TimeSignature: A Universal Method for Robust Detection of Circadian State from Gene Expression

Profiles of circadian gene expression in whole blood from 11 healthy adult subjects. Abstract: Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessment of physiological time using transcriptional biomarkers found in human blood can significantly improve diagnosis of circadian disorders and optimize the delivery time of therapeutic treatments. To be useful, such a test must be accurate, minimally burden some to the patient, and readily generalizable to new data. A major obstacle in development of gene expression biomarker tests is the diversity of measurement platforms and the inherent variability of the data, often resulting in predictors that perform well in the original datasets but cannot be universally applied to new samples collected in other settings. Here we introduce TimeSignature, a new algorithm that robustly infers circadian time from gene expression. We demonstrate its application in data from three independent studies using Pdistinct microarrays, and further validate it against a new set of samples profiled by RNA-Seq. Our results show that TimeSignature is more accurate and efficient than competing methods, estimating circadian time to within 2h for the majority of samples. Importantly, we demonstrate that once trained on data from a single study, the resulting predictor can be universally applied to yield highly accurate results in new data from other studies independent of differences in study population, patient protocol, or assay platform without renormalizing the data or retraining. This feature is unique amongst expression–based predictors, and addresses a major challenge in the development of generalizable, clinically–useful tests. Overall design: Whole blood transcriptional profiles of 11 individuals with intermediate circadian phenotype, were generated by RNA sequencing, using Illumina NextGen 500. Whole blood was collected every 2hr over 28hr (15 time points), yelding total of 165 samples, of which 153 passed the QA and underwent further analysis.