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Digital PCR-based assay: an answer to chromosomal abnormality

Digital PCR, also known as dPCR, was first described by Sykes et al. in 1992 (Sykes et al., n.d.), and although it has been around for a while, it is not as widely practiced as qPCR worldwide. Qualified as a “robust technique”, those who have made the switch appreciate the precision and sensitivity it offers. Particularly relevant for certain fields, it has emerged as a reliable technique for quantifying target sequences and identifying rare variants. It was therefore a logical choice for Stem Genomics’ founders back in 2018.

iPSCs high proliferation rate increases the risk of occurence of genetic abnormalities

Advice on iPSC testing methods for practical and reliable in-process assays

Why it is important to routinely test your iPSC lines for genomic abnormalities… and what you risk if you don’t! Find out why you should regularly test throughout the cell culture process, at which rate and get help on identifying the right technologies to keep time and costs under control. This article will provide you with the answers and the reassurance on quality control that you need.

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

PSC workflow: Introducing practical guidelines for regular in-process testing of PSC lines

It is widely recognised that Pluripotent Stem Cells (PSCs) need close monitoring to ensure their genomic integrity throughout prolonged cultures. However, the challenge remains in putting the theory into practice: How frequently should PSCs be tested? And which steps are critical in the process? In this article, we provide specific guidelines for the genomic integrity characterisation of PSCs. They are based on recognised publications and on Stem Genomics’ experience in PSC quality testing.

Picture of a chromosome

Why you should care about 20q chromosomal abnormality

In this article, you'll find out about the most commun genetic defect in hPSCs found on the chromosome 20q11.21. We'll explain why it is an important abnormality to detect and provide you with advice on the technologies you should be using to that effect.

CRISPR/Cas-9 gene editing can pose a threat to genomic integrity

CRISPR/CAS9 Gene Editing: a threat to genomic integrity

The discovery and recent advances in the CRISPR/Cas9 gene-editing technology have profoundly reshaped the field of genome engineering and allowed the generation of a wide range of mutant cell lines at an unprecedented rate. However, CRISPR/Cas-9 gene editing in hPSCs can also pose a threat to the overall genomic integrity.

Stem Genomics is ISO9001:2015 certified
Big milestone for the team here at Stem Genomics: we have received the ISO 9001:2015 certification! This is an internationally recognised standard that ensures that our products and services meet our clients’ needs through an effective quality management system. Although it represented a rather colossal effort, everyone involved was driven by the conviction that implementing a system of continual improvement in all our processes would result in numerous benefits for our clients. This is the list of reasons that drove us to take on this journey: - Commitment to providing high-quality and consistent services to our existing and future clients - Ensure our clients’ satisfaction in relation with the efficiency of our operations: we have put futureproof processes in place to withstand the constantly changing environment we navigate in, - Show compliance with regulatory requirements and the evolving needs of our customers and their markets so we can better meet them, - Anticipate and prevent non-conformities, which we can’t afford to have with the demanding markets we address, - Remain competitive and relevant with our product and service developments operating within an established framework inspired by best business practices, - Involve and unite the team behind a shared goal. We are confident this recognised quality management system will enable our biotechnology company to provide the peace of mind our clients require when using our tests and services.

Digital-PCR technology

Digital PCR: the most accurate PCR method for assessing the genetic integrity of Stem Cells

Digital PCR is the most accurate PCR method for assessing the genetic integrity of stem cells through the detection of Copy Number Variants (CNVs). At Stem Genomics, we help you assess the genetic integrity of your stem cell lines with digital PCR-based tests designed to suit your organization and the specific features of your cell lines.

The most recurrent abnormality in hPSCs
Many of you asked for a test that would focus on the most common abnormality in hPSCs. So, we made it! You can now detect specifically the sub-karyotypic 20q11.21 amplification, which represents >20% of recurrent genomic abnormalities in hPSCs, with a rapid, sensitive and easy-to-use digital PCR kit.

iCS-digital kit and software
Stem Genomics diversifies its offer by launching the iCS-digital TM PSC kit, allowing you to perform this test, already offered in service for more than 2 years, in your facilities. The iCS-digital TM PSC kit is a precise, fast and sensitive digital PCR test for the detection of more than 90% of the recurrent genomic abnormalities in hPSCs. The iCS-digital TM PSC kit includes eight multiplexed PCR assays that allow the reliable analysis of the 24 regions with the most frequent Copy Number Variations (CNVs) reported in hPSCs. The kit also includes a validated normal genomic DNA control (XY). Data processing, statistical analysis, and graphical representation of the results can be performed in an automated and explicit way using the iCS-digital TM software provided online by Stem Genomics to help users with data interpretation.

The iCS-digital test now published  in Stem Cell Reports
Recurrent Genetic Abnormalities in Human Pluripotent Stem Cells: Definition and Routine Detection in Culture Supernatant by Targeted Droplet Digital PCR In the article published in Stem Cell Reports in January 2020, Assou et al. demonstrate the interest of the iCS-digital TM test for routine human pluripotent stem cell (hPSC) screening. Thanks to the specificity of the digital PCR (dPCR) probe panel, the simplicity of sample collection, and the accuracy of the ddPCR technology, this test allows the fast and straightforward monitoring of hPSC integrity. This innovative test can change how hPSC quality controls are implemented for basic research and cell therapy by increasing the test frequency to secure cell productions and avoid expensive and time-consuming cell cultures. The iCS-digital TM test is exclusively provided by Stem Genomics as a full service. To request technical information or ask for a quote, please follow this link : Link to the publication Discover the test and request a quote

