Abstract: This application provides methods to differentiate between subjects with autism spectrum disorder (ASD) and typically developing (TD) or developmentally delayed (DD) subjects using miRNA and/or microbiome levels detected in saliva samples and patient information. The method can be used to monitor the progress of ASD and guide its treatment. RNA-seq, qPCR, or other methods determine counts and abundance of miRNA or microbiomes. MicroRNA and/or microbiome sequencing data are refined by normalization to expression levels or abundance of time-invariant miRNAs and/or microbial RN As to control for time of sample collection or to compensate for circadian fluctuations in these levels. Multivariate logistic regression and nonlinear classification techniques are further used to select a panel of miRNAs and microbiomes that accurately differentiate between subjects with ASD, DD, and TD in subjects with an unknown ASD status. These panels of miRNAs and microbiomes may be developed into a RNA assay kit.

Abstract: Methods for diagnosing or monitoring a condition, disorder or disease associated with circadian, diurnal or other temporal rhythms by detecting circa-miRNAs and circa-microbiomes associated with said condition, disorder or disease. Methods for correcting or normalizing sequence data to correct for diurnal or circadian fluctuations in quantities of circa-miRNAs and/or circa-microbiomes by adjusting or normalizing values based on the time of day when a saliva sample containing these RNAs was collected.