iCS-digital™ PSC:
fast in-routine genomic testing assay

Detect over 92% of recurrent abnormalities
in hPSCs in record-breaking time!

Human Pluripotent Stem Cells (hPSCs) are particularly prone to developing abnormalities during their time in culture. In 5 passages or less, the variants that appear can rapidly become predominant, compromising your research work.

Traditional G-Banding karyotyping is helpful in providing an exhaustive structural and numerical variant analysis. However, it does not have the required sensitivity to identify the most frequent genomic defects in human pluripotent stem cells.

Additionally, hPSC research scientists need assays designed for in-process testing every 5-10 passages (Assou et al., 2020; McIntire et al., 2020; Pamies et al., 2017) in order to pick up abnormalities as early as possible in their workflow, and G-Banding is not designed to support that level of frequency in testing.

The sensitivity and speed required in delivering a reliable assessment of genomic stability in hPSCs led Stem Genomics to develop the iCS-digital™ PSC range.

High level of performance for optimum detection

Thanks to the high level of performance offered by digital PCR (200 bp and 20% mosaicism) combined with an in-depth analysis of most recurrent abnormalities in hPSCs (see SMART database), the iCS-digital™ PSC range of tests can detect sub-karyotyping abnormalities that G-Banding would miss.

Our iCS-digital™ PSC 24-probe test will capture over 92% of recurrent defects in hPSCs, including the 20q11.21 amplification that accounts for 1⁄4 of recurrent abnormalities in hPSCs worldwide.
Our iCS-digital™ PSC 12-probe assay is based on the same principles and will capture over 77.5% of the most recurrent defects in hPSCs.
Our iCS-digital™ PSC 20q-only test focuses on the gain of 20q11.21 copy-number variant (CNV). It is detected in more than 20% of worldwide cultured human Pluripotent Stem Cells (hPSCs) and represents 22.9% of the recurrent structural variants identified in hPSCs (Assou et al., 2020)[1], making it the most common genomic abnormality in hPSCs.

iCS-digital™ PSC key specifications at a glance

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: 92% 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

Available as a service
(from one sample) or a kit:

For research use only

Practical testing guidelines

Recommended guidelines in terms of genomic stability advise checking the cells every 5-10 passages during their time in culture, but also screening clones after any stressing process (reprogramming, gene editing, etc.) and during banking. It is also advisable when a new line is acquired.

Click on the graph for more details:

The workflow for PSC genetic integrity quality control recommended by Stem Genomics

It’s up to you to...

SMART database

In order to accurately target the abnormalities relevant for hPSC researchers, Stem Genomics specifically analysed the data from +100 scientific publications concerning +900 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™ PSC test.

The test is published in Stem Cell Reports (Assou et al., 2020).

See what our customers say

Ocular Genomics Institute, Harvard Medical School

| Dr Marcela Garita-Hernandez, Pharm D, PhD, Director of the iPSC Research Program, Pierce Lab.

“In my experience, you need to check your cell lines routinely, as nothing that I have found to date can help you predict genomic abnormalities without testing your cell lines regularly. If your raw material is not stable, it is very difficult to trust any differentiation changes down the line. iCS-digital™ PSC is ideal for regular testing and has always been part of our workflow. It is also affordable for most labs, so there is really no excuse not to test your lines”.

University of Freiburg Department of Cardiology and Angiology, AG Hilgendorf

| Dr. Tsai-sang Dederichs, scientist

With Duo iCS-Karyo, Stem Genomics provides a very convenient and good quality service that makes genomic quality control easy. Communication is smooth and instructions are clear.

Cellected

| Claire Richards, CEO and Founder

I would recommend the iCS-digital™ PSC to anyone who wants a good way of keeping an eye on their cells almost in real time and as a complement to traditional techniques that take a lot longer.

DiNAQOR

| Kurt Jacobs, Research scientist

The iCS-digital™ PSC 24-probe kit covers a wide range of mutations in a simple test. It helps us strengthen our quality control at various stages of our workflow. For instance, it picked up the 20q amplicon that was present in some of our hiPSC lines.

denovoMATRIX

| Sandra Segeletz, Head of Innovation

I would recommend the iCS-digital™ tests for anyone looking for a good genomic appraisal at minimum effort. In addition, this is an easy entry to quality control for anyone with a limited budget.

GoLiver Therapeutics

| Angélique Fourrier, R&D project manager

Since we started using the iCS-digital™ PSC for routine control, we have gained a massive degree of confidence in the quality of our cells in long-term culture […] Not surprisingly, by removing the genetic instability factor from the equation, we are rewarded with a highly scalable, efficient and very cost-effective GMP differentiation process for PSCs to produce safe live cell therapy products on a multi-billion cell scale.

