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Supplemental Data Table 1: Patients clinico-pathologic features and CTC status/count data Approach Patient ID used for CTC Primary tumor/ Metastatic lesions n° CTCs/ 5 mL blood ER status detection ** CTC001 CellSearch 203 CTC002 CellSearch CTC003 PR status ** HER2 Stage Line of (AJCC) treatment status *** Pos/Pos Neg/Neg Neg/Neg T3N1M0 III 7 Pos/Pos Pos/Pos Neg/Neg T2N1M0 I AdnaGen * Pos/Pos Pos/Pos Neg/Neg T1N0M0 I CTC004 CellSearch 13 Pos/Pos Neg/Neg Neg/Neg T2N0M0 II CTC005 CellSearch 0 Pos/Pos Neg/Neg Neg/Neg T1N0M0 I CTC006 CellSearch 13 Pos/Pos Pos/Pos Neg/Neg T3N0M0 II CTC007 CellSearch 19 Pos/Pos Pos/Pos Neg/Neg T1N1M0 III * CTC negative by AdnaTest ** evaluated by immunohistochemistry (ER, cut off= 10% positive cells; PR, cut off_10% positive cells) according to Hammond M.E. et al . J Clin Oncol 2010; 28:2784-95. *** evaluated by immunohistochemistry and FISH (for HER2 2+ cases) Supplemental Data Figure 1 Panel A. Pair plots showing correlations between selected samples: Gene expression intensities obtained from samples containing 100 ng of RNA extracted from MDA-MB-468 cells considered as benchmarks and correlated with intensities obtained in profiles using decreasing RNA inputs, respectively 10 ng, 1 ng and 0.5 ng. Panel B. Eulero-Venn diagrams highlighting the numbers of common and exclusive genes detected in samples derived from 100 ng of MDA-MB-468 RNA and from 0.5 of RNA from the same cell line. Gene Ontologies for exclusive genes in each set are reported using character sizes and color intensities directly proportional the p value for to the gene set enrichment. Supplemental Data Figure 2 Eulero-Venn diagrams highlighting the numbers of common and exclusive genes detected in samples derived from 200 MCF7 cells spiked into healthy donor blood (HDB); from HDB not treated with AdnaWash buffer and HDB samples treated with AdnaWash buffer. Gene Ontologies for exclusive genes in each set are reported using character sizes and color intensities directly proportional the p value for to the gene set enrichment. Supplemental Data Figure 3 Distribution plot of signal mean intensities in gene expression data derived from 5-10-25-50 MDAMB-468 (red dots) or MCF7 (blue dots) cells spiked into healthy donor blood (HDB), from cell-free HDB (yellow triangles), and from 100 ng of RNA isolated from MCF-7 and MDA-MB-468 cells (purple and green squares, respectively) profiled with the Illumina Human Whole-Genome DASL HT.