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Figure S1. Reproducibility of microarrays was assessed by hybridization of samples on multiple arrays. Pearson correlations between replicate spots for two different samples are a) 0.96 and b) 0.91. Data is displayed as the log-2 transform of fluorescent intensity.

Figure S2. Plots of autoantibody reactivity medians against SKBR3-arrayed proteins from individual cancer samples separated by clinical characteristics: (A) subject age, (B) tumor stage at time of diagnosis and c) time of blood draw prior to diagnosis of breast cancer. Samples are separated by hormone therapy use and further separated based on the median value of the examined clinical characteristic. The median subject age was 65. The median time of blood draw prior to diagnosis was 150 days. * indicates p<0.05, ** indicates p<0.01, *** indicates p<0.001, **** indicates p<0.0001.

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