Sarah E. Davis

Pathologic Complete Response Predicts Recurrence-Free Survival More Effectively by Cancer Subset: Results From the I-SPY 1 TRIAL—CALGB 150007/150012, ACRIN 6657

PURPOSE Neoadjuvant chemotherapy for breast cancer provides critical information about tumor response; how best to leverage this for predicting recurrence-free survival (RFS) is not established. The I-SPY 1 TRIAL (Investigation of Serial Studies to Predict Your Therapeutic Response With Imaging and Molecular Analysis) was a multicenter breast cancer study integrating clinical, imaging, and genomic data to evaluate pathologic response, RFS, and their relationship and predictability based on tumor biomarkers. PATIENTS AND METHODS Eligible patients had tumors ≥ 3 cm and received neoadjuvant chemotherapy. We determined associations between pathologic complete response (pCR; defined as the absence of invasive cancer in breast and nodes) and RFS, overall and within receptor subsets. RESULTS In 221 evaluable patients (median tumor size, 6.0 cm; median age, 49 years; 91% classified as poor risk on the basis of the 70-gene prognosis profile), 41% were hormone receptor (HR) negative, and 31% were human epidermal growth factor receptor 2 (HER2) positive. For 190 patients treated without neoadjuvant trastuzumab, pCR was highest for HR-negative/HER2-positive patients (45%) and lowest for HR-positive/HER2-negative patients (9%). Achieving pCR predicted favorable RFS. For 172 patients treated without trastuzumab, the hazard ratio for RFS of pCR versus no pCR was 0.29 (95% CI, 0.07 to 0.82). pCR was more predictive of RFS by multivariate analysis when subtype was taken into account, and point estimates of hazard ratios within the HR-positive/HER2-negative (hazard ratio, 0.00; 95% CI, 0.00 to 0.93), HR-negative/HER2-negative (hazard ratio, 0.25; 95% CI, 0.04 to 0.97), and HER2-positive (hazard ratio, 0.14; 95% CI, 0.01 to 1.0) subtypes are lower. Ki67 further improved the prediction of pCR within subsets. CONCLUSION In this biologically high-risk group, pCR differs by receptor subset. pCR is more highly predictive of RFS within every established receptor subset than overall, demonstrating that the extent of outcome advantage conferred by pCR is specific to tumor biology.

Adaptive Randomization of Veliparib–Carboplatin Treatment in Breast Cancer

BACKGROUND The genetic and clinical heterogeneity of breast cancer makes the identification of effective therapies challenging. We designed I-SPY 2, a phase 2, multicenter, adaptively randomized trial to screen multiple experimental regimens in combination with standard neoadjuvant chemotherapy for breast cancer. The goal is to match experimental regimens with responding cancer subtypes. We report results for veliparib, a poly(ADP-ribose) polymerase (PARP) inhibitor, combined with carboplatin. METHODS In this ongoing trial, women are eligible for participation if they have stage II or III breast cancer with a tumor 2.5 cm or larger in diameter; cancers are categorized into eight biomarker subtypes on the basis of status with regard to human epidermal growth factor receptor 2 (HER2), hormone receptors, and a 70-gene assay. Patients undergo adaptive randomization within each biomarker subtype to receive regimens that have better performance than the standard therapy. Regimens are evaluated within 10 biomarker signatures (i.e., prospectively defined combinations of biomarker subtypes). Veliparib-carboplatin plus standard therapy was considered for HER2-negative tumors and was therefore evaluated in 3 signatures. The primary end point is pathological complete response. Tumor volume changes measured by magnetic resonance imaging during treatment are used to predict whether a patient will have a pathological complete response. Regimens move on from phase 2 if and when they have a high Bayesian predictive probability of success in a subsequent phase 3 neoadjuvant trial within the biomarker signature in which they performed well. RESULTS With regard to triple-negative breast cancer, veliparib-carboplatin had an 88% predicted probability of success in a phase 3 trial. A total of 72 patients were randomly assigned to receive veliparib-carboplatin, and 44 patients were concurrently assigned to receive control therapy; at the completion of chemotherapy, the estimated rates of pathological complete response in the triple-negative population were 51% (95% Bayesian probability interval [PI], 36 to 66%) in the veliparib-carboplatin group versus 26% (95% PI, 9 to 43%) in the control group. The toxicity of veliparib-carboplatin was greater than that of the control. CONCLUSIONS The process used in our trial showed that veliparib-carboplatin added to standard therapy resulted in higher rates of pathological complete response than standard therapy alone specifically in triple-negative breast cancer. (Funded by the QuantumLeap Healthcare Collaborative and others; I-SPY 2 TRIAL ClinicalTrials.gov number, NCT01042379.).

