Open Access Research article

Cell Line Derived Multi-Gene Predictor of Pathologic Response to Neoadjuvant Chemotherapy in Breast Cancer: A Validation Study on US Oncology 02-103 Clinical Trial

Kui Shen1, Yuan Qi2, Nan Song1*, Chunqiao Tian1, Shara D Rice1, Michael J Gabrin1, Stacey L Brower1, William Fraser Symmans3, Joyce A O’Shaughnessy4, Frankie A Holmes5, Lina Asmar6 and Lajos Pusztai7

Author Affiliations

1 Department of Product Development, Precision Therapeutics, Inc, 2516 Jane Street, Pittsburgh, PA 15203, USA

2 Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA

3 Department of Pathology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0085, Houston, TX 77030, USA

4 Baylor Sammons Cancer Center, Texas Oncology, US Oncology, Baylor-Sammons Cancer Center, 3535 Worth St., Collins 5, Dallas, TX 75246, USA

5 Texas Oncology, US Oncology, 925 Gessner St #550, Houston, TX 77024, USA

6 Biostatistics and Medical Writing, US Oncology Research, US Oncology, The Woodlands, Woodlands, TX 77380, USA

7 Department of Breast Medical Oncology, Unit 1354, The University of Texas M. D. Anderson Cancer Center, PO Box 301439, Houston, TX 77230, USA

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BMC Medical Genomics 2012, 5:51  doi:10.1186/1755-8794-5-51

Published: 16 November 2012

Additional files

Additional file 1:

Code of developing TFEC-MGP from breast cancer cell lines.

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Additional file 2:

Table S1. AUC values for 42 breast cancer cell lines treated by TFEC. Table S2. Clinical and demographic characteristics of breast cancer patients in this study compared with patients in USO trial. Table S3. Two hundred and ninety one affymetrix probes used in TFEC-MGP. The gene symbols and descriptions of these probes were obtained by using broad institute’s molecular signatures database v3.0 (http://www.broadinstitute.org/gsea/msigdb/index.jsp webcite). Table S4. Identified enriched pathways.

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