Figure 1.

Experimental setup

Wild-type human colorectal organoids were transformed using a CRISPR-Cas9-based strategy.²² Transformed organoids were transduced with a lentiviral library introducing a lineage barcode. Organoids underwent a 26-week in vitro evolution period during which single-cell WGS was performed at regular intervals and culture complexity was assessed weekly. From the single-cell WGS, copy number state, sSNV state, and lineage barcodes were acquired, allowing the construction and validation of highly detailed clonal evolution trees.