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Figure 2. Heatmap of RNA expression (z-scores) of the PAM50 gene set in 1904 breast tumors samples from METABRIC cohort. The
visual representation of clustered gene patterns associated with subtypes Basal, Luminal B, luminal A, HER-enriched and Normal-like (left
to right order). Each rows correspond to a gene and each column to a patient sample. The data of BAG1, PPR160 and TMEM45B were not
included. The heatmap was generated using cBioPortal tools (https://www.cbioportal.org/)

[45]
DX, PAM50, and MammaPrint tests are some examples commercially available . The routine application
of these tests are useful for identifying stage I or stage II lymph node-negative breast cancer patients that
may or may not require adjuvant chemotherapy [30,46] . The Oncotype-DX breast cancer assay quantifies
the transcription for only 21 genes through reverse transcription polymerase chain reaction using in
the breast cancer tissue (lumpectomy, mastectomy, or core biopsy) conserved in FFPE. The Oncotype-
DX test provides a recurrence score (from 1 to 100) that is used to predict the risk of recurrence of DCIS
[45]
breast cancer subtypes and/or the risk of a new invasive cancer . The Oncotype DX DCIS test in woman
diagnosed with DCIS predicts benefit from radiation after surgery. There is currently clinical practice
guideline addressing when biomarker scores might be applied for predicting which women will benefit of
[45]
specific drugs or regimens for adjuvant systemic therapy .

The PAM50 test uses 50 gene expression set to discriminate between each of the 5 breast cancer subtypes.
The PAM50 recurrence score estimate the risk of distant recurrence of hormone-receptor-positive breast
cancer from 5 to 10 years after diagnosis and after 5 years of hormonal therapy treatment in postmenopausal
women [30,45] . For illustrative propose we present a heatmap generated in cBioPortal (https://www.cbioportal.
org/) for PAM50 gene set in 1904 breast tumors samples from METABRIC study [Figure 2]. This colored
representation displays similarities between the tumor samples in terms of messenger RNA expression
levels (z-scores) for the panel of genes. The rows correspond to indicated genes and column to samples. The
gene clusters that define subtypes Basal, Luminal B, luminal A, HER-enriched and Normal-like markers