Quantification of intrinsic subtype ambiguity in Luminal A breast cancer and its relationship to clinical outcomes.

ABSTRACT:

Background

PAM50 gene profiling assigns each cancer to a single intrinsic subtype. However, individual cancers vary in their adherence to a prototype, and due to bulk tissue sampling, some may exhibit expression patterns that indicate intra-tumor admixture of multiple subtypes. Our objective was to develop admixture metrics from PAM50 gene expression profiles in order to stratify Luminal A (LumA) cases according to their degree of subtype admixture, and then relate such admixture to clinical and molecular variables.

Methods

We re-constructed scaled, normalized PAM50 profiles for 1980 cases (674 LumA) in the METABRIC cohort and for each case computed its Mahalanobis (M-) distance from its assigned centroid and M-distance from all other centroids. We used t-SNE plots to visual

SUBMITTER: Kumar N 

PROVIDER: S-EPMC6408846 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature