2.1. RNA-Seq, Whole Exome Sequencing, Single Nucleotide Polymorphism (SNP) Arrays Data Collection

The TCGA data about breast invasive carcinoma (BRCA) were retrieved from the online data portal The Genomic Data Commons (GDC) (https://portal.gdc.cancer.gov accessed on 29 October 2019) [13,14]. Data from the following technologies were selected: (1) RNA-seq data (HTseq counts) from 1222 BRCA-TCGA samples and (2) whole exome sequencing (WES) data by using the available Mutation Annotation Format (MAF) file (variant calling by SomaticSniper algorithms [15]) from a total of 976 samples. Data regarding the cytogenetic features of BRCA were downloaded from cBioPortal for cancer genomics (https://www.cbioportal.org accessed on 29 October 2019) [16,17] for a total of 1084 samples (Affymetrix SNP 6.0 arrays).