High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity (original) (raw)

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Acknowledgements

We are grateful to everyone who has taken care of sample collection and handling: T. Golan-Lev, A. Urrutikoetxea-Uriguen, S. Haupt, P. Koch, I. Laufenberg, B. Ley, A. Hampl, M. Vodinska, K. Koudelkova, S. Ström, F. Holm, A.-M. Strömberg, C. Olsson, M. Mikkola, S. Vuoristo, P. Junni and M. Hakkarainen. We especially acknowledge M. Linja, T. Heinonen and the Finnish DNA Microarray Centre for their excellent technical assistance. We acknowledge the Turku Graduate School of Biomedical Sciences. This study is supported by funding for the ESTOOLS consortium under the Sixth Research Framework Programme of the European Union, Juvenile Diabetes Research Foundation, The Academy of Finland and the Finnish Cancer Organizations, The Improving Outcomes Guidance Trust, The Ministry of Education, Youth, and Sport of the Czech Republic, Ida Montin Foundation, The Academy of Finland, projects no. 129657 (Finnish Centre of Excellence program 2006-11) and no. 134117 and the Medical Research Council, UK.

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Authors and Affiliations

1. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
   Elisa Närvä, Reija Autio, Nelly Rahkonen, Omid Rasool & Riitta Lahesmaa
2. Department of Signal Processing, Tampere University of Technology, Tampere, Finland
   Reija Autio, Lingjia Kong & Olli Yli-Harja
3. Centre for Stem Cell Biology and the Department of Biomedical Science, University of Sheffield, Sheffield, UK
   Neil Harrison & Peter W Andrews
4. Stem Cell Technologies Ltd., Jerusalem, Israel
   Danny Kitsberg
5. Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn and Hertie Foundation, Bonn, Germany
   Lodovica Borghese & Oliver Brüstle
6. Technion-Israel Institute of Technology and Department of Obstetrics and Gynecology, Faculty of Medicine, Rambam Health Care Campus, Haifa, Israel
   Joseph Itskovitz-Eldor
7. Department of Biology, Masaryk University & Department of Molecular Embryology, Faculty of Medicine, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Brno, Czech Republic
   Petr Dvorak
8. Department CLINTEC, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
   Outi Hovatta
9. Program of Molecular Neurology, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
   Timo Otonkoski & Timo Tuuri
10. Children's Hospital, University of Helsinki, Helsinki, Finland
    Timo Otonkoski
11. Institute of Reproductive and Developmental Biology, Faculty of Medicine, Imperial College London, Hammersmith Campus, London, UK
    Wei Cui
12. Sheffield Diagnostic Genetic Services, Sheffield Children's NHS Trust, Sheffield, UK
    Duncan Baker & Edna Maltby
13. Centre for Stem Cell Biology and the Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
    Harry D Moore
14. Department of Genetics, Stem Cell Unit, The Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
    Nissim Benvenisty
15. Institute for Systems Biology, Seattle, Washington, USA
    Olli Yli-Harja

Authors

1. Elisa Närvä
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2. Reija Autio
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3. Nelly Rahkonen
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4. Lingjia Kong
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5. Neil Harrison
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6. Danny Kitsberg
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7. Lodovica Borghese
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8. Joseph Itskovitz-Eldor
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9. Omid Rasool
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10. Petr Dvorak
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11. Outi Hovatta
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12. Timo Otonkoski
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13. Timo Tuuri
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14. Wei Cui
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15. Oliver Brüstle
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16. Duncan Baker
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17. Edna Maltby
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18. Harry D Moore
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19. Nissim Benvenisty
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20. Peter W Andrews
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21. Olli Yli-Harja
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22. Riitta Lahesmaa
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Contributions

E.N., R.A., N.B., P.W.A., O.Y.-H. and R.L. designed the experiments, E.N. and R.L. were responsible for the coordination of the project and microarray experiments. R.A., E.N. and O.Y.-H. were responsible for data analysis, integration and statistical analysis. N.R. performed RNA extractions. L.K. built the gene annotation list of genes overlapping CNVs. D.B. performed conventional karyotyping. E.N. and N.R. performed copy-number state validations with RT-PCR. J.I.-E. provided I3 and I6 lines for the study. P.D., O.H., T.O., T.T., N.B., W.C., O.B., E.M., H.D.M., P.W.A., O.Y.-H. and R.L. provided the samples and coordinated the project in their groups. E.N., R.A., N.R., L.K., N.H., D.K., L.B., J.I.-E., O.R., P.D., O.H., T.O., T.T., N.B., W.C., O.B., D.B., E.M., H.D.M., P.W.A., O.Y.-H. and R.L. contributed to writing the paper.

Corresponding authors

Correspondence toElisa Närvä or Riitta Lahesmaa.

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Competing interests

D.K. is affiliated with Stem Cell Technologies, Ltd. (However, the study was not supported by the company.)

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Närvä, E., Autio, R., Rahkonen, N. et al. High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity.Nat Biotechnol 28, 371–377 (2010). https://doi.org/10.1038/nbt.1615

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• Received: 24 June 2009
• Accepted: 16 February 2010
• Published: 28 March 2010
• Issue Date: April 2010
• DOI: https://doi.org/10.1038/nbt.1615