Detect abnormalities in human Pluripotent Stem Cells

Discover our comprehensive portfolio of PSC tests for accurate and rapid detection of recurrent
genomic abnormalities in human pluripotent stem cells (hPSCs).

iCS-digital TM PSC 24 Probes

iCS-digital TM PSC

24 PROBES

detects more than 90% of recurrent genomic abnormalities in hPSCs

https://www.stemgenomics.com/the-ics-digital-tm-psc-24-probes
Discover the kit version
iCS-digital TM PSC 12 probes

iCS-digital TM PSC

12 PROBES

detects 77.5% of recurrent genomic abnormalities in hPSCs

iCS-digital TM PSC 20q ONLY

iCS-digital TM PSC

20q ONLY

detects the most recurrent abnormality in hPSCs

https://www.stemgenomics.com/detect-the-20q-amplicon-in-hpscs-in-house-kit
Discover the kit version
Fast genomic integrity test
Cell types

Human PSCs:
ESCs & iPSCs

Stages

- In-process control during cell amplification & maintenance
- Clone screening
- Banking characterization

Samples

- gDNA
- Cell pellet
- Cells in fresh culture media
(or in cell culture supernatant)

Shipment

- Room temperature
- Dry ice
- Room temperature

Coverage

Test with 24 probes: 91% of recurrent abnormalities

Test with 12 probes: 77.5% of recurrent abnormalities

Test the 20q11.21 region : the most common genomic abnormality in hPSCs (>20%)

Mosaicism

>20%
(depending on sample quality)

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 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 100 scientific publications concerning 942 hPSC samples. After exclusion of polymorphic variants, we highlighted the presence of 738 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 hPSCs. Our test portfolio also includes :
- a 12-probes version of the iCS-digital TM PSC test allowing the detection of 77.5% of the recurrent genetic abnormalities,
- a single-probe test version specifically dedicated to the sub-karyotypic 20q11.21 amplification detection.

The test is published in Stem Cell Reports**.

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

iCS-digital TM PSC test result

* Assessing the Genome Integrity of Human Induced Pluripotent Stem Cells: What Quality Control Metrics? Stem Cells 2018 Jun;36(6):814-821.
** Recurrent Genetic Abnormalities in Human Pluripotent Stem Cells: Definition and Routine Detection in Culture Supernatant by Targeted Droplet Digital PCR. Stem Cell Reports 2020 Jan14;14(1):1-8.

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.

iCS-digital TM PSC

Published scientific articles citing the iCS-digital™ PSC assay

2022 publications:

• Modeling PRPF31 retinitis pigmentosa using retinal pigment epithelium and organoids combined with gene augmentation rescue
Rodrigues A, Slembrouck-Brec A, Nanteau C, Terray A, Tymoshenko Y, Zagar Y, Reichman S, Xi Z, Sahel JA, Fouquet S, Orieux G, Nandrot EF, Byrne LC, Audo I, Roger JE, Goureau O. Modeling PRPF31 retinitis pigmentosa using retinal pigment epithelium and organoids combined with gene augmentation rescue. NPJ Regen Med. 2022 Aug 16;7(1):39. doi: 10.1038/s41536-022-00235-6. PMID: 35974011; PMCID: PMC9381579.

• CRISPR/Cas9-mediated gene knockout and interallelic gene conversion in human induced pluripotent stem cells using non-integrative bacteriophage-chimeric retrovirus-like particles.
Mianné J, Nasri A, Van CN, Bourguignon C, Fieldès M, Ahmed E, Duthoit C, Martin N, Parrinello H, Louis A, Iché A, Gayon R, Samain F, Lamouroux L, Bouillé P, Bourdin A, Assou S, De Vos J. CRISPR/Cas9-mediated gene knockout and interallelic gene conversion in human induced pluripotent stem cells using non-integrative bacteriophage-chimeric retrovirus-like particles. BMC Biol. 2022 Jan 7;20(1):8.

