AI helping in diagnosis of rare diseases

Detailed in the American Journal of Human Genetics and Genetics in Medicine, the research from Canada's London Health Sciences Centre (LHSC) and Lawson Health Research Institute uses technology called EpiSign, which was developed by Dr Bekim Sadikovic, a Lawson Scientist at LHSC.

EpiSign leverages AI to measure a patient’s epigenome, which is a unique chemical fingerprint that is responsible for turning genes on or off. EpiSign can currently be used to help diagnose over 100 genetic diseases that were previously difficult to diagnose. 

In one of two newly published studies, Dr Sadikovic’s team has found that EpiSign can be used to accurately identify patients affected by birth disorders called recurrent constellation of embryonic malformations (RCEMs).

Since their discovery, attempts to identify the cause and specific diagnostic markers for RCEMs have been unsuccessful, making it challenging to provide patients and families with accurate diagnoses. EpiSign can now be used to accurately identify RCEMs for the first time using a blood test.  

“Reaching an early and accurate diagnosis can be lifechanging. This is a major breakthrough that allows physicians to provide earlier and more accurate diagnosis, resulting in improved disease management,” Dr Sadikovic said in a statement. “It also has the potential to lead to health system cost savings since many patients spend years and even decades being tested to rule out other potential diseases with similar symptoms.” 

In a second study, Dr Sadikovic’s team used EpiSign technology for the first time to develop an accurate biomarker for a group of disorders called fetal valproate syndrome, which is caused by prenatal exposure to toxic levels of medication that may be used to treat bipolar disorder and migraines, or to control seizures in the treatment of epilepsy.

It can result in neurodevelopmental disorders in infants, including learning, communication and motor disorders, autism, and intellectual disabilities.  

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“This is a significant breakthrough as it’s the first time the technology has been used to aid in diagnosis of a disease caused by environmental factors rather than genetics,” said Dr Sadikovic. “It highlights how epigenetics can be influenced by environmental and lifestyle factors, including diet, exercise and exposure to toxins.” 

The research is ongoing as Dr Sadikovic and his team, in collaboration with the global EpiSign Discovery Research network, are currently studying and developing biomarkers for over 700 rare disorders. He noted the potential of this research is endless, showing promise for use in the diagnosis, prognosis and treatment of many other diseases and disorders, including cancer. 

“One in 20 people have a rare disease that could present at any point in their lives and can be caused by genes, environmental exposures, or their combined effects,” said Dr Sadikovic. “We can help diagnose a growing number of genetic diseases and, now for the first time, we can look beyond the genome and accurately measure the impact of the environment.”      

These studies are a collaborative effort involving multidisciplinary teams in Canada, the United States, the United Kingdom and Europe. Funding for the research was provided by Genome Canada and Ontario Genomics, as plus in-kind support from EpiSign Inc.