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The present invention provides novel biomarkers associated with Down syndrome. In particular, biomarkers identified from a proteome analysis of blood samples collected from affected individuals are disclosed that can be used to evaluate the disease spectrum of each individual with Down syndrome. Methods of using such biomarkers to develop diagnostics and therapeutics for prognosis and treatment of the conditions and diseases accompanying Down syndrome, and to develop diagnostics and therapeutics for prognosis and treatment of conditions and diseases prevalent in typical individuals but rare in individuals with Down syndrome are also described.