Specifically, we included: (i) distinguishing treatment-naïve from tyrosine kinase inhibitor (TKI)-treated patients using cancer cells; (ii) differentiating treatment-naïve from anti-PD1–treated BRCA patients using T-cells; (iii) classifying estrogen receptor positive (ER+) versus triple-negative breast cancer (TNBC) patients based on cancer cells; (iv) differentiating exhausted versus non-exhausted T-cell states in BRCA tumors; (v) distinguishing treatment-naïve from neoadjuvant chemotherapy–treated BRCA patients using cancer cells; and (vi) classifying early-stage versus late-stage LUAD. Here, ESR1 is linked to invasive breast carcinoma.