iCS-digital TM Pluri

The in Culture Supernatant – digital PCR Pluri (iCS-digital TM Pluri) test detects more than 90% of human 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

Cell culture supernatant (> 70% confluence)

Shipment

Room temperature

Coverage

Test with 24 probes: 91% of recurrent abnormalities
Test with 12 probes: 76% of recurrent abnormalities

Mosaicism

10%

Time

2-3 days after sample reception

Rationale and definition of recurrence

In culture, human pluripotent stem cells (PSCs) may develop recurrent, or even hyper-recurrent, genomic abnormalities. These recurrent abnormalities, essentially copy number variations (CNV), are a major concern because they reflect a selection pressure that may favour PSC proliferation and survival, or reduce their differentiation capacities*.

We specifically analyzed the data from 110 scientific publications concerning 942 PSC samples with more than 400 000 genomic abnormalities and variants and we highlighted the presence of 757 recurrent genetic abnormalities (i.e., genome sequences with abnormalities found in at least seven different publications) and of 243 hyper-recurrent abnormalities (i.e., found in at least 20 different publications).

The iCS-digital TM Pluri test includes a set of 24 specific probes, designed and optimized based on the 24 most reported altered sequences, to detect, by digital PCR, more than 90% of the recurrent and over 99% of the hyper-recurrent genetic abnormalities in PSC supernatant (patented technology). A version of the iCS-digital TM Pluri test that includes only 12 probes allows the detection of 76% of the recurrent and 99% of the hyper-recurrent genetic abnormalities identified in PSCs.

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

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 Feb 14, Review.

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