Genetic barcoding uncovers the clonal makeup of solid and liquid biopsies and their ability to capture intra tumoral heterogeneity

Intra-tumoral heterogeneity (ITH) drives breast-cancer progression by enabling distinct clonal populations to differentially adapt, metastasize, and resist therapy. To investigate how clonal diversity manifests across tumor sites and sampling methods, we employed genetic barcoding to track the spatial and temporal dynamics of human breast-cancer clones in six preclinical models, including two cell lines and four patient-derived xenografts (PDXs). Barcode sequencing enabled quantitative comparison of intra-tumor clonal composition across solid tumors, matched needle biopsies, and circulating cell-free DNA (cfDNA). Analyses revealed higher clonal diversity in the centers of non-necrotic primary tumors compared to their peripheries, and demonstrated that cfDNA barcode shedding varies with necrosis, tumor burden, and model context. These findings highlight how integrating solid- and liquid-biopsy barcoding data provides a more robust view of tumor composition and underscore the value of barcoded breast-cancer models for studying ITH and metastatic evolution.