title: Breast cancer prognosis risk estimation using integrated gene expression and clinical data.
abstract: BACKGROUND
  Novel prognostic markers are needed so newly diagnosed breast cancer patients do not undergo any unnecessary therapy. Various microarray gene expression datasets based studies have generated gene signatures to predict the prognosis outcomes, while ignoring the large amount of information contained in established clinical markers. Nevertheless, small sample sizes in individual microarray datasets remain a bottleneck in generating robust gene signatures that show limited predictive power. The aim of this study is to achieve high classification accuracy for the good prognosis group and then achieve high classification accuracy for the poor prognosis group.
  
  
  METHODS
  We propose a novel algorithm called the IPRE (integrated prognosis risk estimation) algorithm. We used integrated microarray datasets from multiple studies to increase the sample sizes (∼ 2,700 samples). The IPRE algorithm consists of a virtual chromosome for the extraction of the prognostic gene signature that has 79 genes, and a multivariate logistic regression model that incorporates clinical data along with expression data to generate the risk score formula that accurately categorizes breast cancer patients into two prognosis groups.
  
  
  RESULTS
  The evaluation on two testing datasets showed that the IPRE algorithm achieved high classification accuracies of 82% and 87%, which was far greater than any existing algorithms.
authors.affiliation: School of Information Technology, Deakin University, 221 Burwood Highway, Melbourne, VIC 3125, Australia.
authors.forename: Ashish
authors.identifier: 0000-0002-3723-0809
authors.initials: A
authors.lastname: Saini
authors.affiliation: School of Information Technology, Deakin University, 221 Burwood Highway, Melbourne, VIC 3125, Australia.
authors.forename: Jingyu
authors.identifier: 0000-0002-6403-9786
authors.initials: J
authors.lastname: Hou
authors.affiliation: School of Information Technology, Deakin University, 221 Burwood Highway, Melbourne, VIC 3125, Australia.
authors.forename: Wanlei
authors.initials: W
authors.lastname: Zhou
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D030541:Databases, Genetic; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D016015:Logistic Models; D046228:Microarray Analysis; D011379:Prognosis; D012307:Risk Factors
chemical_list: D014408:Biomarkers, Tumor