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| Status |
Public on Jun 08, 2015 |
| Title |
Effects of Integrating and Non-integrating Reprogramming Methods on Copy Number Variation and Genomic Stability of Human Induced Pluripotent Stem Cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
Human-induced pluripotent stem cells (iPSCs) are derived from differentiated somatic cells using defined factors and provide a renewable source of autologous cells for cell therapy. Many reprogramming methods have been employed to generate human iPSCs, including the use of integrating vectors and non-integrating vectors. Maintenance of the genomic integrity of iPSCs is highly desirable if the cells are to be used in clinical applications. Here, using the Affymetrix Cytoscan HD array, we investigated the genomic aberration profiles of 19 human cell lines: 5 embryonic stem cell (ESC) lines, 6 iPSC lines derived using integrating vectors (“integrating iPSC lines”), 6 iPSC lines derived using non-integrating vectors (“non-integrating iPSC lines”), and the 2 parental cell lines from which the iPSCs were derived. The genome-wide copy number variation (CNV), loss of heterozygosity (LOH) and mosaicism patterns of integrating and non-integrating iPSC lines were investigated. The maximum sizes of CNVs in the genomes of the integrating iPSC lines were 20 times higher than those of the non-integrating iPSC lines. Moreover, the total number of CNVs was much higher in integrating iPSC lines than in other cell lines. The average numbers of novel CNVs with a low degree of overlap with the DGV and of likely pathogenic CNVs with a high degree of overlap with the ISCA database were highest in integrating iPSC lines. Different SNP calls revealed that, using the parental cell genotype as a reference, integrating iPSC lines displayed more single nucleotide variations and mosaicism than did non-integrating iPSC lines. This study describes the genome stability of human iPSCs generated using either a DNA-integrating or non-integrating reprogramming method, of the corresponding somatic cells, and of hESCs. Our results highlight the importance of using a high-resolution method to monitor genomic aberrations in iPSCs intended for clinical applications to avoid any negative effects of reprogramming or cell culture.
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| Overall design |
19 human cell lines: 5 embryonic stem cell (ESC) lines, 6 iPSC lines derived using integrating vectors (“integrating iPSC lines”), 6 iPSC lines derived using non-integrating vectors (“non-integrating iPSC lines”), and the 2 parental cell lines from which the iPSCs were derived.
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| Contributor(s) |
He W, Sun X, Fan Y |
| Citation missing |
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| Submission date |
Jun 07, 2015 |
| Last update date |
Jul 13, 2018 |
| Contact name |
Wenyin HE |
| E-mail(s) |
31848346@qq.com
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| Phone |
8620-81297081
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| Organization name |
The third affiliated hospital of Guangzhou medical university
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| Street address |
No.63, Duobao road
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510150 |
| Country |
China |
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| Platforms (2) |
| GPL16131 |
[CytoScanHD_Array] Affymetrix CytoScan HD Array |
| GPL18637 |
[CytoScan750K_Array] Affymetrix CytoScan 750K Array |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA286044 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE69632_RAW.tar |
2.4 Gb |
(http)(custom) |
TAR (of CEL, CYCHP, TXT) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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