1. Gene SymbolGene Name Fold Difference 1 q-value (%) 2 NL BM? 3 NR2F1nuclear receptor subfamily 2, group F, member 111.95.28No SLC2A10solute carrier family 2, member 109.10.81No EGFL7EGF-like-domain, multiple 78.80.47No PITX2paired-like homeodomain transcription factor 28.81.74No GPR161G protein-coupled receptor 1617.70.00No IGFBP4insulin-like growth factor binding protein 47.55.28No PRSS16serine protease 166.74.42No PDGFRLplatelet-derived growth factor receptor-like6.33.63No PTPRN2protein tyrosine phosphatase, receptor type, N polypeptide 26.23.63No PCpyruvate carboxylase6.21.74No THBS2thrombospondin 26.22.55No TFPItissue factor pathway inhibitor6.04.42No CLEC3BC-type lectin domain family 3, member B5.85.28No SYNPOSynaptopodin5.83.05No PCK1phosphoenolpyruvate carboxykinase 15.64.42No HSPB1heat shock 27kDa protein 15.63.05No KCNAB1potassium voltage-gated channel, shaker-related subfamily, beta member 15.54.42No FLT1fms-related tyrosine kinase 15.54.42No S100A3S100 calcium binding protein A35.53.63No TWIST1twist homolog 15.43.05No DUSP9dual specificity phosphatase 95.44.42No GKN1gastrokine 15.22.55No AKR1C2aldo-keto reductase family 1, member C25.20.15No PDE5Aphosphodiesterase 5A, cGMP-specific5.14.42No PIRpirin (iron-binding nuclear protein)5.00.15No CRISP3cysteine-rich secretory protein 325.60.81Yes S100PS100 calcium binding protein P17.91.51Yes CEACAM6carcinoembryonic antigen-related cell adhesion molecule 616.43.05Yes DEFA4defensin, alpha 4, corticostatin12.54.42Yes KCNJ15potassium inwardly-rectifying channel, subfamily J, member 1511.81.51Yes ENGEndoglin11.70.33Yes CAMPcathelicidin antimicrobial peptide10.62.55Yes MMP9matrix metalloproteinase 910.30.56Yes MGAMmaltase-glucoamylase10.22.12Yes IL8RAinterleukin 8 receptor, alpha10.10.81Yes COL18A1collagen, type XVIII, alpha 18.90.27Yes ORM1orosomucoid 18.91.74Yes FGFR3fibroblast growth factor receptor 37.91.74Yes SCARF1scavenger receptor class F, member 17.83.63Yes LCN2lipocalin 27.82.55Yes IL1R1interleukin 1 receptor, type I7.43.63Yes APOEapolipoprotein E7.00.81Yes PTGESprostaglandin E synthase6.62.55Yes GJA1Connexin 436.65.28Yes TNFRSF10Ctumor necrosis factor receptor superfamily, member 10c6.51.51Yes SEPP1selenoprotein P, plasma, 16.14.42Yes CEACAM8carcinoembryonic antigen-related cell adhesion molecule 86.11.51Yes FCGR3BFc fragment of IgG, low affinity IIIb, receptor5.90.33Yes GNG11guanine nucleotide binding protein, gamma 115.93.63Yes TCN1transcobalamin I5.90.47Yes CLCCharcot-Leyden crystal protein5.63.63Yes G0S2putative lymphocyte G0/G1 switch gene5.61.74Yes GPR109BG protein-coupled receptor 109B5.50.69Yes UBE2Mubiquitin-conjugating enzyme E2M5.44.42Yes LTFLactotransferrin5.40.56Yes NPM3nucleophosmin/nucleoplasmin, 35.34.42Yes SIPA1signal-induced proliferation-associated gene 15.34.42Yes FGF13fibroblast growth factor 135.33.63Yes TSPAN2tetraspan 25.33.63Yes PRV1polycythemia rubra vera 15.23.05Yes ID1inhibitor of DNA binding 1, dominant negative helix-loop-helix protein5.23.05Yes TFF3trefoil factor 35.13.05Yes APEX2APEX nuclease 25.11.74Yes LEPRleptin receptor4.91.74Yes SLPIsecretory leukocyte protease inhibitor4.82.12Yes CA4carbonic anhydrase IV4.81.74Yes TACSTD1tumor-associated calcium signal transducer 14.80.30Yes Supplemental Table 1. 67 Genes over expressed in EpCAM selected cells from bone marrows of patients with stage II/III breast cancer prior to any treatment-analysis of microarray data

2. Footnote for Supplemental Table 1 1: Fold difference: Bone marrow from cancer patients versus normal bone marrow 2: q-value %: measure of false discovery rate 3: Nl BM?: Expression detected in gene array samples from normal bone marrow

3. Supplemental Table 2. Expression of 12 Genes from the 67 Gene Signature in control bone marrow spiked with serial dilutions of Her2/neu positive SKBR3, ER-positive ZR75, or triple negative MDA- MB231 breast tumor cell lines. Cell dilutions (tumors cells per total nucleated bone marrow cells) are displayed on the left of the table. Fold difference in gene expression relative to non-spiked bone marrow is shown for each gene at each dilution for the three cell types. For genes without detectable expression in non-malignant bone marrow, fold differences are calculated by the ddCT method using an arbitrary CT value of 40 for the non-malignant bone marrow sample. (UD=undetected)