Contributor: Dr Mahfuz Chowdhury
Ideally, hESC (human Embryonic Stem Cell) or hiPSC (human induced Pluripotent Stem Cell) has the capability to grow indefinitely. However, hESC/hiPSCs frequently acquire genetic changes during culture, setting a limit on their culture duration.
Genetic changes in hESCs/hiPSCs during the culture can have various irreversible effects on them and their differentiated progeny, e.g., altered growth rate, tumorigenicity, differentiation potential, and functionality, which may significantly impact the reproducibility of stem cell research.
Timing of genomic assessment
To address impact of culture acuired genetic changes on research reproducibility, ISSCR Standards for Human Stem Cell use in Research recommend:
to start experiment by using genetically assessed hESC/hiPSC Master Cell Bank (MCB) or Working Cell Bank (WCB)
during the timespan of experiments, assessing genomic integrity
if any alterations are observed in the growth characteristics of stem cells or in their differentiation pattern
after any major culture bottoleneck e.g., gene editing and clonal cell line establishment
after every 10 passages
genomic assessment at the end of the experimental batch even if hESCs/hiPSCs passaged < 10 times.
Genomic assessment assays
No single assay detects all types of genetic changes with equally high sensitivity and specificity and this area is constantly evolving. Therefore, when choosing an assay for genomic assessment, the specificity and detection limits as well as its trend and update need to be considered. Detail on some assays for genetic assessment is provided in Table A5.2 in ISSCR Standards for Human Stem Cell use in Research.
StemCore provides two assays that are complementary because of their resolution:
hPSC Genetic Analysis Kit - STEMCELL Technologies that detect most common Copy Number Variation (CNV) at chromosomes 1q, 4p, 8q, 10p, 12p, 17q, 18q, 20q, Xp
Karyostat Assay
Karyostat HD Assay
In collaboration with partners, StemCore can provide other genomic assessment assays (e.g., whole genome sequencing). For more, please email at stem.core@uq.edu.au.
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