Human pluripotent stem cells (hPSCs) have transformed regenerative medicine, disease modeling, and drug discovery. From generating patient-specific cell therapies to uncovering insights into complex disease mechanisms, these cells play a central role in advancing biomedical research. But to make a meaningful impact, researchers must be confident in the identity and quality of the hPSCs they use.
Researchers need to confirm cell line identity, verify genomic stability, assess functional pluripotency, and routinely screen for contamination, including mycoplasma. Without these safeguards, even the most carefully designed studies can be compromised.
To help address these risks, the International Society for Stem Cell Research (ISSCR) has established standards for the use of human stem cells that outline best practices for quality control, characterization, and documentation1. While the ISSCR standards do not mandate specific assays, they serve as an important guide for researchers, emphasizing the need for cell line authentication, genetic stability assessment, contamination monitoring, and functional validation to support research integrity and reproducibility.
To help with implementation of these best practices, WiCell’s new QC and Derivation Bundles bring key ISSCR-recommended testing approaches together in a practical format to help labs verify the identity, stability, and pluripotency of their hPSC lines.
The QC Bundle: Core Quality Control for hPSC Research
WiCell’s QC Bundle brings together three key assays recommended by ISSCR to confirm cell line identity, genetic stability, and monitor culture health. The QC Bundle includes karyotyping, STR profiling, and mycoplasma testing.
STR Profiling
Cell line misidentification, contamination, or poor annotation affects scientific reproducibility and can invalidate research results. An estimated 18-36% of all cell lines in use today are misidentified or contaminated2. There are currently 593 misidentified cell lines listed on the ICLAC registry.
Short Tandem Repeats (STR) are short DNA sequences that are highly variable between individuals, allowing for the identification of different samples from one another. STR profiling using the Promega PowerPlex® 16HS system can be used to authenticate cell line identity and detect unwanted cross-contamination.
- STR polymorphisms across 15 loci plus a sex determination marker (amelogenin)
- Probability of matching identity to an existing STR profile
- Detection of cell line cross-contamination at levels of approximately 2–5%
Karyotyping
Over time, hPSCs can acquire genetic abnormalities during routine culture. Cytogenetic karyotyping using G-band analysis provides a comprehensive visual overview of the entire chromosome complement and enables the detection of chromosomal abnormalities and large-scale genomic changes at a single cell level that can affect cellular behavior.
- Microscopic genomic abnormalities (>5-10 Mb)
- Inversions
- Duplications/deletions
- Balanced and unbalanced translocations
- Aneuploidies
- >10% mosaicism (for example: cultures where >1 of 10 cells are trisomy 12)
Mycoplasma Detection (PCR)
Mycoplasma contamination can alter hPSC behavior, affecting protein synthesis, cellular metabolism, and experimental outcomes. An estimated 18-31% of cell cultures are contaminated with mycoplasma3. PCR-based detection using the EZ-PCR Mycoplasma Test Kit enables sensitive and reliable identification of contamination.
- 96 species of mycoplasma contamination from stem cell cultures
- Sensitivity (5-100 CFU/ml)
The QC Bundle is Recommended for: routine hPSC culture monitoring, validation of newly acquired cell lines, shared laboratory environments, and establishing baseline quality control for working cell banks and prior to downstream or translational applications.
The Derivation Bundle: Confidence from the Start
The Derivation Bundle is geared towards for newly derived human pluripotent stem cell lines, adding functional validation on top of core QC assays. It includes karyotyping, STR profiling, mycoplasma testing, and pluripotency testing to provide a comprehensive assessment of a new line’s identity, genomic stability, and functional potential.
Pluripotency testing begins with assessment of the undifferentiated state. to confirm the self-renewal status of stem cell lines by measuring the expression of Oct4 and Nanog. The dual expression of these markers serves as a clear indicator of the undifferentiated state. Pluripotent potential is then evaluated through in vitro differentiation into the three embryonic germ layers, followed by marker expression analysis via flow cytometry to confirm hPSC pluripotency. This is a practical and reliable alternative to xenograft (teratoma) assays4.
The Derivation Bundle aligns with ISSCR guidance for documenting the identity, integrity, and function of new stem cell lines.
Best for:
- Newly derived hPSC lines
- Repository submission and sharing
- Early-stage translational research
- Establishing baseline QC before differentiation, gene editing, or expansion
- Characterizing master stem cell banks (MCBs) for future use
cGMP Testing Options Available
For projects advancing toward translational or clinical applications, WiCell offers cGMP versions of select assays, including karyotyping, STR profiling, as well as Fluorescence In Situ Hybridization (FISH). These services provide enhanced documentation and process controls to meet regulatory quality and compliance expectations.
Make Routine QC Monitoring Part of Your Workflow
Whether you’re maintaining established cell lines or deriving new pluripotent stem cell lines, WiCell’s testing bundles make it easy to safeguard your research while saving time and resources.
Order the QC and Derivation Bundles today and receive a 5% discount on your order.
References
- Ludwig TE, Andrews PW, Barbaric I, et al. ISSCR standards for the use of human stem cells in basic research. Stem Cell Reports. 2023;18(9):1744-1752. doi:10.1016/j.stemcr.2023.08.003
- Horbach, S. P. J. M., & Halffman, W. (2017). The ghosts of HeLa: How cell line misidentification contaminates the scientific literature. PloS one, 12(10), e0186281. https://doi.org/10.1371/journal.pone.0186281
- Corral-Vázquez C, Aguilar-Quesada R, Catalina P, et al. Cell lines authentication and mycoplasma detection as minimum quality control of cell lines in biobanking. Cell Tissue Bank. 2017;18(2):271-280. doi:10.1007/s10561-017-9617-6
- International Stem Cell Initiative. Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells. Nat Commun. 2018;9(1):1925. Published 2018 May 15. doi:10.1038/s41467-018-04011-3