Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer
Fig 1
Schematic diagram of this study.
a Definition of gene signatures to recapitulate the pathways underlying driver genomic aberrations. Here we use three genomic aberrations (TP53 mutation, ERBB2 amplification and ATM deletion) as examples. In ER+ breast cancer, we defined a total of 72 gene signatures, each for a specific genomic aberration. b To predict patient prognosis in ER+ breast cancer, we constructed prediction models to integrate the 72 gene signatures (intrinsic features), 6 types of infiltrating immune cells (extrinsic features), and clinical factors (e.g., age, tumor stage). Gene signature scores and immune cell scores were calculated based on gene expression of tumor samples. Random Forest models were used to classify good versus poor prognosis, and Cox regression models were used to predict prognostic risk scores.