Machine Learning SNP Based Prediction for Precision Medicine

Abstract

In the past decade, precision genomics based medicine has emerged to provide tailored and effective healthcare for patients depending upon their genetic features. Genome Wide Association Studies have also identified population based risk genetic variants for common and complex diseases. In order to meet the full promise of precision medicine, research is attempting to leverage our increasing genomic understanding and further develop personalized medical healthcare through ever more accurate disease risk prediction models. Polygenic risk scoring and machine learning are two primary approaches for disease risk prediction. Despite recent improvements, the results of polygenic risk scoring remain limited due to the approaches that are currently used. By contrast, machine learning algorithms have increased predictive abilities for complex disease risk. This increase in predictive abilities results from the ability of machine learning algorithms to handle multi-dimensional data. Here, we provide an overview of polygenic risk scoring and machine learning in complex disease risk prediction. We highlight recent machine learning application developments and describe how machine learning approaches can lead to improved complex disease prediction, which will help to incorporate genetic features into future personalized healthcare. Finally, we discuss how the future application of machine learning prediction models might help manage complex disease by providing tissue-specific targets for customized, preventive interventions.

Keywords: complex disease risk; genetic disease risk prediction; machine learning; personalized medicine; polygenic risk score; precision medicine.

Figure 1

Workflow for creating a supervised machine learning model from a genotype dataset.

Figure 2

The strengths and weaknesses of polygenic risk scoring and machine learning model.