A machine learning model can improve genetic prediction of type 1 diabetes by as much as 10%, show results from a University of California, San Diego study.
The researchers used the machine‑learning model T1GRS to improve on a gold standard polygenic genetic risk score used to predict who is likely to develop the condition called GRS2.
Type 1 diabetes is an autoimmune condition that impacts around 2 million people in the U.S. While it is a multifactorial condition, genetics plays a big role and around 50% of a person’s susceptibility comes from genetics.
“The natural history of type 1 diabetes suggests that the disease occurs in genetically susceptible individuals exposed to environmental triggers, leading to the development of islet-specific autoantibodies and autoreactive T cells and progressive loss of insulin secretory function, although the underlying etiology is not fully understood,” write lead author Kyle Gaulton, PhD, associate professor of pediatrics at UC San Diego School of Medicine, and colleagues in Nature Genetics.
The GRS2 polygenic risk score has been widely tested and can be used to predict newborns who are at high risk of developing type 1 diabetes. While early prediction can’t necessarily stop the disease it can help to prevent emergencies like diabetic ketoacidosis at diagnosis, allow families time to prepare and could allow use of therapies to delay onset of the condition.
In this study, Gaulton and colleagues carried out a genome‑wide association study in 20,355 people with type 1 diabetes and 797,363 non‑diabetic Europeans, as well as a further analysis around the MHC region in 10,107 diabetic and 19,639 nondiabetic individuals.
“The MHC has ‘blocks’ of co-inherited genetic information that are very highly enriched in individuals with type 1 diabetes,” said co-first author Emily Griffin, PhD, a postdoctoral fellow in Gaulton’s lab. “If you have them, it doesn’t mean that you’re going to get diabetes, but if you don’t have them, it means you have a very low chance of getting diabetes.”
Overall 160 risk signals were identified, and the team trained their T1GRS model to predict who was likely to develop type 1 diabetes based on their genetics. The model was able to improve on the GRS2 model predictions by up to 10% in both populations of European and African American ancestry.
Overall the new score correctly flagged about 89 of 100 people with type 1 diabetes while correctly reassuring about 84 of 100 people without the disease.
“Our results highlight the value of combining the results of genetic association studies with machine learning methods to improve the prediction of complex diseases,” conclude the authors.
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