The iCS-digital TM test is a straightforward method for screening human pluripotent stem cell (hPSC) clones after CRISPR gene editing
The iCS-digital TM test offers fast and reliable detection of the most common genomic abnormalities in CRISPR/Cas9-edited hPSCs By combining human pluripotent stem cells (hPSCs) and the CRISPR/Cas9 genome editing technology, new opportunities are created to study disease mechanisms, with enormous therapeutic potential. Despite the progress in genome engineering, the CRISPR gene editing process consists of major sequential and potentially stressful events, such as clonal expansion, FACS enrichment, drug selection, manual colony picking or stressful single-cell dissociation. By triggering selective pressures on cells, these procedures could favour the generation and selection of genetically abnormal hPSCs, and consequently render these cells unsuitable for further use. Therefore, efficient and rapid screening of CRISPR-modified hPSCs is essential before their use for research purposes or clinical applications. Discover the test and request a quote

28.5% of hPSC samples tested using the iCS-digital PSC test are abnormal
iCS-digital: A method for monitoring hPSC genome integrity that detects more than 90% of recurrent genomic abnormalities. The test is rapid (2-3 days), convenient (full service), straightforward, and can be performed using cell culture supernatant. It is particularly suitable for the routine monitoring of cell lines in culture and for screening genetically stable clones (e.g., CRISPR-edited iPSC clones, patient-derived iPSC clones…).

The Ed-digital PCR test directly informs on the presence and number of transgenes copies  inserted in the genome of CRISPR-edited cells
Thanks to its flexibility and ability to achieve precise targeting, the CRISPR system is a powerful gene editing tool for various molecular biology applications. Precise control of the transgene integration is a major challenge for human cell research biosafety. Despite the improvement of CRISPR specificity, a significant proportion of transgenes integrates at unintended sites. These off-target insertions can cause genomic alterations that may disrupt normal cell functions with dramatic consequences on research outcomes. Therefore, it is crucial to verify the transgene presence at the desired genome site using PCR or sequencing, and also to confirm the absence of any possible additional unwanted insertion using Ed-digital, Stem Genomics digital PCR test for transgene copy number quantification. Ed-digital services The Ed-digital test allows the detection of the number of transgene copies present in the genome of gene-edited cells using digital PCR. Ed-digital targets common resistance cassettes (puromycin, neomycin) as well as the fluorescent reporter gene mCherry. Examples of Ed-digital applications in gene-edited induced pluripotent stem cell (iPSC) lines Analysis of transgene integration in iPSC lines (graph on the left): A. Determination of the number of neomycin gene copies in two iPSC samples. The first sample carries two copies and the second one single copy of the transgene. B. Determination of puromycin gene copies in two iPSC samples. The first one carries two copies and the other one displays mosaic integration (n=2.5) of the transgene. Discover the test and request a quote

straightforward method for monitoring hPSC genome integrity
Now online “Recurrent genetic abnormalities in human pluripotent stem cells: definition and routine detection in culture supernatant by targeted droplet digital PCR” by Assou et al. The unique features of human pluripotent stem cells (hPSCs) open new opportunities for disease modeling, drug discovery and the development of cell-based therapies. However, genetic abnormalities can accumulate during the generation, long-term maintenance or during genome editing of these cells. Therefore, it is crucial to detect these abnormalities as soon as they appear to guaranty the safe and proper use of hPSCs in clinical practice and in research. To address this issue, Assou et al. performed an exhaustive study by combining data from publications describing the occurrence of hPSC aberrations during in vitro culture. Based on this large meta-analysis, a test called iCS-digital (in culture supernatant-digital PCR) has been designed consisting in a panel of digital PCR probes that target the most recurrent abnormalities identified by these studies. Thanks to the precision of the digital PCR technology, the iCS-digital test allows the sensitive and precise quantification of copy number variations (CNVs) and the detection of anomalies that are below the G-banding method resolution, especially the sub-karyotypic 20q11.21 hotspot. Using the iCS-digital test, Assou et al. could monitor cell integrity through regular screenings, and record the moment where genomic aberrations appeared. Furthermore, the iCS-digital test presents the advantage of using cell culture supernatant instead of intact cells as a DNA source, bypassing the inconvenience of dedicating a certain fraction of cell material for control quality testing. To conclude, Assou et al. demonstrated the interest of the iCS-digital test for routine hPSC screening, thanks to the simplicity of the collection procedure, the rapidity of the test, and the accuracy of the digital PCR technology. This innovative test can change how hPSC quality control is implemented for their use in basic research, regenerative medicine, and can contribute to secure genome editing workflows. The iCS-digital TM test is exclusively provided by Stem Genomics as a full service. For more information and quotations, please follow these links: Download the publication Discover the test and request a quote

The iCS-digital TM test was used to evaluate the genomic integrity of hiPSCs in the work published by Neri et al. in Nature Communications in April 2019: "Human pre-valvular endocardial cells derived from pluripotent stem cells recapitulate cardiac pathophysiological valvulogenesis". https://www.nature.com/articles/s41467-019-09459-5

new website Stem Genomics made by Caconcept
Stem Genomics has launched its new website and we are excited to present its new look. Our new website provides a clear message about who we are, what we stand for and about our solutions. The website also boasts a clean design and intuitive and consistent site-wide navigation system with improved menu functionalities that direct you to the most relevant information for your needs. It is also fully responsive on mobile devices, and the website pages are easy to navigate using a wide range of web browsers and portable devices.

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