Analysis of 10086 Microarray Gene Expression Data Uncovers Genes that Subclassify Breast Cancer Intrinsic Subtypes

Breast cancer is a complex disease comprising molecularly distinct subtypes. The prognosis and treatment differ between subtypes; thus, it is important to distinguish one subtype from another. In this chapter, we make use of high-throughput microarray dataset to perform breast cancer subtyping of 10086 samples. Aside from the four major subtypes, that is, Basal-like, HER2-enriched, luminal A, and luminal B, we defined a normal-like subtype that has a gene expression profile similar to that found in normal and adjacent normal breast samples. Also, a group of luminal B-like samples with better prognosis was distinguished from the high-risk luminal B breast cancer. We additionally identified 33 surface-protein encoding genes whose gene expression profiles were associated with survival outcomes. We believe these genes are potential therapeutic targets and diagnostic biomarkers for breast cancer.