iCS-digital TM Pluri

The in Culture Supernatant – digital PCR Pluri (iCS-digital TM Pluri) test detects more than 90% of recurrent genomic abnormalities in human pluripotent stem cells (PSC), i.e. human embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC).

iCS-digital TM pluri test steps Stem Genomics
Cell types

Human PSC: ESC & iPSC

Stages

- Reprogramming
- Derivation
- Maintenance
- Differentiation
- Gene editing

Sample

- DNA
- Cell culture supernatant (> 70% confluence)
- Cell pellet

Shipment

- Room temperature
- Dry ice

Coverage

Test with 24 probes: 91% of recurrent abnormalities

Test with 12 probes: 76% of recurrent abnormalities

Mosaicism

30%

Time

2-3 days 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 recurrent defects, essentially copy number variations (CNV), are a major concern because they reflect a selection pressure that may favour hPSC proliferation and survival, or reduce their differentiation capacities*.

We specifically analysedthe data from 104 scientific publications concerning 942 hPSC samples. After exclusion of polymorphic variants, we identified more than 25 000 genomic defects and highlighted the presence of 786 recurrent genetic abnormalities (i.e., genome sequences with abnormalities found in at least five different publications).

We then used these data to develop the iCS-digital TM Pluri test. This assay includes a set of 24 specific probes that were designed and optimized based on the 24 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 Pluri test that includes 12 probes allows the detection of 76% of the recurrent genetic abnormalities identified in hPSCs.

We found that the CNVs detected by the iCS-digital TM Pluri test in DNA extracted from hPSC supernatants are highly correlated with the CNVs detected in DNA from cultured hPSCs.

Thanks to the simplicity of the collection method and the rapidity of the analysis, the iCS-digital TM Pluri test is a straightforward method for monitoring cell linesat regular intervals in culture, for controlling the cells before initiating critical and costly steps (banking, differentiation), and for screening hPSCclones after reprogramming or gene editing.

Percentage of cumulated recurrent abnormalities detected in function of the number of probes targeting specific genomic sequences

iCS-digital TM Pluri test result

* 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 Pluri 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.

iCS-digital TM Pluri