The mechanisms underlying the low efficiency of reprogramming somatic cells into induced pluripotent stem (iPS) cells are poorly understood. There is a clear need to study whether the reprogramming process itself compromises genomic integrity and, through this, the efficiency of iPS cell establishment. Using a high-resolution single nucleotide polymorphism array, we compared copy number variations (CNVs) of different passages of human iPS cells with their fibroblast cell origins and with human embryonic stem (ES) cells. Here we show that significantly more CNVs are present in early-passage human iPS cells than intermediate passage human iPS cells, fibroblasts or human ES cells. Most CNVs are formed de novo and generate genetic mosaicism in early-passage human iPS cells. Most of these novel CNVs rendered the affected cells at a selective disadvantage. Remarkably, expansion of human iPS cells in culture selects rapidly against mutated cells, driving the lines towards a genetic state resembling human ES cells.

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Gene Expression Omnibus

Data deposits

Affymetrix SNP array 6.0 data from each individual sample have been deposited with the NCBI Gene Expression Omnibus (http:// www.ncbi.nlm.nih.gov/geo/) under accession number GSE26173.


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This work was supported by funding for the ESTOOLS consortium under the Sixth RFP of the EU (S.M.H., T.O., R.L. and O.B.), the Academy of Finland (T.O. and R.A.), the Finnish Cancer Organizations (R.L.), the Research Funds of the Helsinki University Hospital (T.O.), the Sigrid Jusélius Foundation (T.O.), the Stem Cell Network Canada, GL2 and CIHR (A.N.). S.M.H. is a recipient of a McEwen Post-doctoral Fellowship from the McEwen Centre for Regenerative Medicine. N.N.B. is the recipient of a New Investigator Award from the Ontario Institute for Cancer Research, through the Ontario Ministry of Research and Innovation. A.N. is Tier 1 Canada Research Chair in Stem Cells and Regeneration. We are grateful to I. Rogers, M. Faiz and K. Nagy for critically reading and editing the manuscript, and J. Ustinov, H. Sariola and J. Palgi for skilled assistance in the characterization of human iPS cells. We thank N. Rahkonen for sample processing, as well as the Finnish Microarray and Sequencing Centre (http://www.btk.fi/), and the Institute of Human Genetics, University of Bonn, for array processing.

Author information

Author notes

    • Samer M. Hussein
    •  & Nizar N. Batada

    These authors contributed equally to this work.


  1. Samuel Lunenfeld Research Institute, Toronto, Ontario M5T 3H7, Canada

    • Samer M. Hussein
    • , Michel Sourour
    • , Riikka Hämäläinen
    •  & Andras Nagy
  2. Research Program Unit, Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki FI-00014, Finland

    • Samer M. Hussein
    • , Sanna Vuoristo
    • , Riikka Hämäläinen
    • , Cia Olsson
    • , Karolina Lundin
    • , Milla Mikkola
    • , Ras Trokovic
    •  & Timo Otonkoski
  3. Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada

    • Nizar N. Batada
    •  & Siemon Ng
  4. Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada

    • Reagan W. Ching
    •  & David P. Bazett-Jones
  5. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland

    • Reija Autio
    • , Elisa Närvä
    •  & Riitta Lahesmaa
  6. Department of Signal Processing, Tampere University of Technology, Tampere 33101, Finland

    • Reija Autio
  7. Institute of Reconstructive Neurobiology, Life and Brain Center, University of Bonn and Hertie Foundation, D-53127 Bonn, Germany

    • Michael Peitz
    •  & Oliver Brüstle
  8. Molecular Cancer Biology Laboratory, University of Helsinki and Helsinki University Central Hospital, Helsinki FI-00014, Finland

    • Kari Alitalo
  9. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada

    • Andras Nagy
  10. Children’s Hospital, University of Helsinki, Helsinki FI-00029, Finland

    • Timo Otonkoski


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S.M.H. coordinated and performed most of the experiments in this project, analysed and interpreted the data, and prepared the manuscript. N.N.B. analysed and interpreted the data and prepared an early version of the manuscript. S.V. provided essential experimental assistance and performed some experiments in this study. R.W.C. performed, and advised on the planning of, FISH experiments. R.A. and E.N. analysed and interpreted the data and coordinated the sample processing of the arrays. O.B. and M.P. provided analysed data and samples from Illumina arrays for validation. M.S., S.N., R.H., R.T., M.M., C.O. and K.L. contributed experimentally. D.P.B-J. and K.A. provided essential experimental material and support. R.L. directed the SNP array data generation and analysis. T.O. directed, coordinated and supervised the first stage of the project and contributed to the preparation of the manuscript. A.N. prepared the manuscript, supervised the second stage of the project and helped to interpret the data. K.A. and R.L. contributed equally as co-authors. A.N. and T.O. contributed equally as senior authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Andras Nagy or Timo Otonkoski.

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