Abstract S5-02: Veliparib/carboplatin plus standard neoadjuvant therapy for high-risk breast cancer: First efficacy results from the I-SPY 2 TRIAL

Background: I-SPY 2 is a multicenter, phase 2 screening trial using adaptive randomization within biomarker subtypes to evaluate a series of novel agents/combinations when added to standard neoadjuvant therapy (paclitaxel q wk x 12, doxorubicin & cyclophosphamide q 2-3 wk x 4, T/AC) vs. T/AC (control arm) for women with high-risk stage II/III breast cancer. The primary endpoint is pathologic complete response (pCR) at surgery. Our goal is to identify/graduate regimens that have ≥85% Bayesian predictive probability of success (statistical significance) in a 300-patient biomarker-linked Phase 3 neoadjuvant trial. Experimental regimens can “graduate” in at least 1 of 10 possible signatures defined by hormone-receptor (HR) & HER2 status & MammaPrint (MP), with a maximum number of 120 total patients enrolled. We report final efficacy results of the oral PARP inhibitor veliparib (V, ABT-888) in combination with carboplatin (carbo), 1 of 7 experimental regimens evaluated in the trial to date. Methods: Women with tumors ≥2.5 cm by clinical exam and ≥2 cm by imaging are eligible for screening. Tumors that are MP low/HR+/HER2- are ineligible for randomization. MRI scans (baseline, 3 weeks after start of therapy, at completion of weekly T, and prior to surgery) were used in a longitudinal statistical model to improve the efficiency of adaptive randomization. V+carbo was assigned to HER2- tumors only, which limits its possible signatures to: all HER2-, HR+/HER2-, HR-/HER2-. For these 3 signatures we provide estimated pCR rates with associated 95% Bayesian probability intervals for V+carbo and concurrently randomized controls. Analysis is intent to treat with patients who switched to non-protocol therapy regarded as non-pCRs. For each signature we provide probabilities of superiority for V+carbo over control and Bayesian predictive probabilities of success in a neoadjuvant Phase 3 trial equally randomized between V+carbo and control. Results: When V+carbo met the 85% predictive probability criterion in HR-/HER2- and all HER2-, this regimen graduated and accrual to V+carbo was stopped. V+carbo was assigned to 72 patients, and there were 62 concurrently randomized controls (44 HER2- controls). The following table shows final results based on available pCR information. Two patients assigned to V+carbo withdrew consent during treatment and are not included in the table. Conclusion: Adaptive randomization successfully identified a biomarker signature for V+carbo on the basis of a modest number of patients. V+carbo has graduated with a triple-negative (TN) breast cancer signature, and is the subset recommended for this regimen9s subsequent development. There is a suggestion that HR+/HER2- tumors benefit little from this regimen and inclusion of tumors in this subset would therefore dilute its effect in a subsequent trial. Analyses are currently underway to define additional biomarkers that may be predictive of response. The I-SPY 2 standing trial mechanism efficiently evaluates agents/combinations in biomarker-defined patient subsets, with future agents/combinations reported as available. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S5-02.

Abstract CT227: Neratinib plus standard neoadjuvant therapy for high-risk breast cancer: Efficacy results from the I-SPY 2 TRIAL

