Abstract
Due to their unique cellular features, pluripotent stem cells (PSCs) acquire chromosomal aberrations at a rather high frequency during their growth in culture. Analysis of chromosomal integrity should be routinely performed and usually is done at the DNA level of the cells. RNA sequencing (RNA-Seq) has recently become the basic tool for transcriptional studies. Therefore, methods that utilize this already available data to inspect the genomic integrity are very valuable. In this chapter, we provide a practical guide to implement methods of detection of chromosomal aberrations, which are based on RNA-Seq data. The expression-based karyotyping (e-Karyotyping) method is based on global gene expression analysis, while the expressed-SNP-karyotyping (eSNP-Karyotyping) method is based on changes in the ratio between alleles.
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References
Weissbein U, Benvenisty N, Ben-David U (2014) Genome maintenance in pluripotent stem cells. J Cell Biol 204:153–163
Lamm N, Ben-David U, Golan-Lev T et al (2016) Genomic instability in human pluripotent stem cells arises from replicative stress and chromosome condensation defects. Cell Stem Cell 18:253–261
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
Ben-David U, Arad G, Weissbein U et al (2014) Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells. Nat Commun 5:4825
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
Nguyen HT, Geens M, Mertzanidou A et al (2014) Gain of 20q11.21 in human embryonic stem cells improves cell-survival by increased expression of Bcl-xL. Mol Hum Reprod 20:168–177
Ben-David U, Mayshar Y, Benvenisty N (2013) Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles. Nat Protoc 8:989–997
Mayshar Y, Ben-David U, Lavon N et al (2010) Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell 7:521–531
Ben-David U, Mayshar Y, Benvenisty N (2011) Large-scale analysis reveals acquisition of lineage-specific chromosomal aberrations in human adult stem cells. Cell Stem Cell 9:97–102
Weissbein U, Ben-David U, Benvenisty N (2014) Virtual karyotyping reveals greater chromosomal stability in neural cells derived by transdifferentiation than those from stem cells. Cell Stem Cell 15:687–691
Weissbein U, Schachter M, Egli D et al (2016) Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq. Nat Commun 7:12144
Kim D, Pertea G, Trapnell C et al (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36
Dobin A, Davis CA, Schlesinger F et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21
Trapnell C, Williams BA, Pertea G et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515
Anders S, Pyl PT, Huber W (2015) HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169
Lingjaerde OC, Baumbusch LO, Liestol K et al (2005) CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics 21:821–822
DePristo MA, Banks E, Poplin R et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498
Kent WJ, Sugnet CW, Furey TS et al (2002) The human genome browser at UCSC. Genome Res 12:996–1006
Leinonen R, Sugawara H, Shumway M (2011) The sequence read archive. Nucleic Acids Res 39:2010–2012
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Weissbein, U. (2019). Computational Analysis of Aneuploidy in Pluripotent Stem Cells. In: Cahan, P. (eds) Computational Stem Cell Biology. Methods in Molecular Biology, vol 1975. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9224-9_18
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DOI: https://doi.org/10.1007/978-1-4939-9224-9_18
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