Cross-species genomics matches driver mutations and cell compartments to model ependymoma (original) (raw)

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Gene Expression Omnibus

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The microarray data generated during this study has been deposited in GEO under the accession number GSE21687.

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Acknowledgements

R.J.G. holds the Howard C. Schott Research Chair from the Malia’s Cord Foundation, and is supported by grants from the National Institutes of Health (R01CA129541, P01CA96832 and P30CA021765), the Collaborative Ependymoma Research Network (CERN) and by the American Lebanese Syrian Associated Charities (ALSAC). K.D.W. is supported by NRSA Training Grant T32 CA070089. We are grateful to N. Heintz for providing the Blbp–eGFP mouse, T. Pawson for providing mouse Ephb2 cDNA, M. Roussel for the pCX4-IRES-RFP virus, J. Downing and M. Relling for access to 500K SNP profiles of normal human DNA, and the staff of the Hartwell center for Bioinformatics and Biotechnology, Vector Production Core, ARC, AIC and Cell and Tissue Imaging at St Jude Children’s Research Hospital for technical assistance.

Author information

Author notes

  1. Robert A. Johnson and Karen D. Wright: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Developmental Neurobiology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA,
    Robert A. Johnson, Karen D. Wright, Helen Poppleton, Kumarasamypet M. Mohankumar, Elsie White, Christopher Eden, Twala Hogg, Jennifer Atkinson, Tanya A. Kranenburg & Richard J. Gilbertson
  2. Department of Oncology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA,
    Karen D. Wright, Mariko DeWire, Amar Gajjar & Richard J. Gilbertson
  3. Hartwell Centre for Bioinformatics and Biotechnology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA ,
    David Finkelstein, Geoffrey Neale & Yong-Dong Wang
  4. Department of Biostatistics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA,
    Stanley B. Pounds
  5. Northern Institute for Cancer Research, University of Newcastle upon Tyne, Newcastle upon Tyne, NE2 4HH, UK
    Vikki Rand
  6. Hematology-Oncology, Seattle Children's Hospital, Seattle, 98105, Washington, USA
    Sarah E. S. Leary
  7. Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario M4N 1X8, Canada,
    Paul Northcott, Stephen Mack & Michael D. Taylor
  8. Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, NG7 2RD, UK
    Beth Coyle & Richard G. Grundy
  9. Department of Surgery, University of Alabama, 1900 University Boulevard, Birmingham, 35294, Alabama, USA
    Yancey Gillespie
  10. New York University, Langone Medical Center, 550 First Avenue, New York, 10016, New York, USA
    Jeffrey C. Allen
  11. Department of Radiological Sciences, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA,
    Thomas Merchant
  12. Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA,
    Fredrick A. Boop & Robert. A. Sanford
  13. Department of Pathology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA,
    David W. Ellison

Authors

  1. Robert A. Johnson
  2. Karen D. Wright
  3. Helen Poppleton
  4. Kumarasamypet M. Mohankumar
  5. David Finkelstein
  6. Stanley B. Pounds
  7. Vikki Rand
  8. Sarah E. S. Leary
  9. Elsie White
  10. Christopher Eden
  11. Twala Hogg
  12. Paul Northcott
  13. Stephen Mack
  14. Geoffrey Neale
  15. Yong-Dong Wang
  16. Beth Coyle
  17. Jennifer Atkinson
  18. Mariko DeWire
  19. Tanya A. Kranenburg
  20. Yancey Gillespie
  21. Jeffrey C. Allen
  22. Thomas Merchant
  23. Fredrick A. Boop
  24. Robert. A. Sanford
  25. Amar Gajjar
  26. David W. Ellison
  27. Michael D. Taylor
  28. Richard G. Grundy
  29. Richard J. Gilbertson

Contributions

R.J.G., R.G.G. and M.D.T. conceived the research and planned experiments. R.A.J. and K.D.W. also planned and conducted the great majority of the experiments under the direction of R.J.G.; A.G., Y.G., J.C.A., M.D.T. and R.G.G. provided human tumour material. All authors contributed experimental expertise and participated in the writing of the manuscript. D.F., S.B.P., Y.-D.W. and G.N. provided bioinformatic expertise. D.W.E. provided pathology review and iFISH analysis.

Corresponding author

Correspondence toRichard J. Gilbertson.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, References, Supplementary Figures 1-6 with legends, Supplementary Table legends 1-6 (see pages 32-33) and Supplementary Tables 1-6. (PDF 9737 kb)

Supplementary Information

This file contains gene cards, which contain a comprehensive summary of the DNA alteration and gene expression within each validated focal amplification and deletion identified in Figure 1 of the main paper. (PDF 24320 kb)

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Johnson, R., Wright, K., Poppleton, H. et al. Cross-species genomics matches driver mutations and cell compartments to model ependymoma.Nature 466, 632–636 (2010). https://doi.org/10.1038/nature09173

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