Background: I-SPY 2 is a multicenter, phase II neoadjuvant trial in women with high-risk stage II/III breast cancer using adaptive randomization within biomarker subtypes to evaluate novel agents added to standard chemotherapy. Primary endpoint is pathologic complete response (pCR). Goal is to identify regimens that meet a high Bayesian predictive probability of statistical significance in a neoadjuvant 300-patient phase III trial defined by hormone-receptor (HR), HER2 status, and MammaPrint (MP). Experimental regimens may “graduate” in 1 of 10 signatures, with a maximum of 120 patients. We report efficacy results for neratinib (N). Methods: Tumors ≥2.5cm by clinical exam & ≥2cm by imaging are eligible for screening. MP low risk/HR+/HER2- tumors are ineligible for randomization. Patients receive chemotherapy (paclitaxel qwk x 12, doxorubicin and cyclophosphamide q2-3 wk x 4, T->AC). HER2- pts were randomized to N+T->AC vs. T->AC and HER2+ pts to N+T->AC vs. trastuzumab+T->AC. Analysis is intent-to-treat with pts who switch to non-protocol therapy regarded as non-pCRs. We provide estimated pCR rates (95% Bayesian probability intervals), probabilities of superiority of neratinib over control, and Bayesian predictive probabilities of success in an equally randomized phase III trial. Results: Neratinib met the predictive probability criterion in HR-/HER2+, “graduated”, and accrual ceased [115 N patients (65 HER2+), 78 concurrently randomized controls (22 HER2+)]. The table shows results for all 10 signatures. Two patients (1 N and 1 control) withdrew consent and are not included. Conclusion: I-SPY 29s standing trial mechanism efficiently evaluates agents in biomarker-defined patient subsets. In a modest number of patients, adaptive randomization successfully identified a biomarker signature (HR-/HER2+) for neratinib9s further development. All HER2+ and MP+ tumors may also benefit from this regimen, consistent with preclinical data. Evaluation in I-SPY 3, a phase III registration trial, is planned. Citation Format: John W. Park, Minetta C. Liu, Douglas Yee, Angela DeMichele, Laura van 9t Veer, Nola Hylton, Fraser Symmans, Meredith B. Buxton, A. Jo Chien, Amy Wallace, Michelle Melisko, Richard Schwab, Judy Boughey, Debashish Tripathy, Hank Kaplan, Rita Nanda, Stephen Chui, Kathy S. Albain, Stacy Moulder, Anthony Elias, Julie E. Lang, Kirsten Edminston, Donald Northfelt, David Euhus, Qamar Khan, Julia Lyandres, Sarah E. Davis, Christina Yau, Ashish Sanil, Laura J. Esserman, Donald A. Berry. Neratinib plus standard neoadjuvant therapy for high-risk breast cancer: Efficacy results from the I-SPY 2 TRIAL. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr CT227. doi:10.1158/1538-7445.AM2014-CT227

Serial expression analysis of breast tumors during neoadjuvant chemotherapy reveals changes in cell cycle and immune pathways associated with recurrence and response

IntroductionThe molecular biology involving neoadjuvant chemotherapy (NAC) response is poorly understood. To elucidate the impact of NAC on the breast cancer transcriptome and its association with clinical outcome, we analyzed gene expression data derived from serial tumor samples of patients with breast cancer who received NAC in the I-SPY 1 TRIAL.MethodsExpression data were collected before treatment (T1), 24–96 hours after initiation of chemotherapy (T2) and at surgery (TS). Expression levels between T1 and T2 (T1 vs. T2; n = 36) and between T1 and TS (T1 vs. TS; n = 39) were compared. Subtype was assigned using the PAM50 gene signature. Differences in early gene expression changes (T2 − T1) between responders and nonresponders, as defined by residual cancer burden, were evaluated. Cox proportional hazards modeling was used to identify genes in residual tumors associated with recurrence-free survival (RFS). Pathway analysis was performed with Ingenuity software.ResultsWhen we compared expression profiles at T1 vs. T2 and at T1 vs. TS, we detected significantly altered expression of 150 and 59 transcripts, respectively. We observed notable downregulation of proliferation and immune-related genes at T2. Lower concordance in subtype assignment was observed between T1 and TS (62 %) than between T1 and T2 (75 %). Analysis of early gene expression changes (T2 − T1) revealed that decreased expression of cell cycle inhibitors was associated with poor response. Increased interferon signaling (TS − T1) and high expression of cell proliferation genes in residual tumors (TS) were associated with reduced RFS.ConclusionsSerial gene expression analysis revealed candidate immune and proliferation pathways associated with response and recurrence. Larger studies incorporating the approach described here are warranted to identify predictive and prognostic biomarkers in the NAC setting for specific targeted therapies.Clinical trial registrationClinicalTrials.gov identifier: NCT00033397. Registered 9 Apr 2002.

