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Recurrent copy number variations in human induced pluripotent stem cells

Nature Biotechnology volume 29, pages 488–491 (2011)Cite this article

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Human induced pluripotent stem cells (hiPSCs) have been shown to acquire genomic and epigenomic aberrations1,2,3,4,5,6,7 that are also frequently observed in human embryonic stem cells (hESCs)7,8,9,10,11,12, including recurrent duplications of chromosome 12 (refs. 1,4,7) and 20q11.2 (refs. 3,4). To date, however, no recurrent subchromosomal abnormalities specific to hiPSC lines have been identified. We monitored the genomic stability of 32 hiPSC lines by G-banded karyotyping and high-resolution array-based comparative genomic hybridization (aCGH). Few aneuploidies were detected in hiPSCs by karyotyping after extended periods in culture. However, aCGH analysis identified unique copy number variation (CNV) signatures for hiPSC lines derived from specific sources of parental fibroblasts, including CNVs acquired specifically during culture. Recurrent CNVs at 1q31.3 and 17q21.1 were shared by >25% of hiPSCs. Furthermore, the loss of 8q24.3 was unique to hiPSCs.

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Figure 1: Karyotype of the ICF-TK4 hiPSC line determined by multiple assays.
Figure 2: Venn diagrams for total CNVs acquired during prolonged culture of hiPSCs and hESCs.
Figure 3: Large chromosomal aberrations >1 Mb in hiPSC samples and analysis of some affected genes.

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Acknowledgements

We thank J. Thomson for the iPS (foreskin) and iPS (IMR90) lines, G. Daley for the hFIB2-iPS4 line and Cell Line Genetics for analysis, comments and suggestions for the FISH analysis. We also would like to thank all the members of the Xu laboratory for their kind help and support, S. Chamberlain for her careful reading of the manuscript, and M. Ikeda for the development of the dual labeling protocol used in the aCGH. This work was mainly supported by Connecticut Stem Cell Research Grants 06SCD02 and 09SCD01 to R.-H.X. The contents in this work are solely the responsibility of the authors and do not necessarily represent the official views of the State of Connecticut. aCGH of hESC lines was funded in part by the National Center for Research Resources, National Institutes of Health, under contract no. HHSN309200582085C.

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Authors and Affiliations

  1. University of Connecticut Stem Cell Institute and Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut, USA

    Kristen Martins-Taylor, Tiwanna Compton, Leann Crandall, Marc Lalande & Ren-He Xu

  2. WiCell Cytogenetics Laboratory, WiCell Research Institute, Madison, Wisconsin, USA

    Benjamin S Nisler, Seth M Taapken & Karen Dyer Montgomery

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  1. Kristen Martins-Taylor
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Correspondence to Ren-He Xu.

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Martins-Taylor, K., Nisler, B., Taapken, S. et al. Recurrent copy number variations in human induced pluripotent stem cells. Nat Biotechnol 29, 488–491 (2011). https://doi.org/10.1038/nbt.1890

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