Fig. 1: Breast cancer PDX collection.

a Schematic of live biobanking protocol of primary and metastatic breast cancer (BrCa). Fresh breast tumors were divided for traditional biobanking (FFPE and snap frozen) and generation of PDX. These samples underwent molecular (WGS/RNA-seq and RPPA) and functional (in vivo drug sensitivity, metastasis assays) analyses. FFPE formalin-fixed paraffin-embedded, PDX patient-derived xenograft, WGS whole-genome sequencing, RNA-seq RNA-sequencing, RPPA reverse-phase protein array. b Bar chart of success rate for engraftment attempts per tumor sample. Success (n = 36), failure (n = 45). c Kaplan–Meier analysis of progression-free survival (PFS) for patients whose tumors successfully generated PDXs versus those that failed. d Bar chart of growth kinetics (time to endpoint, defined as growth to 10 mm) across passage 1–3 (P1, P2, P3) of PDX models (P1 median n = 2.5, range 1–11; P2 median n = 6, range 3–29; P3 median n = 4, range 3–15). Mean ± SD. Patient follow-up (Pt F/U) time and time to progression (Pt progression) are overlaid. *Mouse sacrificed before endpoint reached. e Representative H&E, estrogen receptor (ER) and HER2 staining from patient tumor and corresponding PDXs, representing the four major clinical subtypes. Left, whole-image scale bar 200 μm; right higher-magnification scale bar 50 μm. Complete staining panel in Supplementary Fig. 3. f Sankey diagrams for patient (Pt) and PDX concordance for estrogen receptor (ER) status, HER2 status, histological subtype and gene expression subtype (AIMS, absolute intrinsic molecular subtype) (left to right). ACC adenoid cystic carcinoma, IDC (pleo) invasive ductal carcinoma (pleomorphic), IDC (MGA) IDC in microglandular adenosis background, ILC invasive lobular carcinoma, MBC metaplastic breast cancer, Muc mucinous, NE neuroendocrine, BL basal-like, HER2E HER2-enriched, NL normal-like, LumB luminal B.