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E-GEOD-20194 - Transcription profiling by array of human breast cancer: MAQC-II project

Status
Released on 4 February 2010, last updated on 12 February 2014
Organism
Homo sapiens
Samples (278)
Array (1)
Protocols (7)
Description
The human breast cancer (BR) data set (endpoints D and E) was contributed by the University of Texas M. D. Anderson Cancer Center (MDACC, Houston, TX, USA). Gene expression data from 230 stage I-III breast cancers were generated from fine needle aspiration specimens of newly diagnosed breast cancers before any therapy. The biopsy specimens were collected sequentially during a prospective pharmacogenomic marker discovery study between 2000 and 2008. These specimens represent 70-90% pure neoplastic cells with minimal stromal contamination. Patients received 6 months of preoperative (neoadjuvant) chemotherapy including paclitaxel, 5-fluorouracil, cyclophosphamide and doxorubicin followed by surgical resection of the cancer. Response to preoperative chemotherapy was categorized as a pathological complete response (pCR = no residual invasive cancer in the breast or lymph nodes) or residual invasive cancer (RD), and used as endpoint D for prediction. Endpoint E is the clinical estrogen-receptor status as established by immunohistochemistry. RNA extraction and gene expression profiling were performed in multiple batches over time using Affymetrix U133A microarrays. Genomic analysis of a subset of this sequentially accrued patient population were reported previously. For each endpoint, the first 130 cases were used as a training set and the next 100 cases were used as an independent validation set. Gene expression data from 230 stage I-III breast cancers
Experiment type
transcription profiling by array 
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Citation
DACH1: Its Role as a Classifier of Long Term Good Prognosis in Luminal Breast Cancer. Powe DG, Dhondalay GK, Lemetre C, Allen T, Habashy HO, Ellis IO, Rees R, Ball GR. PLoS One 9(1):e84428 (2014), PMID:24392136
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