Recurrent Genetic Abnormalities in Human Pluripotent Stem Cells: Definition and Routine Detection in Culture Supernatant by Targeted Droplet Digital PCR

Genomic integrity of human pluripotent stem cells (hPSCs) is essential for research and clinical applications. However, genetic abnormalities can accumulate during hPSC generation and routine culture and following gene editing. Their occurrence should be regularly monitored, but the current assays to assess hPSC genomic integrity are not fully suitable for such regular screening. To address this issue, we first carried out a large meta-analysis of all hPSC genetic abnormalities reported in more than 100 publications and identified 738 recurrent genetic abnormalities (i.e., overlapping abnormalities found in at least five distinct scientific publications). We then developed a test based on the droplet digital PCR technology that can potentially detect more than 90% of these hPSC recurrent genetic abnormalities in DNA extracted from culture supernatant samples. This test can be used to routinely screen genomic integrity in hPSCs. [Display omitted] •A meta-analysis was carried out to list genetic abnormalities detected in hPSCs•Recurrent genetic abnormalities in hPSCs were precisely defined•ddPCR is a robust and sensitive approach to screen these recurrent abnormalities•In culture supernatant digital test can be used to rapidly screen iPSC clones In this article, De Vos and colleagues performed a comprehensive meta-analysis of genetic abnormalities detected in hPSC lines. They then used this information to devise a ddPCR test targeting the majority of recurrent abnormalities and show that this test can be applied to the cell culture supernatant. Finally, they illustrate the interest of this test for routine hPSC screening.