Elevated pretreatment autoantibody profiles in etanercept responders compared with nonresponders in the ABCoN cohort. Significance analysis of microarrays (SAM) and hierarchical clustering were applied to identify and display autoantibody profiles that differentiate etanercept responders from nonresponders; results from one of several representative experiments are presented. SAM was utilized to identify antigens with statistical differences in antibody reactivity between etanercept responders (≥ ACR50) and nonresponders (< ACR20), and the statistically significant hits are listed to the right of the heatmap (false discovery rate q < 4.3%). The SAM-identified variables and individual patients were then hierarchically clustered, and results presented in tree dendrograms that represent the relationships in reactivities between patients as well as between antigens. Red font, citrullinated antigens; black font, native antigens. Patients are listed across the top of the heatmap image, and the ACR response rate for each patient is indicated. Red bar, responder cluster; green bar, nonresponder cluster. Numbers of misclassified samples are shown for each cluster. Array fluorescence units are color coded and indicated in the bar in the right upper corner of the image. ACR, American College of Rheumatology response; CCP, cyclic citrullinated peptide.