iCS-digital TM PSC
The in Culture Supernatant – digital PCR (iCS-digital TM) PSC test detects more than 90% of recurrent genomic abnormalities in human pluripotent stem cells (hPSCs).
ESCs & iPSCs
- Gene editing
- Cell culture supernatant
(> 70% confluence)
- Cell pellet
- Room temperature
- Room temperature
- Dry ice
Test with 24 probes: 91% of recurrent abnormalities
Test with 12 probes: 76% of recurrent abnormalities
after sample reception
Definition of recurrent genomic abnormalities and rationale for regular testing
In culture, human pluripotent stem cells (hPSCs) may develop recurrent genomic abnormalities. These defects, essentially copy number variations (CNVs), are a major concern because they reflect a selection pressure that may favour hPSC proliferation and survival, or reduce their differentiation capacities*.
We specifically analysed the data from 104 scientific publications concerning 942 hPSC samples. After exclusion of polymorphic variants, we highlighted the presence of 786 recurrent genetic abnormalities (i.e., genomic defects found in at least five different publications).
We then used these data to develop the iCS-digital TM PSC test. This assay includes a set of 24 specific probes that were designed and optimized based on the most reported altered sequences and that allows detecting, by digital PCR, more than 90% of recurrent genetic abnormalities in hPSC supernatant (patented technology). A version of the iCS-digital TM PSC test that includes 12 probes allows the detection of 76% of the recurrent genetic abnormalities.
Thanks to the simplicity of the collection method and the rapidity of the analysis, the iCS-digital TM PSC test is a straightforward method for monitoring cell lines at regular intervals in culture, for controlling the cells before initiating critical and costly steps (banking, differentiation), and for screening hPSC clones after reprogramming or gene editing.
Percentage of cumulated recurrent abnormalities detected in function of the number of probes targeting specific genomic sequences
* Assou S, Bouckenheimer J, De Vos J. Assessing the Genome Integrity of Human Induced Pluripotent Stem Cells: What Quality Control Metrics? Stem Cells. 2018 Jun;36(6):814-821.
The iCS-digital TM PSC test is a non-invasive tool to detect the vast majority of recurrent genomic abnormalities for the routine monitoring of human PSC genomic stability. This new test can change how quality control is implemented for PSC use in basic research and regenerative medicine.