Human Stem Cell Karyotyping and Digital PCR

For human stem cells, we recommend our Standard G-band Chromosome Analysis.  This service includes brief cell culture, processing to arrest the cells in metaphase, cell fixation, preparation of stained/banded slides, and microscope analysis of the karyotypes of 20 chromosome spreads.

The final report of 20 metaphase chromosome spreads includes:

  • Information on chromosome count and gender
  • Description of any aberrations detected (deletions, additions, breaks, translocation trisomies, monosomies, duplication, inversions, isochromosomes, polyploidy, and more)
  • A written summary of the findings
  • One representative karyotype image
  • Typical turnaround time of 10 business days (Saturdays, Sundays, and Federal Holidays excluded from TAT)
  • Work performed in the spirit of Good Laboratory Practice (GLP)

Other information to consider:

  • Discounts for academic, non-profit research institution, and government labs
  • Volume discounting available
  • Option to submit cryopreserved samples for an extra fee (with longer turnaround time)
  • Rush service available for an extra fee
  • Additional images may be included for an extra fee
  • Additional spreads may be analyzed for an extra fee
  • Add on the digital PCR assay below for an extra fee

We will customize to your needs.  Please email [email protected] with special requests.

Human Stem Cell Karyotyping Plus Digital PCR Package – Duo iCS-Karyo

Human Pluripotent Stem Cells (hPSCs) are prone to developing genetic aberrations during their time in culture.  Variants that arise can rapidly become predominant in cell cultures, thus compromising research studies.  While traditional G-band karyotyping provides thorough structural and numerical variant analysis, and is able to detect defects down to the level of 5 to 10 Megabases, digital PCR has the ability to detect even smaller aberrations.  Each of these assays, karyotyping and digital PCR, covers a range of detection that the other cannot. For example, G-band karyotyping is able to detect balanced translocations and inversions, however, as there is no change in gene copy number with these defects and only rearrangement of DNA, digital PCR is not able to detect them.  Therefore, we highly recommend both assays to verify the genomic integrity of your stem cells.

Consider ordering Duo-iCS-karyo, the combination package of G-band karyotyping and digital PCR

From one cell sample submission, we are able to perform both the G-band karyotype analysis and also the digital PCR assay, in conjunction with our partner, Stem Genomics.  Twenty four different probes for the most frequent abnormalities found in human pluripotent stem cells will be assayed by state of the art digital PCR. Included in this panel is assessment of the chromosome 20q11.21 band amplification which is too small to be detected by G-band karyotyping. This chromosome 20q variant has been detected in more than 20% of the worldwide cultured human pluripotent stem cells making it the most common genetic abnormality in hPSC’s.  (Avery et al., 2013; Halliwell et al., 2020)  The final analysis will be sent to you by email within approximately 10 working days of receipt of your live cells.  The final report will consist of a full interpretation of the results with representative images and a summary of the analysis.


Halliwell, J. Barbaric, I., and Andrews, P.W.  Acquired genetic changes in human pluripotent stem cells: origins and consequences.  Nature Reviews Molecular Cell Biology 21, 715 – 728. (2020)

Avery, S., Hirst, A.J., Baker, D., Lim, C.Y., Alagaratnam, S., Skotheim, R.I., Lothe, R.A., Pera, M.F., Colman, A., Robson, P., Andrews, P.W., and Knowles, B.B.  BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures.  Stem Cell Reports 1 (5), 379-386, 2013.