug conjugate for triple-negative breast cancer, now in a Phase I clinical trial at Princess Margaret Cancer Centre in Toronto. ProteinQure has experience across 80+ clinical trials and advanced PQ203 from discovery to IND-enabling studies in just two years—and into clinical trials 18 months later—demonstrating exceptional execution in translating preclinical programs into clinical assets.

Building on the innovation of PQ203, an AI-designed SORT1-binding peptide, they further modified and optimized this scaffold for CNS delivery of therapeutic payloads, having the potential to unlock an estimated $100B global market across neurology and neurodegenerative disease indications.

The CNS-delivery program leverages this optimized SORT1-binding peptide to deliver siRNA molecules for targeted gene knockdown in the brain. The program is supported by an advanced data package: best-in-class delivery across multiple in vivo models, including rodents and, more recently, non-human primates. For the lead CNS indication, they selected Glioblastoma Multiforme (GBM), a lethal brain cancer with relatively high incidence in Canada and few effective treatment options.

The interest in glioblastoma (GBM) is guided by ProteinQure’s existing expertise in cancer biology and, importantly, through a partnership with Dr. Stéphane Angers, Director of the Donnelly Centre at the University of Toronto and an internationally recognized leader in GBM genetics. Dr. Angers brings unparalleled leadership, drug development experience, and state-of-the-art tools that will support the advancement of our therapeutic candidate for GBM.

Also on the project team is Dr. Peter Dirks, a world-renowned neurosurgeon at SickKids and pioneer in brain cancer stem cell biology, whose lab has developed and validated in vivo GBM models. Dr. Douglas Cook, Professor and Chair of Neurosurgery at Queen’s University, adds expertise in translational neuroscience and access to a world-class non-human primate facility with established models for CNS therapeutics.

ProteinQure has a proven track record advancing oncology programs into the clinic, and unlike more prevalent diseases such as Alzheimer’s, GBM represents an area to independently advance and commercialize a program. By leveraging Toronto’s world-class ecosystem in GBM and oncology clinical trials, the same roadmap that was successfully executed with PQ203 can be applied to develop and commercialize a life-changing therapy for patients with GBM, who face a dire need for new treatment options.

SmartRequisition: Scalable Genomic Test Requisitions

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Overview

Genomic medicine is entering mainstream care, but interpretation remains a critical bottleneck: accurate variant analysis depends on structured phenotypes, yet requisitions are often incomplete, unstructured, and still on paper.

Manual entry of Human Phenotype Ontology (HPO) codes is slow, inconsistent, and labour-intensive, delaying care and limiting scalability as sequencing expands across specialties. This project will advance SmartRequisition, a software portal that automates HPO capture at ordering and generates HL7 FHIR/LIS-ready requisitions.

By Month 24, it will be implemented at IWK Health and partner Canadian sites, with a 67% reduction in phenotype coding time, 80% requisition completeness, and a solution with 30% attach-rate goal across current deployments and an ARR trajectory toward ~CA$6M.

To address the existing need, the Clinical Intelligence for Phenotyping and Genomics Research (CIPHER) network has been established. Co-led by PhenoTips and IWK Health, partners include Alberta Health Services, CHU Sainte-Justine, CHEO, and SickKids. The network will co-design and validate SmartRequisition, embedding it into intake workflows.

Using large language models with retrieval-augmented generation, the tool extracts HPO terms from free text and structured inputs, supports multimodal data, and enables clinician-in-the-loop review. Requisitions export via HL7 FHIR, LIS, or PDF for integration into lab and EHR systems.

The market opportunity is significant. The global genetic testing market was US$11.9B in 2024 and is projected to reach US$91.3B by 2034 (22.6% CAGR). Growth depends on digital infrastructure that enables high-quality requisition and interpretation. PhenoTips already serves 26 hospitals worldwide with its genomic workflow platform, anchoring an immediate ~CA$200M addressable market in hospitals with in-house genetics labs.

SmartRequisition strengthens PhenoTips’ AI-driven suite, positioning the company to capture this segment and expand into the ~CA$2B serviceable market of large health systems, with future application in oncology, neurology, cardiology, and population health.

IWK was the first centre in Atlantic Canada to deliver local clinical exome services, with phenotypes integrated into sequencing through a multi-year development and privacy/legal program. This foundation de-risks the project, allowing immediate focus on validation and roll-out within the two-year GAPP timeframe.

For Canada, SmartRequisition strengthens national genomic capacity, reduces reliance on foreign software, and improves patient care. For the CIPHER network, it supports more timely diagnoses while demonstrating a solution that can scale across provinces. By transforming a universal bottleneck into a validated product, SmartRequisition positions Canada as a leader in digital infrastructure for precision medicine.