Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model

MOTIVATION Tissue microarrays (TMAs) quantify tissue-specific protein expression of cancer biomarkers via high-density immuno-histochemical staining assays. Standard analysis approach estimates a sample mean expression in the tumor, ignoring the complex tissue-specific staining patterns observed on tissue arrays. METHODS In this article, a cell mixture model (CMM) is proposed to reconstruct tumor expression patterns in TMA experiments. The concept is to assemble the whole-tumor expression pattern by aggregating over the subpopulation of tissue specimens sampled by needle biopsies. The expression pattern in each individual tissue element is assumed to be a zero-augmented Gamma distribution to assimilate the non-staining areas and the staining areas. A hierarchical Bayes model is imposed to borrow strength across tissue specimens and across tumors. A joint model is presented to link the CMM expression model with a survival model for censored failure time observations. The implementation involves imputation steps within each Markov chain Monte Carlo iteration and Monte Carlo integration technique. RESULTS The model-based approach provides estimates for various tumor expression characteristics including the percentage of staining, mean intensity of staining and a composite meanstaining to associate with patient survival outcome. AVAILABILITY R package to fit CMM model is available at http://www.mskcc.org/mskcc/html/85130.cfm