Biology of breast cancers that present as interval cancers and at young age should inform how we approach early detection and prevention.

Abstract #6034 Population screening has increased the absolute number of breast cancer cases. In spite of widespread screening, there are still many patients who present with locally advanced breast cancer, often women who are young or who present with a mass between annual screens (“interval cancers”). Molecular profiling provides the opportunity to determine whether mammographically detected cancers are biologically distinct from locally advanced breast cancers. Methods: Tumor samples from the time of diagnosis (2002-2006), from patients with locally advanced breast cancers enrolled on the multi-site I-SPY TRIAL (CALGB 150007/150012 and ACRIN 6657) were compared to stage 1 & 2 tumor samples collected in 2004 from multiple community Netherlands hospitals (RASTER dataset). The NKI 70 gene set was performed on 100 of 221 patients (80 more samples pending) from I-SPY and 228 of 242 patients from the RASTER dataset. The proportion of good vs. poor prognosis profiles were compared. Additionally, we have collected data on response to chemotherapy from the I-SPY patients. Finally, mammograms from the I-SPY and RASTER datasets are being reviewed to enable classification of tumors by presentation (palpable, screen detected, and interval cancer and negative prior mammogram within 1 year). Results: I-SPY data includes 221 patients with tumors ≥3cm in size; median tumor size is 6cm; 55% were 50, with a good prognosis is 10%, 23%, and 22%, respectively. The RASTER dataset included 427 patients from age 30 to 61. NKI 70 gene profiles are available in 219 patients: 66% were Stage 1; 33% were Stage 2. Overall, 51% had a NKI 70 gene good prognosis profile. For women under the age of 40, 31% had a NKI 70 gene poor prognosis. For women 40-50, and >50, the fraction of NKI 70 gene poor prognosis is 55% and 56%, respectively. Data will be presented based on mode of detection: screen vs. palpation (never screened vs. interval). Conclusion: The key observation is that the fraction of good prognosis tumors substantially increases with age. In patients too young for screening, the fraction of poor prognosis tumors is 69%. Patients who present with locally advanced breast cancers who are too young to be screened almost always have a poor prognosis signature. This may extend to those with interval cancers. This suggests that the tumors identified by screening, although they are early stage cancers, are not the precursors of the poor prognosis tumors in young women and those with locally advanced disease. Therefore, we may not be able to rely on current screening approaches to improve outcomes for young women and those with interval cancers. Further analysis will include reviewing interval cancer cases within the I-SPY dataset and assessing prognostic indicators. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 6034.

Abstract P1-08-01: MammaPrint ultra-high risk score is associated with response to neoadjuvant chemotherapy in the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657)

Background: Increasingly, gene expression tests are being used with standard clinicopathological markers to assess risk of recurrence in breast cancer and to guide treatment. The 70-gene signature (MammaPrint™) was recently validated in a prospective study as an effective tool for identifying low risk patients who may avoid chemotherapy without compromising outcome. MammaPrint scores have been shown to differentiate likelihood of neoadjuvant chemotherapy response. Here we hypothesize that a further stratification of the 70-gene signature into ‘high-risk’ and ‘ultra-high risk’ groups might yield improved predictors of chemo-sensitivity and patient outcome. Methods: Agilent 44K array data from pre-treatment biopsies were obtained from 149 I-SPY 1 TRIAL patients treated with neoadjuvant anthracycline-based chemotherapy. These data were used to compute each patient9s MammaPrint score and risk category (good vs. poor threshold 0.4). Of these patients, 138 were either in the ‘poor’ outcome group (136) or in the ‘good’ outcome group but Her2+ (2). The median score cut-point based on these 138 patients equals -0.154, and was used to further stratify patients into MammaPrint High1 (MP1) or MammaPrint (ultra) High2 (MP2) groups, with MP1 defined as ≤ -0.154 and MP2 defined as >-0.154 (69 MP1, 69 MP2). Outcome parameters included pathologic complete response (pCR) after therapy and recurrence free survival (RFS). Fisher9s exact test was used to assess association with pCR overall and within hormone receptor (HR) and Her2 subtypes, and Cox proportional hazards modeling to assess association with RFS. 29 patients who received Herceptin and 4 without pCR data were excluded from analysis, yielding 105 evaluable patients. Results: Though all receptor subtypes were represented in MP1 and MP2 subgroups, the majority of MP1 patients were HR+/Her2- (54%), whereas MP2 patients were more evenly distributed among triple negative (TN; 38%), HR+/Her2- (22%), HR-/Her2+ (22%) and HR+/Her2+ (18%) subtypes. 25/105 patients achieved pCR: 8 (15%) in the MP1 group and 17 (33%) in the MP2 group. Applying Fisher9s exact test, we found that a significantly higher percentage of pCR was observed for MP2 patients in the overall population (p = 0.038), but not within receptor subtypes; though there was a trend towards a higher pCR rate in MP2 patients within the HR+/Her2- subset (p = 0.071). The greater sensitivity of MP2 to chemotherapy may in part be driven by differences in receptor subtype distribution, as well as a relationship between MP2 status and proliferation; we found that MP1/2 classification was highly associated with Ki67 (low/intermediate: 25% positive) (p = 3.3E-5), with MP2 patients having more Ki67 positive cells. No significant differences in RFS were observed between MP1 and MP2 subsets, likely because MP2 patients, who respond best, are also at the highest risk of relapse. Conclusion: These analyses suggest that additional MammaPrint score stratification within the ‘poor’ biology group might be a useful for developing companion diagnostics to neoadjuvant therapies, a hypothesis currently being tested in the adaptive randomization engine of the I-SPY 2 clinical trial. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-01.

