HIGHLIGHTS
SUMMARY
Transcriptomic (RNAseq and microarray-based) and mass spectrometry-(MS-) and reverse phase proteomics (RPPA) gene_expression profiles correlate well with those of patientmatched tissue. Omics, gene_expression at the mRNA level was only evaluated at baseline (T0, pre-treatment). Permutation of Baseline mRNA Expression For the clinical gene_expression dataset, gene level batch-corrected and normalized RNA expression data from the I-SPY2 trial (GSE194040) representing TNBC patients were used as pre-treatment (T0) gene_expression data for the prototype patient dataset. To simulate T1 gene_expression data, the T0 expression tables were randomly permuted by multiplying each data . . .
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