Genomic stability:
Karyotyping assays

Robust, fast and cost-effective genomic stability testing for the success of your research work

Stem cell research scientists need reassurance concerning the genomic stability of the cells they are using in their experiments. The validity of their research work relies in part on the implementation of a robust genomic quality control system.

Traditional karyotyping methods alone will not always provide the level of sensitivity required to reliably detect the most common abnormalities found in stem cells.

In addition, they are generally not suited to regular testing at each step that cells are put under stress due to their processing lead times.

With these constraints in mind, Stem Genomics has developed a range of tests to match your specific requirements and put your mind at rest.

The iCS-digital™ range: a sensitive detection solution, specifically designed for your cell type

The iCS-digital™ range has been designed to target specific abnormalities relevant to hPSCs & hMSCs, as well as aneuploidy detection. These assays use highly sensitive digital PCR (dPCR) technology, ideal for small size CNV detection that other traditional methods like G-Banding will miss.

The 5 main advantages of the iCS-digital™ range:

  1. Speed: you can get your results within 3 days or even faster if you use our in-house kit.
  2. Robustness: you get a high level of confidence in your results thanks to the high sensitivity of dPCR combined with our specific set of probes.
  3. Cost effectiveness: Cheaper than G-Banding, the iCS-digital™ range enables you to test more regularly during culture, or introduce an entry level genomic screening in your process.
  4. Convenience: you can choose to do it yourself or have us perform the service for you. Regarding the service, you have several easy options to choose from to send your samples: genomic DNA, cell pellets or cells in fresh culture media (or in cell culture supernatant).
  5. Straightforward results: you get easy data analysis and interpretation of results delivered to your inbox when you choose the service, or you can download the results from the iCS- digital™ software with your kit.

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

Detect over 80% of recurrent abnormalities in hMSCs in record-breaking time !

Detect aneuploidy in any
human cell type in
record-breaking time !

A combined solution for hPSCs only

The Duo iCS-Karyo assay* will provide you with a combined G-Banding and iCS-digital PSC solution for assessing the genomic integrity of your cells with high precision.

4 main advantages:

  1. High-resolution detection: identify the most recurrent altered regions in hPSCs, including the sub-karyotypic 20q.11.21 abnormality.
  2. Exhaustivity: G-Banding will provide you with an exhaustive structural and numerical variant analysis.
  3. Peace of mind: we provide full processing services from simultaneous metaphase chromosome preparation and DNA extraction to the final report.
  4. Straightforward results: you will get both assay results sent to you at the same time with a fully interpreted report.

* Only available in Europe and North America. Outside these geographical locations, you can combine your traditional G-Banding analysis with our iCS- digital™ PSC solution.

If you only need a G-Banding analysis to be performed, please follow this link. 

The ultimate combined solution for hPSC in-process genomic stability testing

The Stem-Seq™ range: sequence multiple genes simultaneously and get a clear and meaningful interpretation

The Stem-Seq™ Panel enables stem cell scientists to look deeper into targeted regions of interest. Based on NGS technologies, the Stem-Seq™ Panel detects Single-Nucleotide Variants (SNVs) associated with cancer (including TP53, BCOR, etc.), but also selected variants specific to pluripotent stem cells and their impact on the natural development of cells in culture.

Stem-Seq™ Plus offers a more comprehensive analysis including the molecular abnormalities detection from the Stem-Seq™ panel (SNVs) as well as the chromosomal abnormalities detection of Copy Number Variations (CNVs) on the whole cell.

The 5 main advantages of the Stem-Seq™ range:

  1. A custom-made panel: 361 genes selected for their relevance to stem cell researchers, and particularly hPSC research scientists, whose cells are the most prone to genomic abnormalities.
  2. High-performance: its high resolution and average coverage of 1000x ensure you can identify SNVs and Indels at up to 2% mosaicism/VAF and 20% for CNVs.
  3. Several levels of reports: from filtered to fully interpreted, get a clear interpretation of significant variants and the potential pathogenicity on your cells.
  4. Convenience: all you need to do is send genomic DNA at room temperature and we handle the whole process for you.
  5. Speed: Analysis available starting from 1 sample so you do not need to wait for other samples before processing begins!

Look deeper into any human cell type and detect targeted SNVs & CNVs

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”.  
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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”.  
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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.
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The Regenerative Medicine Center Utrecht
| Renee Maas, PhD candidate
Since establishing a QC strategy involving iCS-digital™ PSC, we realized that the 20q appears very often. We really did not expect it to be present so frequently! This led us to implement iCS-digital™ PSC every 10 passages.
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Toxys
| Luke Flatt, Senior Scientist
“The iCS-digital™ PSC test enabled us to efficiently monitor the genomic stability of iPSC lines that are crucial for our in vitro toxicity assays. The high quality of the results and short turn-around times provided by Stem Genomics helps us to ensure the quality of our cell-based assays and services to our clients”.
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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.
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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.
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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.
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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.
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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.
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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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