Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [DNA-seq_distribution]

Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant models of bladder and prostate cancer. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes. Overall design: 2-step PCR was performed on prostate organoid cells transduced with a pooled lentivirus containing candidate oncogenic events to amplify the oncogenic barcode region, helping deconvolute distribution of each oncogenic event transduced in the cells. The distributions of oncogenic barcode were retrieved in each sample. Th distribution was used to determine if each oncogenic events were evenly distributed in the transduced cells.