P1-06-11: Comparison of Community and Central Her2 Assessment on Outcome of Neoadjuvant Chemotherapy in the I-SPY Trial.

Background: Her-2/neu overexpression, by immunohistochemistry (IHC) or fluorescence in-situ hybridization (FISH), is highly correlated with response to trastuzumab and these are currently the gold-standard, FDA-cleared testing methods for assigning treatment to Her-2-directed therapies. However, substantial variability has been documented between community and central laboratory IHC and FISH testing. Biologically, Her-2 overexpression may reflect increased gene copy number, gene expression and/or protein production, and these can be measured by other platforms, including comparative genomic hybridization (CGH), expression arrays and quantitative protein assays, respectively. We sought to determine the degree to which community IHC/FISH results differed from centrally-assessed IHC, FISH, and other assessment platforms within the I-SPY Trial and whether response to neoadjuvant chemotherapy (NAC) differed by platform. Methods: The I-SPY Trial enrolled 237 women 2002–06 with invasive breast tumors at least 3 cm in clinical/radiographic size who subsequently underwent anthracycline/taxane NAC, serial core biopsies and imaging. Pathologic complete response (pCR) was determined at time of surgery and 3-year follow up has been reached. Trastuzumab was given to Her2+ patients at physician discretion, based upon community IHC/FISH results, and became more widespread after 2005. Central I-SPY laboratories determined Her2 copy number by MIP array, gene expression by Affymetrix and Agilent arrays, and Her2 protein by reverse-phase protein array (RPMA). Unsupervised clustering algorithms were used to evaluate expression patterns. Composite variables were constructed for DNA, RNA and protein positivity as well as for community and central IHC/FISH. Platforms were compared and Kaplan-Meier curves were constructed to compare outcomes by platform. Results: 222 women were evaluable, though not all patients had results for all platforms. Community composite IHC/FISH was positive in 64/214 (30%) but only 41 of these (64%) were confirmed by central IHC/FISH and 4 additional cases were centrally positive despite negative community testing. Concordance was high among centrally-assessed Her2 platforms, but was lower between community IHC/protein and central RNA (90%), DNA (91%) and protein (91%). Among patients receiving trastuzumab (n=36), the pCR rate was ∼50% regardless of Her2-assessment platform; in contrast, those not receiving trastuzumab had pCR rates below 30%. Among the 64 patients deemed Her2+ by community IHC/FISH, 30 (48%) had pCR and 15 (25%) have had distant relapse. Five distant relapses have occurred despite pCR; all received trastuzumab, all were Her2 positive by multiple central platforms and 3/5 were ER-positive. Sites of distant relapse included brain, bone and viscera; only 1 of 5 had isolated brain relapse. Conclusions: Community IHC/FISH testing for Her2 expression in the I-SPY Trial overcalled Her2 positivity compared to central testing while central results were highly concordant among DNA, RNA and protein platforms. Despite the high rate of community “false positives”, relapse after pCR occurred only in central Her2 “true positives,” exclusively among those receiving trastuzumab, and was rarely isolated to CNS sanctuary sites. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-06-11.

