Addendum to Method section:

Gene expression data analysis

Seven other reported studies of gene expression profiling of breast cancer samples from patients receiving neoadjuvant taxane were not retained for validation for different reasons: Chang et al[1] (24 patients treated with docetaxel single-agent, but annotated for the clinical (and not pathological) response, and profiled using first-generation Affymetrix microarrays: HgU95-Av2 GeneChip), Iwao-Koizumi et al[2] (44 patients treated with docetaxel single-agent, but annotated only for the clinical reponse, and profiled using RT-PCR), Ayers et al[3] (42 patients treated with paclitaxel-FAC, annotated for the pathological response, but profiled using high-density nylon cDNA arrays, andre-included in Hess et aldataset [4]), Gianni et al[5] (89 patients treated with paclitaxel-doxorubicin, annotated for the pathological response, but profiled using RT-PCR), Hannemann et al[6] (48 patients including 24 treated with doxorubicin-docetaxel combination, but profiled using 18k human cDNA and without publicly-available expression data), Rouzier et al[7] (82 patients treated with paclitaxel-FAC, annotated for the pathological response, profiled using Affymetrix microarrays (U133A), but also included in Hess et al dataset [4]), and Bonnefoi et al[8] (125 ER-negative patients, including 55 treated with docetaxel followed by epirubicine-docetaxel, annotated for the pathological response, but profiled using Affymetrix X3P microarrays and with recent concern about validity of data [9]). Thus, only Hess dataset, which also includes dataset from Ayers et al, and Rouzier et al, (Affymetrix U133, pathological response documented) was retained for clinical validation of the Tax-predictor.

1.Chang JC, Wooten EC, Tsimelzon A, Hilsenbeck SG, Gutierrez MC, Elledge R, Mohsin S, Osborne CK, Chamness GC, Allred DC et al (2003) Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer. Lancet 362:362-369.

2.Iwao-Koizumi K, Matoba R, Ueno N, Kim SJ, Ando A, Miyoshi Y, Maeda E, Noguchi S, Kato K (2005) Prediction of Docetaxel Response in Human Breast Cancer by Gene Expression Profiling. Journal of Clinical Oncology 23:422-431.

3.Ayers M, Symmans WF, Stec J, Damokosh AI, Clark E, Hess K, Lecocke M, Metivier J, Booser D, Ibrahim N et al (2004) Gene Expression Profiles Predict Complete Pathologic Response to Neoadjuvant Paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide Chemotherapy in Breast Cancer. Journal of Clinical Oncology 22:2284-2293.

4.Hess KR, Anderson K, Symmans WF, Valero V, Ibrahim N, Mejia JA, Booser D, Theriault RL, Buzdar AU, Dempsey PJ et al (2006) Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J Clin Oncol 24:4236 - 4244.

5.Gianni L, Zambetti M, Clark K, Baker J, Cronin M, Wu J, Mariani G, Rodriguez J, Carcangiu M, Watson D et al (2005) Gene Expression Profiles in Paraffin-Embedded Core Biopsy Tissue Predict Response to Chemotherapy in Women With Locally Advanced Breast Cancer. Journal of Clinical Oncology 23:7265-7277.

6.Hannemann J, Oosterkamp HM, Bosch CAJ, Velds A, Wessels LFA, Loo C, Rutgers EJ, Rodenhuis S, van de Vijver MJ (2005) Changes in Gene Expression Associated With Response to Neoadjuvant Chemotherapy in Breast Cancer. Journal of Clinical Oncology 23:3331-3342.

7.Rouzier R, Rajan R, Wagner P, Hess KR, Gold DL, Stec J, Ayers M, Ross JS, Zhang P, Buchholz TA et al (2005) Microtubule-associated protein tau: a marker of paclitaxel sensitivity in breast cancer. Proc Natl Acad Sci U S A 102:8315-8320.

8.Bonnefoi H, Potti A, Delorenzi M, Mauriac L, Campone M, Tubiana-Hulin M, Petit T, Rouanet P, Jassem J, Blot E et al (2007) Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial. Lancet Oncol 8:1071-1078.

9.David C Expression of concern-validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial. The Lancet Oncology 11:813-814.