Pac Symp Biocomput. 2016:21:405-16.


The cellular composition of a tumor greatly influences the growth, spread, immune activity, drug response, and other aspects of the disease. Tumor cells are usually comprised of a heterogeneous mixture of subclones, each of which could contain their own distinct character. The presence of minor subclones poses a serious health risk for patients as any one of them could harbor a fitness advantage with respect to the current treatment regimen, fueling resistance. It is therefore vital to accurately assess the make-up of cell states within a tumor biopsy. Transcriptome-wide assays from RNA sequencing provide key data from which cell state signatures can be detected. However, the challenge is to find them within samples containing mixtures of cell types of unknown proportions. We propose a novel one-class method based on logistic regression and show that its performance is competitive to two established SVM-based methods for this detection task. We demonstrate that one-class models are able to identify specific cell types in heterogeneous cell populations better than their binary predictor counterparts. We derive one-class predictors for the major breast and bladder subtypes and reaffirm the connection between these two tissues. In addition, we use a one-class predictor to quantitatively associate an embryonic stem cell signature with an aggressive breast cancer subtype that reveals shared stemness pathways potentially important for treatment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / classification
  • Breast Neoplasms / genetics
  • Breast Neoplasms / pathology
  • Computational Biology / methods
  • Computational Biology / statistics & numerical data
  • Embryonic Stem Cells / pathology
  • Female
  • Gene Expression Profiling / statistics & numerical data
  • Humans
  • Logistic Models
  • Neoplasms / classification*
  • Neoplasms / genetics
  • Neoplasms / pathology*
  • Neoplastic Stem Cells / pathology
  • Precision Medicine
  • Support Vector Machine
  • Urinary Bladder Neoplasms / classification
  • Urinary Bladder Neoplasms / genetics
  • Urinary Bladder Neoplasms / pathology