3/24/2023 0 Comments Tt2 compendium![]() Microarray analysis was performed using Affymetrix Mouse Genome 430 2.0 arrays on three to four mice per treatment group, and a total of 70 mice were analyzed and used as the MAQC-II's training set (GEO Series GSE6116). If successful, the results may form the basis of a more efficient and economical approach for evaluating the carcinogenic activity of chemicals. The study objective was to apply microarray gene expression data from the lung of female B6C3F1 mice exposed to a 13-week treatment of chemicals to predict increased lung tumor incidence in the 2-year rodent cancer bioassays of the National Toxicology Program. The Hamner data set (endpoint A) was provided by The Hamner Institutes for Health Sciences (Research Triangle Park, NC, USA). ![]() 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. Genomic analysis of a subset of this sequentially accrued patient population were reported previously. RNA extraction and gene expression profiling were performed in multiple batches over time using Affymetrix U133A microarrays. Endpoint E is the clinical estrogen-receptor status as established by immunohistochemistry. 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. Patients received 6 months of preoperative (neoadjuvant) chemotherapy including paclitaxel, 5-fluorouracil, cyclophosphamide and doxorubicin followed by surgical resection of the cancer. These specimens represent 70-90% pure neoplastic cells with minimal stromal contamination. The biopsy specimens were collected sequentially during a prospective pharmacogenomic marker discovery study between 20. 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. Anderson Cancer Center (MDACC, Houston, TX, USA). The human breast cancer (BR) data set (endpoints D and E) was contributed by the University of Texas M. Sex, Specimen part, Compound View Samples a common array platform (Affymetrix Rat 230 2.0 microarray), experimental procedures and data retrieving and analysis processes. All eight compounds were studied using standardized procedures, i.e. The gene expression compendium data set was collected from 418 rats exposed to one of eight compounds (1,2-dichlorobenzene, 1,4-dichlorobenzene, bromobenzene, monocrotaline, N-nitrosomorpholine, thioacetamide, galactosamine, and diquat dibromide). The study objective was to use microarray gene expression data acquired from the liver of rats exposed to hepatotoxicants to build classifiers for prediction of liver necrosis. The NIEHS data set (endpoint C) was provided by the National Institute of Environmental Health Sciences (NIEHS) of the National Institutes of Health (Research Triangle Park, NC, USA). Publication TitleĮffect of training-sample size and classification difficulty on the accuracy of genomic predictors. A gene expression model of high-risk multiple myeloma was developed and validated by the data provider and later on validated in three additional independent data sets. ![]() Dichotomized overall survival (OS) and eventfree survival (EFS) were determined based on a two-year milestone cutoff. All samples applied to the microarray contained more than 85% plasma cells as determined by 2-color flow cytometry (CD38+ and CD45-/dim) performed after selection. Plasma cells were enriched by anti-CD138 immunomagnetic bead selection of mononuclear cell fractions of bone marrow aspirates in a central laboratory. The training set consisted of 340 cases enrolled on total therapy 2 (TT2) and the validation set comprised 214 patients enrolled in total therapy 3 (TT3). Gene expression profiling of highly purified bone marrow plasma cells was performed in newly diagnosed patients with MM. The multiple myeloma (MM) data set (endpoints F, G, H, and I) was contributed by the Myeloma Institute for Research and Therapy at the University of Arkansas for Medical Sciences (UAMS, Little Rock, AR, USA). ![]()
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