2021 publications :

Optogenetically controlled human functional motor endplate for testing botulinum neurotoxins
de Lamotte JD, Polentes J, Roussange F, Lesueur L, Feurgard P, Perrier A, Nicoleau C, Martinat C. Optogenetically controlled human functional motor endplate for testing botulinum neurotoxins. Stem Cell Res Ther. 2021 Dec 5;12(1):599.

PCSK9 regulates the NODAL signaling pathway and cellular proliferation in hiPSCs
Roudaut M, Idriss S, Caillaud A, Girardeau A, Rimbert A, Champon B, David A, Lévêque A, Arnaud L, Pichelin M, Prieur X, Prat A, Seidah NG, Zibara K, Le May C, Cariou B, Si-Tayeb K. PCSK9 regulates the NODAL signaling pathway and cellular proliferation in hiPSCs. Stem Cell Reports. 2021 Dec 14;16(12):2958-2972.

Allele-Specific Knockout by CRISPR/Cas to Treat Autosomal Dominant Retinitis Pigmentosa Caused by the G56R Mutation in NR2E3
Diakatou M, Dubois G, Erkilic N, Sanjurjo-Soriano C, Meunier I, Kalatzis V. Allele-Specific Knockout by CRISPR/Cas to Treat Autosomal Dominant Retinitis Pigmentosa Caused by the G56R Mutation in NR2E3. Int J Mol Sci. 2021 Mar 5;22(5):2607.

2020 publications :

Generation of a human induced pluripotent stem cell line (iPSC) from peripheral blood mononuclear cells of a patient with a myasthenic syndrome due to mutation in COLQ
Barbeau S, Desprat R, Eymard B, Martinat C, Lemaitre JM, Legay C. Generation of a human induced pluripotent stem cell line (iPSC) from peripheral blood mononuclear cells of a patient with a myasthenic syndrome due to mutation in COLQ. Stem Cell Res. 2020 Dec;49:102106.

Effective Differentiation and Biological Characterization of Retinal Pigment Epithelium Derived from Human Induced Pluripotent Stem Cells
Shrestha R, Wen YT, Tsai RK. Effective Differentiation and Biological Characterization of Retinal Pigment Epithelium Derived from Human Induced Pluripotent Stem Cells. Curr Eye Res. 2020 Sep;45(9):1155-1167.

2019 publications :

Generation of hiPSC line TCIERi001-A from normal human epidermal keratinocytes
Shrestha R, Wen YT, Tsai RK. Generation of hiPSC line TCIERi001-A from normal human epidermal keratinocytes. Stem Cell Res. 2019 Dec;41:101590.

Genome Editing in Patient iPSCs Corrects the Most Prevalent USH2A Mutations and Reveals Intriguing Mutant mRNA Expression Profiles
Sanjurjo-Soriano C, Erkilic N, Baux D, Mamaeva D, Hamel CP, Meunier I, Roux AF, Kalatzis V. Genome Editing in Patient iPSCs Corrects the Most Prevalent USH2A Mutations and Reveals Intriguing Mutant mRNA Expression Profiles. Mol Ther Methods Clin Dev. 2019 Nov 27;17:156-173.

Human pre-valvular endocardial cells derived from pluripotent stem cells recapitulate cardiac pathophysiological valvulogenesis
Neri T, Hiriart E, van Vliet PP, Faure E, Norris RA, Farhat B, Jagla B, Lefrancois J, Sugi Y, Moore-Morris T, Zaffran S, Faustino RS, Zambon AC, Desvignes JP, Salgado D, Levine RA, de la Pompa JL, Terzic A, Evans SM, Markwald R, Pucéat M. Human pre-valvular endocardial cells derived from pluripotent stem cells recapitulate cardiac pathophysiological valvulogenesis. Nat Commun. 2019 Apr 26;10(1):1929.

Aberrant hiPSCs-Derived from Human Keratinocytes Differentiates into 3D Retinal Organoids that Acquire Mature Photoreceptors
Shrestha R, Wen YT, Ding DC, Tsai RK. Aberrant hiPSCs-Derived from Human Keratinocytes Differentiates into 3D Retinal Organoids that Acquire Mature Photoreceptors. Cells. 2019 Jan 9;8(1):36. 

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