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The Impact of Psychopathology, Social Adversity and Stress-Relevant DNA Methylation on Prospective Risk for Post-Traumatic Stress: A Machine Learning Approach

Citation

Wani, Agaz H.; Aiello, Allison E.; Kim, Grace S.; Xue, Fei; Martin, Chantel L.; Ratanatharathorn, Andrew; Qu, Annie; Koenen, Karestan C.; Galea, Sandro; & Wildman, Derek E., et al. (2021). The Impact of Psychopathology, Social Adversity and Stress-Relevant DNA Methylation on Prospective Risk for Post-Traumatic Stress: A Machine Learning Approach. Journal of Affective Disorders, 282, 894-905. PMCID: PMC7942200

Abstract

BACKGROUND: A 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.
METHODS: We 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).
RESULTS: ML 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 R(2) 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.
CONCLUSION: Multiple 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.
LIMITATION: One of the limitations of this study is small sample size.

URL

http://dx.doi.org/10.1016/j.jad.2020.12.076

Reference Type

Journal Article

Article Type

Regular

Year Published

2021

Journal Title

Journal of Affective Disorders

Author(s)

Wani, Agaz H.
Aiello, Allison E.
Kim, Grace S.
Xue, Fei
Martin, Chantel L.
Ratanatharathorn, Andrew
Qu, Annie
Koenen, Karestan C.
Galea, Sandro
Wildman, Derek E.
Uddin, Monica

PMCID

PMC7942200

Data Set/Study

Detroit Neighborhood Health Study (DNHS)

Continent/Country

United States of America

State

Nonspecific