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273 fresh frozen tissue samples. 74 excluded 47 with highly degraded RNA 16 with low concentration of RNA 5 with good quality RNA, but no microarray performed, 6 without RNA extracted. 199 microarray analysis performed. 8 excluded 4 with microarray of inferior quality

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## Supplementary Figure 1. Flowchart of patients included in the training set.

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**273**fresh frozen tissue samples 74 excluded 47 with highly degraded RNA 16 with low concentration of RNA 5 with good quality RNA, but no microarray performed, 6 without RNA extracted 199 microarray analysis performed 8 excluded 4 with microarray of inferior quality 4 with good quality array, but with < 5% invasive carcinoma in frozen sample 191 successful microarray analysis from verified tumor tissue (FFT) 191 training set FFT 45 excluded 33 with no corresponding paraffin blocks available 4 with < 5% invasive carcinoma 8 with insufficient RNA yield 146 available from formalin-fixed, paraffin-embedded (FFPE) 146 training set FFPE Supplementary Figure 1.Flowchart of patients included in the training set.

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