Genetic integrity of human pluripotent stem cells (hPSCs) is essential for their sustained use in regenerative medicine, and as a tool in modelling development and disease. Though the majority of hPSC lines derived are euploid, over the last several years it has been well established that hPSCs are subject to mutation and can acquire recurrent genetic abnormalities upon culture. The recurrent abnormalities observed commonly present as either copy number variants or gains of whole or regions of chromosomes; 1, 12, 17, 20 and X.     

 

Despite being widely documented, changes in the frequency of recurrent chromosomal abnormalities over time and their correlation to culture conditions have not yet been investigated. Utilizing an annotated dataset of almost 20,000 karyotypes, containing cytogenetic analysis and information on the corresponding culture conditions, acquired between 2009 - 2022 we show the correlation of karyotypic changes with culture conditions used to grow hPSCs. We further identified a gain of chromosome 1q as one of the most frequent aberrations in hPSCs in feeder-free cultures and characterized the features that provide these cells with selective advantage over their wild-type counterparts. Finally, we carried out functional assays to identify a putative driver gene in the amplified region on chromosome 1q. Overall, our data reveals which recurrent genetic changes represent a current threat to applications of hPSCs in research and cell therapy and establish the molecular basis for the selective advantage of variant cells with a gain of chromosome 1q.