The present invention relates to a system utilizing biochemical markers and genetic markers to diagnose, predict, and / or monitor intervention of a number of diseases and conditions that have unresolved oxidative stress as an important component. The present invention relates generally to markers and assays for diagnosing, predicting, and monitoring disease, particularly disease-relevant oxidative stress and lipid metabolites and mediators. The oxidative stress, lipid metabolite and lipid mediator biochemical and genetic markers may be further combined with other disease associated or disease relevant markers in methods and assays for diagnosis, monitoring, and assessment of disease, particularly of complex diseases with multi-component factors. The system, methods and assays are applicable to various diseases, including autism, asthma, and Alzheimer's disease.