Supplementary Figure 1. Supplementary Figure 2 All patients CharacteristicN% Median Age of patients 58 yrs ER Positive 40 69 Negative 18 31 PR Positive.

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Supplementary Figure 1

Supplementary Figure 2

All patients CharacteristicN% Median Age of patients 58 yrs ER Positive Negative PR Positive Negative HER2 Positive 7 12 Negative Status Stable Progression Supplementary Table 1: Classification of patients based on receptor and disease status

AssayBlood volume per testCTC enrichment principleDetection method CellSearch Method7.5 mLImmunomagnetic using EpCAM Visual confirmation of CK + /DAPI +/ CD45 - cells using automated fluorescence imaging CSV Method 7.5 mL (for comparative analysis) Depletion of CD45 + cells and positive selection of cell-surface vimentin positive cancer cells using 84-1 antibody Visual confirmation of CSV + /Cancer specific marker using Confocal Imaging Supplementary Table 2 Comparison between two detection techniques Abbreviations: CSV= Cell-surface vimentin, CK= Cytokeratin,

K coefficientDegree of AgreementAgreement (%) Comparison of Progressive population with the CellSearch CTC test Poor45% Comparison of Stable population with the CellSearch CTC test 0.440Moderate66.67% Supplementary Table 3 Concordances between CSV and CellSearch detection techniques Abbreviations: CSV= Cell-surface vimentin, CTC= Circulating tumor cells.

Triple NegativeLuminal ALuminal BHER2 Type CTCs<5 StableProgressionStableProgressionStableProgressionStableProgression CSV < CellSearch < CTCs≥ 5 CSV ≥ CellSearch ≥ CSV: Cell-surface vimentin; CTCs: Circulating tumor cells; ER: Estrogen receptor; PR: Progesterone receptor ; HER2: HER2/neu receptor; Triple negative: ER - PR - HER2 - ; Luminal A: ER/PR + HER2 - Luminal B: ER/PR + HER2 +, HER2 Type: ER/PR - HER2 + Supplementary Table 4: Receptor based classification for individual samples with stable/progression status as determined by both techniques

Triple Negative (n=16) SensitivitySpecificity Positive Predictive Value Negative Predictive Value CSV66.67%100% 50% CellSearch33.34%50%66.67%20% Summation (T h 5)83.33%25%76.92%33.33% Summation (T h 8)83.33%75%90.91%60% Luminal A (n=35) CSV91.67%90.91%95.65%83.33% CellSearch50%90.91%92.3%45.45% Summation (T h 5)95.83%72.73%88.46%88.89% Summation (T h 8)95.83%81.82%92%90% Supplementary Table 5: Analysis of Sensitivity, Specificity, Positive Predictive Value, and Negative Predictive Value based on receptor status of patients CSV: Cell-surface vimentin Summation: sum of CTC counts from 84-1 and CellSearch methods. Triple negative: ER - PR - HER2 - ; Luminal A: ER/PR + HER2 - T h 5 indicates a threshold of 5 CTCs/ 7.5 mL as cutoff. T h 8 indicates a threshold of 8 CTCs/ 7.5 mL as cutoff.

n=20ProgressionStable Nuclear EpCAM131 No Nuclear EpCAM24 Supplementary Table 6: Analysis of Nuclear EpCAM Status

SensitivitySpecificityPositive Predictive ValueNegative Predictive Value n= %80%92.86%66.67% Supplementary Table 7: Sensitivity, Specificity, Positive prediction and Negative prediction values for Nuclear EpCAM method

