The Impact of Psychopathology, Social Adversity and Stress-relevant DNAm on Prospective Risk for Post-traumatic Stress: A Machine Learning Approach

Wani, A. H.; Aiello, A. E.; Kim, G. S.; Xue, F.; Martin, C. L.; Ratanatharathorn, A.; Qu, A.; Koenen, K.; Galea, S.; Wildman, D. E.; Uddin, M.

doi:10.1101/2020.09.25.313635

bioRxiv · 10.1101/2020.09.25.313635

The Impact of Psychopathology, Social Adversity and Stress-relevant DNAm on Prospective Risk for Post-traumatic Stress: A Machine Learning Approach

Wani, A. H.·Aiello, A. E.·Kim, G. S.·Xue, F.·Martin, C. L.·Ratanatharathorn, A.·Qu, A.·Koenen, K.·Galea, S.·Wildman, D. E.·Uddin, M.

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Abstract

BackgroundA range of factors have been identified that contribute to greater incidence, severity, and prolonged course of post-traumatic stress disorder (PTSD), including: comorbid and/or prior psychopathology; social adversity such as low socioeconomic position, perceived discrimination, and isolation; and biological factors such as genomic variation at glucocorticoid receptor regulatory network (GRRN) genes. This complex etiology and clinical course make identification of people at higher risk of PTSD challenging. Here we leverage machine learning (ML) approaches to identify a core set of factors that may together predispose persons to PTSD. MethodsWe used multiple ML approaches to assess the relationship among DNA methylation (DNAm) at GRRN genes, prior psychopathology, social adversity, and prospective risk for PTS severity (PTSS). ResultsML models predicted prospective risk of PTSS with high accuracy. The Gradient Boost approach was the top-performing model with mean absolute error of 0.135, mean square error of 0.047, root mean square error of 0.217, and R2 of 95.29%. Prior PTSS ranked highest in predicting the prospective risk of PTSS, accounting for >88% of the prediction. The top ranked GRRN CpG site was cg05616442, in AKT1, and the top ranked social adversity feature was loneliness. ConclusionMultiple factors including prior PTSS, social adversity, and DNAm play a role in predicting prospective risk of PTSS. ML models identified factors accounting for increased PTSS risk with high accuracy, which may help to target risk factors that reduce the likelihood or course of PTSD, potentially pointing to approaches that can lead to early intervention.

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Wani, A. H., Aiello, A. E., Kim, G. S., Xue, F., Martin, C. L., Ratanatharathorn, A., Qu, A., Koenen, K., Galea, S., Wildman, D. E., Uddin, M.. 2020-09-28. The Impact of Psychopathology, Social Adversity and Stress-relevant DNAm on Prospective Risk for Post-traumatic Stress: A Machine Learning Approach. https://doi.org/10.1101/2020.09.25.313635

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