Fig. 1.

Steps 1–3: Discovery, prioritization and validation. a Cohorts used in study, depicting flow of discovery, prioritization, and validation of biomarkers from each step. b Discovery cohort longitudinal within-subject analysis. Phchp### is study ID for each subject. V# denotes visit number. c Discovery of possible subtypes of stress based on High Stress visits in the discovery cohort. Subjects were clustered using measures of mood and anxiety (from Simplified Affective State Scale (SASS)) [7], as well as psychosis (PANNS Positive). d Differential gene expression in the Discovery cohort—number of genes identified with differential expression (DE) and absent–present (AP) methods with an internal score of ≥2. Red—increased in expression in High Stress, blue—decreased in expression in High Stress. At the discovery step, probesets are identified based on their score for tracking stress with a maximum of internal points of 6 (33% (2 pt), 50% (4 pt) and 80% (6 pt)). e Prioritization with Convergent Functional Genomics (CFG) for prior evidence of involvement in stress. In the prioritization step, probesets are converted to their associated genes using Affymetrix annotation and GeneCards. Genes are prioritized and scored using CFG for stress evidence with a maximum of 12 external points. Genes scoring at least 6 points out of a maximum possible of 18 total internal and external scores points are carried to the validation step. f Validation in an independent cohort of psychiatric patients with clinically severe trait stress and high-state stress. In the validation step, biomarkers are assessed for stepwise change from the discovery groups of subjects with Low Stress, to High Stress, to Clinically Severe Stress, using analysis of variance. N = number of testing visits. Two hundred and thirty-two biomarkers were nominally significant, NUB1 and ASCC1 were the most significant increased and decreased biomarkers, respectively, and 1130 biomarkers were stepwise changed