SampleAgeER/PR/HER2 statusTreatmentDisease status84-1CellSearch S165ER+/PR-/HER2+TaxolProgression201 S342ER+/PR+/HER2-letrozoleStable00 S448ER+/PR+/HER2+trastuzumabStable00 S561ER+/PR+/HER2-paclitaxelStable10 S778ER+/PR+/HER2-everolimus, exemestane and zoledronic acidProgression12 S953ER+/PR+/HER2+Ixabepilone plus capecitabine, zoladex + AIProgression3274 S1044ER-/PR-/HER2+docetaxel, pertuzumab and trastuzumabProgression1244 S1127ER-/PR-/HER2-Abraxane and bevacizumabProgression222 S1272ER+/PR+/HER2-tamoxifenProgression010 S1358ER+/PR+/HER2-TaxolProgression569 S1467ER+/PR+/HER2-letrozoleStable00 S1561ER-/PR-/HER2-Taxol and AvastinStable21 S1649ER+/PR+/HER2-Afinitor and tamoxifenProgression754 S1746ER-/PR-/HER2-eribulinProgression734 S1837ER-/PR-/HER2-TaxolStable14 S1969ER+/PR-/HER2-everolimus, exemestane and zoledronic acidStable21 S2064ER+/PR+/HER2-TaxolStable01 S2231ER+/PR+/HER2+TaxolStable34 S2353ER+/PR-/HER2-capecitabineProgression613 S2466ER+/PR+/HER2-docetaxel and zoledronicProgression811 S2658ER-/PR-/HER2-eribulinProgression13 S2748ER-/PR-/HER2-gemcitabine and carboplatinProgression171 S2836ER+/PR+/HER2-Gemzar, carboplatinProgression241 S2947ER-/PR-/HER2-MK-2206Stable411 S3052ER+/PR+/HER2-tamoxifenStable41 S3140ER-/PR-/HER2-Taxol and AvastinProgression481 S3342ER+/PR-/HER2-abraxane plus bevacizumabProgression634 S3567ER+/PR+/HER2-everolimusProgression81 S3668ER+/PR+/HER2-everolimus, exemestane and zoledronic acidStable09 S3851ER+/PR+/HER2-Avastin and eribulinProgression133 S3965ER-/PR-/HER2-Taxol and AvastinStable05 S4060ER+/PR-/HER2-everolimus, exemestane and zoledronic acidProgression151 S4157ER-/PR-/HER2-GemzarProgression2374 S4262ER+/PR-/HER2-vinorelbineProgression167 S4354ER+/PR-/HER2+TamoxifenProgression66221 S4441ER+/PR+/HER2-AbraxaneProgression63 S4556ER-/PR-/HER2+Pertuzumab, trastuzumab, docetaxelStable11 S4635ER-/PR-/HER2-erlotinib plus pralatrexateProgression601 S4769ER+/PR-/HER2-everolimus and exemestaneProgression3010 S4966ER-/PR-/HER2-cisplatin and etoposideProgression155 S5067ER+/PR+/HER2-ArimidexStable00 S5267ER+/PR+/HER2-letrozoleStable90 S5365ER+/PR-/HER2-anastrozoleProgression72 S5452ER+/PR+/HER2-everolimus and exemestaneStable00 S5563ER-/PR-/HER2-capecitabineProgression20 S5647ER-/PR-/HER2-Avastin and eribulinProgression S5759ER+/PR+/HER2-Taxol and AvastinProgression243 S5866ER-/PR-/HER2-AbraxaneProgression962 S5941ER+/PR+/HER2-eribulinProgression62 S6059ER+/PR+/HER2-Avastin and eribulinProgression660 S6192ER+/PR+/HER2-fluoxymesteroneProgression280 S6245ER+/PR+/HER2-gemcitabineProgression14226 S6376ER+/PR-/HER2-fulvestrantStable00 S6459ER+/PR+/HER2-anastrozoleProgression621 S6567ER+/PR+/HER2-everolimus and exemestaneProgression1800 S6630ER-/PR-/HER2-T-FACProgression120 S6758ER+/PR-/HER2-Abraxane and AvastinProgression30124 S6840ER+/PR+/HER2-exemestane, everolimus, and denosumabProgression1442 Supplementary Table 8: Clinical parameters, disease status and CTC counts from patients