Statistical framework for gene expression data analysis.

DNA (mRNA) microarray, a highly promising technique with a variety of applications, can yield a wealth of data about each sample, well beyond the reach of every individual's comprehension. A need exists for statistical approaches that reliably eliminate insufficient and uninformative genes (probe sets) from further analysis while keeping all essentially important genes. This procedure does call for in-depth knowledge of the biological system to analyze.

The erbB2+ cluster of the intrinsic gene set predicts tumor response of breast cancer patients receiving neoadjuvant chemotherapy with docetaxel, doxorubicin and cyclophosphamide within the GEPARTRIO trial.

Gene expression profiling using Affymetrix HG-U133 Arrays (22,500 genes) was performed on fresh frozen pretherapeutic core biopsies from 50 patients undergoing neoadjuvant chemotherapy (NAC) with docetaxel, adriamycin, cyclophosphamide (TAC) within the GEPARTRIO trial. The Sorlie classification based on the "intrinsic gene set" revealed four different subgroups in our cohort (normal-like: 14%, basal-like: 20%, erbB2+: 22% and luminal: 44%), which is in line with the original description. High genomic grade but not histopathological grading was statistically different within the four subgroups (P<0.

Gene expression profiling of breast cancer patients treated with docetaxel, doxorubicin, and cyclophosphamide within the GEPARTRIO trial: HER-2, but not topoisomerase II alpha and microtubule-associated protein tau, is highly predictive of tumor response.

Gene expression analysis in breast cancer patients undergoing neoadjuvant chemotherapy is an interesting tool for identification of gene signatures and new markers to predict tumor response. However, the detection of predictive markers strongly depends on the drugs used in the specific therapeutic setting. There is growing evidence that topoisomerase II-alpha (TOPO IIalpha) is a marker for anthracycline-, and microtubule-associated protein tau (MAPT) for taxane sensitivity.

Gene expression profiles of breast cancer obtained from core cut biopsies before neoadjuvant docetaxel, adriamycin, and cyclophoshamide chemotherapy correlate with routine prognostic markers and could be used to identify predictive signatures.

Background: Neoadjuvant administration of chemotherapy provides a unique opportunity to monitor response to treatment in breast cancer and assesses response exactly. Global gene expression profiling by microarrays has been used as a valuable tool for the identification of prognostic and predictive marker genes. Even though this technology is now wide spread and relatively standardized, there are only few data available which compare established parameters with expression values to determine reliability of this method.

Predictors of primary breast cancers responsiveness to preoperative epirubicin/cyclophosphamide-based chemotherapy: translation of microarray data into clinically useful predictive signatures.

Background: Our goal was to identify gene signatures predictive of response to preoperative systemic chemotherapy (PST) with epirubicin/cyclophosphamide (EC) in patients with primary breast cancer.

Methods: Needle biopsies were obtained pre-treatment from 83 patients with breast cancer and mRNA was profiled on Affymetrix HG-U133A arrays. Response ranged from pathologically confirmed complete remission (pCR), to partial remission (PR), to stable or progressive disease, "No Change" (NC).