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

Detect over 93% 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.

  1. Our iCS-digital™ PSC 24-probe test will capture over 93% of recurrent defects in hPSCs, including the 20q11.21 amplification that accounts for 1⁄4 of recurrent abnormalities in hPSCs worldwide.
  2. 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.
  3. 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.3

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

 

Shipment

Room temperature

Dry ice

 

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

Amplification

iCS-digital PSC
every 5 passages

STR

Mycoplasma

Amplification

iCS-digital PSC
every 5 passages

STR

Mycoplasma

 Differentiation
monitoring

iCS-digital PSC

Mycoplasma

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

Acquisition
of a new line

Duo iCS-Karyo

Stem-Seq™ range

STR

Clone
screening

iCS-digital PSC

STR

Amplification & Maintenance

iCS-digital PSC
every 5 passages

STR

Bank characterization

Duo iCS-Karyo

Stem-Seq™ range

STR

Clone
screening

iCS-digital PSC

STR

Amplification & Maintenance

iCS-digital PSC
every 5 passages

STR

Bank characterization

Duo iCS-Karyo

Stem-Seq™ range

STR

 Differentiation
monitoring

iCS-digital PSC

SMART database

In order to accurately target the abnormalities relevant for hPSC researchers, Stem Genomics specifically analysed the data from 132 scientific publications concerning 1485 hPSC samples. After exclusion of polymorphic variants, we highlighted the presence of 949 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

EditCo Bio
| Alexander Brown, Associate director, Scientific Development and Montse Morell, Director of scientific development.
“We evaluated a lot of karyotyping technologies and only Stem Genomics’ digital PCR-based assay enabled the scalability, sensitivity, repeatability, and speed we needed to rapidly iterate and improve our processes. In addition, we have automated much of our cell-editing workflow and we found that only this technology was compatible with the speed and scale that we wanted in-house”.  
,,
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”.  
,,
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.
,,
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.
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Published scientific articles
citing the iCS-digital™ PSC assay

2023

Lab Resource: Single Cell Line Generation of an induced pluripotent stem cell line (ITXi012-A) from a patient with genetically determined high-lipoprotein(a) plasma levels

Amandine Caillaud a, Lise Bray a, Aurore Girardeau a, Zoé Begué-Racapé a, Lucie Vince a, Murielle Patitucci a, Cédric Le May a, Gilles Lambert b, Bertrand Cariou a, Antoine Rimbert a
a Université de Nantes, CHU Nantes, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France b Inserm UMR 1188 DéTROI, Université de La Réunion, Saint- Denis de La Réunion, France
2023

Establishment of induced pluripotent stem cells IRMBi005-A from a patient with sporadic Alzheimer’s disease

C. Clua Provost a 1, L. Auboyer b 1, A. Rovelet-Lecrux c, C. Monzo a, Eliot Schob a, S. Lehmann a, D. Wallon d, C. Crozet a b
a INM, Univ Montpellier, INSERM, Montpellier, France b Institute for Regenerative Medicine and Biotherapy (IRMB), Univ Montpellier, INSERM, CHU Montpellier, Montpellier, France c Normandie Univ, UNIROUEN, INSERM U1245, Rouen University Hospital, Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, F 76000 Rouen, France d Normandie Univ, UNIROUEN, INSERM U1245, Rouen University Hospital, Department of Neurology and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, F 76000 Rouen, France
2023

Lab Resource: Multiple Cell Lines Generation and characterization of novel human induced pluripotent stem cell (iPSC) lines originating from five asymptomatic individuals carrying the PLN-R14del pathogenic variant and a non-carrier relative

Valentina Balducci a 1, Francesco Scardigli b 1, Magdalena Harakalova b c, J. Peter. van Tintelen d, Pieter A. Doevendans b e, Kevin D. Costa f, Irene C. Turnbull f, Joost P. G. Sluijter b c, Francesca Stillitano b c f
a Department of Neurosciences, Psychology, Drugs and Child Health, University of Florence, Florence, Italy b Department of Cardiology, Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands c Regenerative Medicine Utrecht, Circulatory Health Research Center, Utrecht University, Utrecht, The Netherlands d Department of Genetics, University Medical Center Utrecht, The Netherlands e Netherlands Heart Institute, Utrecht, The Netherlands f Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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.
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.
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.
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.
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.
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.
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.
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.
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.
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