On average it takes five to seven years to diagnose a rare disease. But, for growing numbers of rare diseases, that is all about to change with new artificial intelligence-led technology developed by researchers at London Health Sciences Centre (LHSC) and Lawson Health Research Institute that will be going global.

With funding of $7,551,693 that includes a Genome Canada Genomic Applications Partnership Program (GAPP) grant and support from Illumina Inc., a leading developer of tools for analysis of genetic variation, research led by Dr. Bekim Sadikovic will change what has been years of trial and error in the search for a diagnosis into a simple blood test that could ultimately be available in any lab around the world.

“Despite advances in genome sequencing, it is estimated that nearly 70 per cent of people with a rare genetic disease are not diagnosed,” says Dr. Sadikovic, Research Chair in Clinical Genomics and Epigenomics with the Archie and Irene Verspeeten Clinical Genome Centre at LHSC, and
Scientist at Lawson.

“To receive specialized care, you need a specific genetic diagnosis. Without one, you can’t access therapy and, unlike other types of diseases, genetic diseases don’t only affect the patient, they affect whole family because they can be inherited,” he says.

Using machine learning, Dr. Sadikovic has developed EpiSign^™, the first technology that uses a patient’s epigenome to diagnose genetic disorders. At its most basic level this means that artificial intelligence is used to detect the pattern of chemical signals, called epigenetics, that turn genes within a person’s DNA on or off. The position of this on-off switch for any specific gene could mean someone has blue eyes versus brown eyes, or it could mean they have a rare genetic disease. 

Over the last ten years, Dr. Sadikovic has been researching epigenetics and has created a database that contains the epigenetics of hundreds of genetic diseases, and diseases caused by toxic environmental exposures, the largest database of its kind in the world. 

This decade of research has culminated in an ongoing national trial of this diagnostic technology called EpiSign-CAN. Funded by Genome Canada, the trial involves testing of thousands of patients across 14 Canadian academic hospitals.

 Dr. Bekim Sadikovic and Jen Kerkhof, Senior Laboratory Technologist, Molecular Genetics, in the lab where samples are analyzed.

“It is these episignatures that allow us to diagnose patients that otherwise cannot be diagnosed with standard genetic techniques,” Dr. Sadikovic explains. “So, we can now interpret this genetic data that we couldn’t understand before, and provide critical answers for patients and families affected by hundreds of rare diseases.”

This $7.44 million grant funding from the Government of Canada through Genome Canada will enable the next phase of the project in which EpiSign™ technology will be implemented in labs at academic institutions in 15 countries around the world. 

“This research is a great example of LHSC’s commitment to supporting the world-leading advances in diagnosis of patients with rare diseases,” says Brad Campbell, Corporate Hospital Administrative Executive at LHSC.

Along with Dr. Sadikovic’s laboratory at LHSC, two industry partners will be involved in this project. Illumina Inc. will be developing custom microchip hardware to facilitate streamlined sample collection, and EpiSign Inc., a Canadian startup biotechnology company which is a partnered venture between LHSC and Dr. Sadikovic, will develop end-user software for automated data analysis in labs around the world.

“The support provided by Genome Canada and Illumina will enable adoption of EpiSign technology and place it at the forefront of patient care globally,” Campbell says.

Dr. Sadikovic’s work has also been supported with funding through LHSC’s Academic Realignment Initiative Awards and generous donor support through London Health Sciences Foundation, including through the Archie and Irene Verspeeten Clinical Genome Centre. 

By Roxanne Beaubien

Roxanne Beaubien is a Senior Media Relations Consultant  at London Health Sciences Centre