Abstract
Culturing stem cells for an extended period of time can lead to acquired chromosomal aberrations. Determining the copy number variant (CNV) profile of stem cell lines is critical since CNVs can have dramatic effects on gene expression and tumorigenic potential. Here, we describe an improved version of our StemArray, a stem-cell-focused comparative genomic hybridization (aCGH) microarray, which contains 135,000 probes and covers over 270 stem cell and cancer related genes at the exon level. We have dramatically increased the median probe spacing throughout the genome in order to obtain a higher resolution genetic profile of the cell lines. To illustrate the importance of using the StemArray, we describe a karyotypically normal iPSC line in which we detected acquired chromosomal variations that could affect the cellular phenotype of the cells. Identifying adaptive chromosomal aberrations in stem cell lines is essential if they are to be used in regenerative medicine.
Highlights
Several studies have demonstrated that human embryonic and induced pluripotent stem cells (ESCs, iPSCs) acquire genomic abnormalities during prolonged culture [1,2,3]
IPSC lines are generally derived by transforming fibroblast cells with retroviral vectors containing OCT4, SOX2, KLF4, and c-MYC [10]
These genes provide good positive controls for iPSC array-based comparative genomic hybridization (aCGH) data since multiple copies of these transgenes integrate into the DNA
Summary
Several studies have demonstrated that human embryonic and induced pluripotent stem cells (ESCs, iPSCs) acquire genomic abnormalities during prolonged culture [1,2,3]. These chromosomal aberrations can have dramatic effects on the survival, proliferative ability, and differentiation potential of the cells, which can result in unreliable experimental results and jeopardize their potential use in regenerative medicine. The most common method used by stem cell researchers to monitor the genomic stability of the cell lines is G-banded karyotype analysis. The use of the 12 × 135 K array platform, which allows 12 samples to be run per slide, significantly reduces the costs of the array and makes it competitive in pricing with karyotype analysis
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