Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles

• Published in: Nature protocols Vol. 8; no. 5; pp. 989 - 997
• Main Authors: Ben-David, Uri, Mayshar, Yoav, Benvenisty, Nissim
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.05.2013; Nature Publishing Group
• Subjects: 38/61; 45/100; 631/114; 631/1647/1407/1405; 631/1647/2217/2018; 631/532/2064; Analytical Chemistry; Biological Techniques; Chromosome Aberrations; Chromosome abnormalities; Chromosomes; Computational Biology; Computational Biology/Bioinformatics; Databases, Genetic; Deoxyribonucleic acid; DNA; Gene expression; Genetic aspects; Genetic engineering; Genomes; Genomic Instability; Genomics; Karyotyping; Karyotyping - methods; Laboratories; Life Sciences; Methods; Microarrays; Oligonucleotide Array Sequence Analysis; Organic Chemistry; Physiological aspects; Pluripotent Stem Cells; Protocol; Risk factors; Stem cell research; Stem cells; Transcriptome; United States
• ISSN: 1754-2189; 1750-2799; 1750-2799
• DOI: 10.1038/nprot.2013.051

The genomic instability of stem cells in culture, caused by their routine in vitro propagation or by their genetic manipulation, is deleterious both for their clinical application and for their use in basic research. Frequent evaluation of the genomic integrity of stem cells is thus required, and it is usually performed using cytogenetic or DNA-based methods at variable sensitivities, resolutions and costs. Here we present a detailed protocol for determining the genomic integrity of pluripotent stem cells (PSCs) using their global gene expression profiles. This expression-based karyotyping (e-karyotyping) protocol uses gene expression microarray data (either originally generated or derived from the literature) and describes how to organize it properly, subject it to two complementary bioinformatic analyses and conservatively interpret the results in order to generate an accurate estimation of the chromosomal aberrations in the autosomal genome of examined stem cell lines. The experimental steps of e-karyotyping can be carried out in ∼20–30 h.