ICM

| Stéphanie Bigou, Responsable Opérationnelle

We have been using the (iCS-Digital™) tests since their launch in 2018 and find them to be very reliable.

Ncardia

| Arie Reijerkerk, Director Manufacturing Technology

The results are obtained very quickly; the reports are clearly interpreted and there is a smooth line of communication between Ncardia and Stem Genomics whenever we require further clarifications.

Previous slide

Next slide

Published scientific articles
citing the iCS-digital™ PSC assay

2023

Lab Resource: Genetically-Modified Multiple Cell Lines Generation of gene corrected human isogenic iPSC lines (IDVi003-A_CR13, IDVi003-A_CR21, IDVi003-A_CR24) from an inherited retinal dystrophy patient-derived IPSC line ITM2B-5286-3 (IDVi003-A) carrying the ITM2B c.782A>C variant using CRISPR/Cas9

Tasnim Ben Yacoub1, Camille Letellier1, Juliette Wohlschelegel1, Christel Condroyer1, Amélie Slembrouck-Brec1, Olivier Goureau1, Christina Zeitz1, Isabelle Audo1,2,3

Affiliations: 1 Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France. 2 CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, 75012 Paris, France 3 Institute of Ophthalmology, University College of London, London EC1V 9EL, United Kingdom.

Link to the publication

2023

AAV-mediated gene augmentation therapy of CRB1 patient-derived retinal organoids restores the histological and transcriptional retinal phenotype

Nanda Boon, Xuefei Lu, Charlotte A. Andriessen, Ioannis Moustakas, Thilo M. Buck, Christian Freund, Christiaan H. Arendzen, Stefan Bo¨hringer, Hailiang Mei, and Jan Wijnholds.

Link to the publication

2023

Generation of AAVS1 and CLYBL STRAIGHT-IN v2 acceptor human iPSC lines for integrating DNA payloads

Albert Blanch-Asensio, Babet van der Vaart, Mariana Vinagre, Eline Groen, Christiaan Arendzen, Christian Freund, Niels Geijsen, Christine L. Mummery, Richard P. Davis.

Link to the publication

2022

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.

Link to the publication

2022

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.

Link to the publication

2021

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.

Link to the publication

2021

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.

Link to the publication

2021

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.

Link to the publication

2020

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.

Link to the publication

2020

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.

Link to the publication

2020

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

Assou S, Girault N, Plinet M, Bouckenheimer J, Sansac C, Combe M, Mianné J, Bourguignon C, Fieldes M, Ahmed E, Commes T, Boureux A, Lemaître JM, De Vos J. Stem Cell Reports 2020 Jan 14;14(1):1-8

Link to the publication

2019

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.

Link to the publication

Previous slide

Next slide

iCS-digital™ PSC: fast in-routine genomic testing assay

Detect over 92% of recurrent abnormalities in hPSCs in record-breaking time!

High level of performance for optimum detection

iCS-digital™ PSC key specifications at a glance

Practical testing guidelines

It’s up to you to...

SMART database

See what our customers say

Published scientific articles citing the iCS-digital™ PSC assay

Lab Resource: Genetically-Modified Multiple Cell Lines Generation of gene corrected human isogenic iPSC lines (IDVi003-A_CR13, IDVi003-A_CR21, IDVi003-A_CR24) from an inherited retinal dystrophy patient-derived IPSC line ITM2B-5286-3 (IDVi003-A) carrying the ITM2B c.782A>C variant using CRISPR/Cas9

AAV-mediated gene augmentation therapy of CRB1 patient-derived retinal organoids restores the histological and transcriptional retinal phenotype

Generation of AAVS1 and CLYBL STRAIGHT-IN v2 acceptor human iPSC lines for integrating DNA payloads

Modeling PRPF31 retinitis pigmentosa using retinal pigment epithelium and organoids combined with gene augmentation rescue.

CRISPR/Cas9-mediated gene knockout and interallelic gene conversion in human induced pluripotent stem cells using non-integrative bacteriophage-chimeric retrovirus-like particles.

PCSK9 regulates the NODAL signaling pathway and cellular proliferation in hiPSCs.

Optogenetically controlled human functional motor endplate for testing botulinum neurotoxins.

Allele-Specific Knockout by CRISPR/Cas to Treat Autosomal Dominant Retinitis Pigmentosa Caused by the G56R Mutation in NR2E3.

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.

Effective Differentiation and Biological Characterization of Retinal Pigment Epithelium Derived from Human Induced Pluripotent Stem Cells.

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

Generation of hiPSC line TCIERi001-A from normal human epidermal keratinocytes.

Download this file immediately

iCS-digital™ PSC:
fast in-routine genomic testing assay

Detect over 92% of recurrent abnormalities
in hPSCs in record-breaking time!

Published scientific articles
citing the iCS-digital™ PSC assay