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The Stem-Seq™ range:
In-depth genomic knowledge
without the data overload

Expand your genomic knowledge using advanced sequencing technology

Human stem cells can develop molecular and genomic abnormalities, arising at a very low level of mosaicism. These defects, primarily Copy Number Variations (CNV) and Single Nucleotide Variants (SNV), need to be identified as quickly as possible in the process, as they can rapidly develop and overtake cell cultures. Their impact can be detrimental to the quality of the final product.

With the advent of cutting-edge technologies such as next-generation sequencing (NGS), the ability to detect novel abnormalities has greatly improved. Unlike traditional methods such as G-banded karyotyping, which are less sensitive and have limited resolution, NGS can detect variants with unprecedented precision. This new technology is making a significant contribution to our understanding of genomic variation and its potential impact in various clinical and research settings.

However, the main constraint of this method is the vast amount of information it can generate. This turns result interpretation into a time consuming and challenging exercise for most teams.

This is what led Stem Genomics to design a range of NGS-based sequencing assays with fully interpreted results that mean something to you.

View key specifications

Discover the Stem-Seq™ range in video

Watch short videos for a visual presentation of our latest NGS-targeted assays and discover the main benefits they offer scientists working on stem cells.

Stem-Seq™ Panel: Detect SNVs with a panel of 361 genes

Stem-Seq™ Plus: detect CNVs and SNVs in just one test.

A deeper understanding of targeted regions of interest

Based on innovative NGS technology, the Stem-Seq™ range enables scientists to target copy number variations (CNVs) throughout the genome and specific genes for single nucleotide variants (SNV detection). This is particularly suited to pluripotent stem cell scientists who encounter the highest level of mutations in their cells.

2 levels of tests:

  1. Stem-Seq™ Panel: a custom-made, targeted NGS panel composed of 361 genes that have been selected for their relevance to stem cell scientists. It 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.
  2. Stem-Seq™ Plus: it includes the Stem-Seq™ Panel for SNV detection as well as the additional capability to detect copy number variations (CNVs) across the entire genome. This powerful assay will allow the detection of CNVs in regions that may not have been considered previously or that could harbor unexpected variations. This comprehensive and unbiased view adds significant information on the genomic stability of your cells.

A clear and meaningful report

Once sequencing has been completed, our expertise continues to add value to the end result. No need to have a team of in-house bioinformaticians or dedicate time for deciphering and interpreting results. Our specialists 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 the copy number variation (CNV) analysis, our expert team will prioritize your variant by comparing it against Stem Genomics’ proprietary database (Smart database) and the ACMG (American College of Medical Genetics and Genomics) classification standards. Your data will be thoroughly scrutinized to ensure the most accurate and clinically relevant findings for your specific application.

Stem-Seq™ Panel key specifications at a glance

  • A wide range of 361 genes with known associations to cancer according to recognized database references (including TP53, etc.), and genes known to be recurrently mutated in hPSC (Salomonis N. et al. 2016, Merkle et al. 2020, Avior et al. 2020, Merkle et al. 2022).
  • Deep sequencing of targeted genes with 1000x coverage, and a high resolution of 1% mosaicism/VAF to capture SNVs and Indels.
  • 2 levels of reports: automatically or fully interpreted.
  • Delivery in 4-5 weeks (depending on the report option selected).
  • Just send your gDNA sample at room temperature.
  • Analysis available starting from 1 sample so you do not need to wait for other samples before processing begins!
See list of genes
Cell types

All human cell types

Stages

Acquisition of a new line

Bank characterization

End of process

Samples

gDNA

 

Shipment

Room temperature

Coverage

1000 x

Mosaicism

1%

Time

4-5 weeks depending on report selection

 

Available from 1 sample

Stem-Seq™ Plus key specifications at a glance

  • A comprehensive solution that combines both SNV and CNV detection in one assay.
  • SNVs and Indels capture: deep sequencing of targeted genes with 1000x coverage, and a high resolution of 2% mosaicism/VAF.
    • The panel contains 361 genes with known associations to cancer according to recognized database references (including TP53, etc.), and genes known to be recurrently mutated in hPSC (Salomonis N. et al. 2016, Merkle et al. 2020, Avior et al. 2020, Merkle et al. 2022).
  • CNV detection: deep sequencing across the genome with 1000x and a high resolution of 20% mosaicism*.
    • This sequencing approach uses a backbone and a Pool of Normal (PON) to enable a more accurate analysis of the large regions covered by CNVs and reduce false positives.
  • Several levels of reporting available from filtered to fully interpreted.
  • Delivery in 4 to 5 weeks, depending on the selected report.
  • Just send your gDNA sample at room temperature.
  • Analysis available starting from 1 sample so you do not need to wait for other samples before processing begins!

*A lower mosaicism can be obtained from the raw data that we will supply. However, we will not produce any interpretation under the 15-20% threshold.

Cell types

All human cell types

Stages

Acquisition of a new line

Bank characterization

End of process

Samples

gDNA

 

Shipment

Room temperature

Coverage

1000 x

Mosaicism

2% for SNVs

20% for CNVs*

300 kb

Time

4-5 weeks depending on report selection

 

*A lower mosaicism can be obtained from the raw data that we will supply. However, we will not produce any interpretation under the 20% threshold.

Available from 1 sample

A comprehensive service to make your life easier

Stem Genomics handles the whole process for you from receipt of DNA samples to the delivery of the results. The library is built using Twist capture technology and the sequencing is performed on Illumina NovaSeq as paired-end reads. The final analysis will be sent to you within 4-5 weeks depending on the level of reporting you need or the type of analysis required (SNV only or SNV + CNV).    

How it works:

Follow the step-by-step guidance to perform your assay: view useful documents

Practical testing guidelines

Recommended guidelines on genomic stability advise checking cells at various key steps in the workflow. Due to its exhaustivity and strong technical performance, the Stem-Seq™ range is best suited for the acquisition stage, when banking cells and/or at the end of the workflow. It strengthens the RUO process overall and supports the application for entering the clinical stage.

Click on the graphs below for more details

Guidelines for human Pluripotent Stem cell workflow

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

End
of process

Duo iCS-Karyo

Stem-Seq™ range

STR

Guidelines for human Mesenchymal Stromal cell workflow

workflow msc

Cell acquisition

G-Banding karyotype

Stem-Seq™ range

STR

Mycoplasma

Amplification

iCS-digital™ MSC

WCB

G-Banding karyotype

Stem-Seq™ range

STR

Mycoplasma

Clone screening

iCS-digital™ MSC

Amplification

iCS-digital™ MSC

WCB

G-Banding karyotype

Stem-Seq™ range

STR

Mycoplasma

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Upcoming webinar

Join us LIVE for our webinar “Genomic stability made easy” to discover how Stem Genomics has turned cutting-edge technologies into easy testing solutions accessible to most labs.

Get expert opinions and user perspectives on our genomic stability assays in the context of iPSC research.

Happening on Tuesday, November 14, 6 pm CET

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