P1-06-09: Patient-Specific Integrative Pathway Analysis Using PARADIGM Identifies Key Activities in I-SPY 1 Breast Cancer Patients (CALGB 150007/150012; ACRIN 6657).

Background: A major challenge in interpreting high-throughput multianalyte genomic data sets such as those produced by the ISPY clinical trials is data integration and interpretation within the context of biologically relevant pathways. To address this need, the data analysis tool PARADIGM (PAthway Recognition Algorithm using Data Integration on Genomic Models) was developed to infer the activities of genetic pathways by integrating any number of functional genomic data sets for a given patient sample into a pathway activity profile. Methods: We used PARADIGM to integrate gene expression (Agilent 44K) and DNA copy number data (AFFY 22K and 330K MIP) from 133 ISPY-1 patients into pathway component activity levels for approximately 1400 curated signal transduction, transcriptional and metabolic pathways superimposed onto a single non-redundant ‘SuperPathway9. These pathway activities then become the substrate for statistical analyses to identify pathways characterizing different breast cancer subtypes, as well as those associated with recurrence and response to neoadjuvant chemotherapy within breast cancer subgroups. To identify subtype-specific pathway activities, we used ANOVA for initial feature filtering followed by Tukey analysis with Benjamini Hochberg multiple testing correction. For other binary outcome comparisons we used Mann-Whitney (2-sample Wilcoxon) analysis. PARADIGM results were corroborated with pathway enrichment analysis and filtered for significance. Results: In agreement with breast cancer cell line and other prior studies, basal-like and triple negative cancers are dominated by upregulation of the FOXM1 and MYC/Max subnetworks and downregulation of the FOXA1/ER signal transduction pathway, the converse of the activity pattern seen in luminal breast cancers. These and other subtype associations pass stringent multiple testing corrected significance tests. Though an association study of recurrence over the entire patient cohort mostly yields pathways characteristic of basal-like tumors, alternative pathway associations emerge when subtypes are analyzed individually for outcome and significance tests are relaxed to include features that pass un-corrected Wilcoxon significance tests and also generate highly significant pathway enrichment scores. Subtype-specific drivers of recurrence and chemo-resistance supported by this level of evidence include ALK1/2 (TGFB-BMP) and p53 effector signaling for basals and Syndecan-1 and c-MYC for luminals. Chemo-sensitivity pathways, assessed by association with pCR and RCB1, appear to be subtype-specific as well, with HDAC class 1 signaling, LRP6-Wnt, and IRE1alpha chaperones dominating basal-like cancers and c-MYB activity dominating Her2+ cancers, whereas chemo-sensitivity of HR+Her2- cancers though rare appears to be driven by the DNA damage axis (BRCA/BARD1). Conclusion: These and other similar analyses suggest that patients with TN or basal-like disease might benefit from the addition of ALK1 pathway inhibitors to treatment, whereas high risk HR+ patients might benefit from Syndecan-1 inhibitors. C-MYC/MAX inhibitors might benefit all high risk patients. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-06-09.

Gene expression in serial biopsies in locally advanced breast cancer patients who failed to respond to neoadjuvant chemotherapy.

10515 Background: To elucidate candidate genes and pathways associated with poor response, we retrospectively analyzed gene expression profiles in serial biopsies from women with locally advanced breast cancer who failed to respond to anthracycline-based chemo followed by taxane in the I-SPY TRIAL (CALGB150007/150012/ACRIN 6657). Methods: Of the 221 patients who completed neoadjuvant chemotherapy, 215 patients had surgery with 73% not achieving a pathologic complete response (pathCR). In these patients, cDNA microarray expression profiles from pretreatment biopsy (T1) were compared to those biopsy specimens obtained 24-72 hours after initiation of treatment (T2) or in tumors surgically removed after chemotherapy (TS). Paired expression data for T1vsT2 and T1vsTS were available for 29 and 39 patients with no pathCR, respectively. Paired differential expression analyses were performed via significance analysis of microarrays (SAM) and differentially expressed genes were subjected to ingenuity pathway analys...