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

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. 2-step PCR was performed on laser captured section of FFPF samples of bladder tumors generated by transducing the bladder urothelial cells with a pooled lentivirus containing candidate oncogenic events to amplify the oncogenic barcode region, helping deconvolute oncogenic events involved in initiating the tumors. The distributions of oncogenic barcode were retrieved in each sample. The overlapping enriched factors for different histology were identified to be potentially invovled in the histology initiation.