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Characterizing the Genetic Stability of Human Naïve and Primed Pluripotent Stem Cells

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Human Naïve Pluripotent Stem Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2416))


The presence of genetic changes in human pluripotent stem cells (hPSCs) can affect their behavior and impact on the utility of hPSC-based applications in research and clinic. The spectrum of spontaneously arising genetic abnormalities in hPSCs is wide and ranges from numerical and structural chromosomal anomalies down to point mutations. The detection of genetic changes in hPSCs is confounded by the fact that no single method detects all types of abnormalities with the same accuracy and sensitivity, therefore necessitating the use of a combination of different methods. Here, we provide detailed protocols for two methods commonly utilized for the detection of genetic changes in naïve and primed hPSCs: karyotyping by G-banding and fluorescent in situ hybridization (FISH).

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  1. Thomson JA, Itskovitz-Eldor J, Shapiro SS et al (1998) Embryonic stem cell lines derived from human blastocysts. Science 282:1145–1147

    Article  CAS  Google Scholar 

  2. Takahashi K, Tanabe K, Ohnuki M et al (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131:861–872

    Article  CAS  Google Scholar 

  3. Andrews PW, Ben-David U, Benvenisty N et al (2017) Assessing the safety of human pluripotent stem cells and their derivatives for clinical applications. Stem Cell Rep 9:1–4

    Article  Google Scholar 

  4. Draper JS, Smith K, Gokhale P et al (2004) Recurrent gain of chromosomes 17q and 12 in cultured human embryonic stem cells. Nat Biotechnol 22:53–54

    Article  CAS  Google Scholar 

  5. Amps K, Andrews PW, Anyfantis G et al (2011) Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol 29:1132–1144

    Article  CAS  Google Scholar 

  6. Merkle FT, Ghosh S, Kamitaki N et al (2017) Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 545:229–233

    Article  CAS  Google Scholar 

  7. Avior Y, Lezmi E, Eggan K, Benvenisty N (2021) Cancer-related mutations identified in primed human pluripotent stem cells. Cell Stem Cell 28:10–11

    Google Scholar 

  8. Baker D, Hirst AJ, Gokhale PJ et al (2016) Detecting genetic mosaicism in cultures of human pluripotent stem cells. Stem Cell Rep 7:998–1012

    Article  CAS  Google Scholar 

  9. Guo G, von Meyenn F, Santos F et al (2016) Naive pluripotent stem cells derived directly from isolated cells of the human inner cell mass. Stem Cell Rep 6:437–446

    Article  CAS  Google Scholar 

  10. Bredenkamp N, Yang J, Clarke J et al (2019) Wnt inhibition facilitates RNA-mediated reprogramming of human somatic cells to naïve pluripotency. Stem Cell Rep 13:1083–1098

    Article  CAS  Google Scholar 

  11. Halliwell J, Barbaric I, Andrews PW (2020) Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat Rev Mol Cell Biol 21:715–728

    Article  CAS  Google Scholar 

  12. Olariu V, Harrison NJ, Coca D et al (2010) Modeling the evolution of culture-adapted human embryonic stem cells. Stem Cell Res 4:50–56

    Article  Google Scholar 

  13. Avery S, Hirst AJ, Baker D et al (2013) BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures. Stem Cell Rep 1:379–386

    Article  CAS  Google Scholar 

  14. Price CJ, Stavish D, Gokhale PJ et al (2021) Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition. Dev Cell S1534-5807(21)00602-X

    Google Scholar 

  15. Shaffer LG, McGowan-Jordan J, Schmid M (2013) ISCN 2103: an international system for human cytogenetic nomenclature (S. Karger)

    Google Scholar 

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This work was supported by the grant from the UK Regenerative Medicine Platform, MRC reference MR/R015724/1.

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Correspondence to Ivana Barbaric .

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Baker, D., Barbaric, I. (2022). Characterizing the Genetic Stability of Human Naïve and Primed Pluripotent Stem Cells. In: Rugg-Gunn, P. (eds) Human Naïve Pluripotent Stem Cells. Methods in Molecular Biology, vol 2416. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1907-0

  • Online ISBN: 978-1-0716-1908-7

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