Clin Psychopharmacol Neurosci.  2017 Feb;15(1):47-52. 10.9758/cpn.2017.15.1.47.

Predicting Autism Spectrum Disorder Using Blood-based Gene Expression Signatures and Machine Learning

Affiliations
  • 1Institute for Health and Society, Hanyang University, Seoul, Korea.
  • 2Translational Neurogenetics Laboratory, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.
  • 3Department of Psychiatry and Institute of Mental Health, Hanyang University College of Medicine, Seoul, Korea. ahndh@hanyang.ac.kr

Abstract

OBJECTIVE: The aim of this study was to identify a transcriptomic signature that could be used to classify subjects with autism spectrum disorder (ASD) compared to controls on the basis of blood gene expression profiles. The gene expression profiles could ultimately be used as diagnostic biomarkers for ASD.
METHODS
We used the published microarray data (GSE26415) from the Gene Expression Omnibus database, which included 21 young adults with ASD and 21 age- and sex-matched unaffected controls. Nineteen differentially expressed probes were identified from a training dataset (n=26, 13 ASD cases and 13 controls) using the limma package in R language (adjusted p value <0.05) and were further analyzed in a test dataset (n=16, 8 ASD cases and 8 controls) using machine learning algorithms.
RESULTS
Hierarchical cluster analysis showed that subjects with ASD were relatively well-discriminated from controls. Based on the support vector machine and K-nearest neighbors analysis, validation of 19-DE probes with a test dataset resulted in an overall class prediction accuracy of 93.8% as well as a sensitivity and specificity of 100% and 87.5%, respectively.
CONCLUSION
The results of our exploratory study suggest that the gene expression profiles identified from the peripheral blood samples of young adults with ASD can be used to identify a biological signature for ASD. Further study using a larger cohort and more homogeneous datasets is required to improve the diagnostic accuracy.

Keyword

Autism spectrum disorder; Blood; Microarray analysis; Transcriptome; Machine learning; Decision support techniques
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