Autoantibodies and cytokine levels stratified according to presence of a shared epitope allele. Autoantibody levels are higher in RA patients with one or two shared-epitope alleles than in those with no shared-epitope alleles. Serum samples from 74 RA patients with either one or two copies of the shared epitope and from 46 RA patients with no shared epitope were characterized with the IMPACT platform. Autoantibody reactivity was assessed on the IMPACT platform and cytokine levels were measured in a bead-based assay run on the Luminex platform. For assays run on the IMPACT platform, values were normalized as described in the methods. Significance Analysis of Microarrays (SAM) followed by a hierarchical clustering algorithm were used to determine cluster relations that group patient samples (top dendrogram) and antigen reactivities (right dendrogram) on the basis of similarities in patient autoantibody and cytokine profiles (false discovery rate < 1). Dendrogram branch lengths and distances between nodes illustrate the extent of similarities in antigen reactivity and cytokine levels, with blue representing a decrease relative to the mean value obtained in samples from healthy individuals, yellow no change, and red an increase. Cit, citrullinated; RF, rheumatoid factor.