CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models.

ABSTRACT: Colorectal cancers (CRCs) can be divided into four gene expression-based biologically distinct consensus molecular subtypes (CMS). This classification provides a potential framework for stratified treatment, but to identify novel CMS-drug associations, translation of the subtypes to pre-clinical models is essential. The currently available classifier is dependent on gene expression signals from the immune and stromal compartments of tumors and fails to identify the poor-prognostic CMS4-mesenchymal group in immortalized cell lines, patient-derived organoids and xenografts. To address this, we present a novel CMS classifier based on a filtered set of cancer cell-intrinsic, subtype-enriched gene expression markers. This new classifier, referred to as CMScaller, recapitulated the subtypes in b

SUBMITTER: Eide PW 

PROVIDER: S-EPMC5709354 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature