The FDA’s latest draft guidelines on “Safety Testing of Human Allogeneic Cells Expanded for Use in Cell-Based Medical Products” recommend performing whole-genome sequencing (WGS) on cell banks of continuous cell lines and genome-edited cells, at a minimum read depth of 50x. While this represents an important regulatory baseline, a 50x WGS analysis has a key limitation: insufficient sensitivity for detecting low-level mosaicism. Since genomic abnormalities in hPSCs can arise at very low variant allele frequencies and rapidly expand to dominate a culture, early detection is critical. For this reason, Stem Genomics recommends complementing WGS with a targeted NGS (or dPCR test such as iCS-digital™ PSC) assay in your iPSC workflow is highly advisable.
Its significantly deeper detection provides the sensitivity needed to identify emerging variants that WGS at 50x would likely miss, adding a meaningful layer of robustness to your genomic safety strategy. WGS in turn will provide a broader analysis to a targeted approach that will ensure a comprehensive view of the cell genome. Together, this will efficiently de-risk your final cell product. At another level, if you face budget constraints, or if your entire QC process is audited by regulatory authorities, targeted NGS is an effective option either on its own, when regulatory guidelines is not the primary constraint, or combined with WGS for a robust quality control strategy.
As CNVs represent large regions of the genome, they are complex to analyze. Consequently, Stem Genomics introduced a backbone and a Pool of Normal (PON) in the Stem-Seq™ Plus assay to enable a more robust analysis of significant variants. The backbone of probes covers the entire genome. Combined with the PON, they enable data normalization between the target sample and the normal sample and effectively reduce background noise.
Specialists at Stem Genomics are committed to providing a comprehensive interpretation of single nucleotide variants (SNVs) by meticulously examining each variant in multiple databases such as Cosmic and ClinVar, as well as conducting an extensive literature review. In addition, for copy number variation (CNV) analysis, our team will prioritize your variant by comparing it against our proprietary database, the SMART database and the ACMG (American College of Medical Genetics and Genomics) classification standards.
Bioinformatics interpretation comes in several tiers, and it’s worth understanding what each one actually delivers. The first question is whether the analysis is fully automated or reviewed by a domain expert. Expert review matters because it’s what surfaces pathogenic variants and clinically relevant findings from the raw data a generic, automated interpretation with no bioinformatics support behind it won’t be of much use to you or your team.
A second consideration is analytical accuracy. Using multiple variant callers and filters reduces false positives, which are a common pitfall in WGS analysis. It’s also worth checking whether a given vendor supports downstream interpretation and any additional analysis you might need beyond the initial deliverables—not all of them do.
Finally, report clarity matters just as much as the analysis itself. Results should be presented clearly and accessibly, translating complex data into insights you can actually act on.
Yes, it is. We offer a transparent and comprehensive analysis process, starting with the provision of the raw data containing all the variants identified in your samples.
The price will depend on the level of interpretation you require for the reports. Discounts are also available for large volume orders.
The Stem-Seq™ range has been designed to provide pertinent information to all stem cell scientists working on human stem cells. It is particularly suited to pluripotent stem cell scientists who encounter the highest level of mutations in their cells.
These Stem Genomics’ assays are complementary. Together, they will strengthen your stem cell workflow genomic stability. The iCS-digital™ range is ideal for regular in-process checks during amplification and maintenance and detects CNVs. As for the Duo iCS-Karyo, it will de facto detect CNVs, but will also show aneuploidies or chromosomal structural abnormalities such as translocations and inversions. The Stem-Seq™ range will complement these two tests at acquisition, banking characterization or end of workflow. It will complement the analysis with the identification of potential SNVs (punctual mutations) and small insertions/deletions (indels).
In accordance with the ISSCR’s latest quality standard recommendations, Stem Genomics strongly recommends regularly checking the identity of your stem cells during their time in culture with our STR assay. Mycoplasma testing is also critical for robust science and we have a digital PCR solution called Myco-digital that can do that for you.
Comprehensive detection of SNVs, SVs/CNVs
Unparalleled interpretation by iPSC specialists
4-week turnaround
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Join us LIVE for a Q&A session on the latest iCS-digital™ PSC upgrade.
Find out what it means for you and ask all your questions
Juline VINCENT our R&D Project Manager and Digital PCR expert will answer you LIVE.
SAVE THE DATE: Thursday, November 7, 6pm CET/9am PDT/12 pm EDT.
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Best Practices: Making your hPSC Quality Control workflow more efficient
Join Juline VINCENT, our R&D Project Manager, as she presents efficient quality control strategies specifically designed to address the unique characteristics of pluripotent stem cells.
Thursday, October 23, 12:00 PM EST / 6:00 PM CET
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