Predicting Clinical Dementia Rating Using Blood RNA Levels

• Main Authors: Justin B. Miller, John S. K. Kauwe
• Format: Article
• Language: English
• Published: MDPI AG 2020-06-01
• Series: Genes
• Subjects: diagnosis; machine learning; chloride intracellular channel 1 (<i>CLIC1</i>); clinical dementia rating; Alzheimer’s disease
• Online Access: https://www.mdpi.com/2073-4425/11/6/706

The Clinical Dementia Rating (CDR) is commonly used to assess cognitive decline in Alzheimer’s disease patients and is included in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. We divided 741 ADNI participants with blood microarray data into three groups based on their most recent CDR assessment: cognitive normal (CDR = 0), mild cognitive impairment (CDR = 0.5), and probable Alzheimer’s disease (CDR ≥ 1.0). We then used machine learning to predict cognitive status using only blood RNA levels. Only one probe for chloride intracellular channel 1 (<i>CLIC1</i>) was significant after correction. However, by combining individually nonsignificant probes with <i>p</i>-values less than 0.1, we averaged 87.87% (s = 1.02) predictive accuracy for classifying the three groups, compared to a 55.46% baseline for this study due to unequal group sizes. The best model had an overall precision of 0.902, recall of 0.895, and a receiver operating characteristic (ROC) curve area of 0.904. Although we identified one significant probe in <i>CLIC1</i>, <i>CLIC1</i> levels alone were not sufficient to predict dementia status and cannot be used alone in a clinical setting. Additional analyses combining individually suggestive, but nonsignificant, blood RNA levels were significantly predictive and may improve diagnostic accuracy for Alzheimer’s disease. Therefore, we propose that patient features that do not individually predict cognitive status might still contribute to overall cognitive decline through interactions that can be elucidated through machine learning.