The genomic landscape of hypodiploid acute lymphoblastic leukemia (original) (raw)

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References

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Acknowledgements

We thank J. Morris, E. Walker and A. Merriman for performing SNP and gene expression microarrays and G. Zambetti and P. Brindle for insightful discussions of TP53 and CREBBP mutational data, respectively. We also thank H. Mulder, R. Collins, M. Barbato, E. Stonerock, E. Pinto and M. Ellis for technical assistance, the Tissue Resources Core facility and the Flow Cytometry and Cell Sorting Core facility of the St. Jude Children's Research Hospital (SJCRH). This work was supported by The Henry Schueler 41&9 Foundation in conjunction with Partnership for Cures, the St. Baldrick's Foundation, US National Cancer Institute (NCI) grant RC4CA156329, US National Institutes of Health (NIH) grants CA21765 and U01 GM92666, the American Association for Cancer Research (AACR) Gertrude B. Elion Cancer Research Award and the American Lebanese and Syrian Associated Charities (ALSAC) of SJCRH. Support was also provided by NCI grants to the Children's Oncology Group, including CA98543, CA98413 and CA114766. L.H. was supported by the Swedish Research Council. S.P.H. is the Ergen Family Chair in Pediatric Cancer. M.L.L. is a Clinical Scholar in the Leukemia Lymphoma Society and supported by the Frank A. Campini Foundation. C.G.M. is a Pew Scholar in the Biomedical Sciences and a St. Baldrick's Scholar. M.L.L. and E.D.-F. were supported by the Team Connor Foundation, and S.N.P. was supported by 5R25CA023944 from NCI. This paper is dedicated to Henry 'Hank' Schueler who died from complications of hypodiploid ALL and whose Foundation is dedicated to finding a cure for hypodiploid ALL in his memory and to James B. Nachman who was instrumental in the genesis of this project and who recently passed away.

Author information

Author notes

  1. Samir N Patel & Susan L Heatley
    Present address: Present addresses: Weill Cornell Medical College, Cornell University, New York, New York, USA (S.N.P.) and Human Immunology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia (S.L.H.).,
  2. Linda Holmfeldt and Lei Wei: These authors contributed equally to this work.
  3. Department of Pathology, Ohio State University, Columbus, Ohio, USA.

Authors and Affiliations

  1. Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
    Linda Holmfeldt, Lei Wei, Debbie Payne-Turner, Michelle Churchman, Anna Andersson, Shann-Ching Chen, Kelly McCastlain, Jing Ma, Samir N Patel, Susan L Heatley, Letha A Phillips, Guangchun Song, David W Ellison, Sheila A Shurtleff, Susana C Raimondi, James R Downing & Charles G Mullighan
  2. Department of Pediatrics, University of California School of Medicine, San Francisco, California, USA
    Ernesto Diaz-Flores & Mignon L Loh
  3. Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
    Michael Walsh, Ching-Hon Pui & Raul C Ribeiro
  4. Department of Computational Biology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
    Jinghui Zhang, Jared Becksfort, Gang Wu, Matthew Parker, Xiang Chen, Michael Rusch, Erin Hedlund, Robert Huether, Elaine R Mardis & Richard K Wilson
  5. The Genome Institute at Washington University, St. Louis, Missouri, USA
    Li Ding, Charles Lu, Robert S Fulton, Lucinda L Fulton, Yashodhan Tabib, David J Dooling, Kerri Ochoa, Elaine R Mardis & Richard K Wilson
  6. Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
    Li Ding, Robert S Fulton, Lucinda L Fulton & David J Dooling
  7. Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
    Anna Andersson
  8. Pediatric Cancer Genome Project, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
    John Easton, Kristy Boggs & Bhavin Vadodaria
  9. Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
    Christina Drenberg & Sharyn Baker
  10. Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
    Deqing Pei & Cheng Cheng
  11. Princess Margaret Hospital/University Health Network, University of Toronto, Ontario, Canada
    Mark Minden
  12. Division of Haematology, Institute of Medical and Veterinary Science, Adelaide, South Australia, Australia
    Ian D Lewis & L Bik To
  13. Oncology/Haematology Unit, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
    Paula Marlton
  14. Department of Clinical Haematology and Bone Marrow Transplant, Royal Melbourne Hospital, Melbourne, Victoria, Australia
    Andrew W Roberts
  15. Section of Hematology/Oncology, University of Chicago Medicine, Chicago, Illinois, USA
    Gordana Raca & Wendy Stock
  16. The Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
    Geoffrey Neale
  17. Department of Human and Animal Cell Cultures, Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
    Hans G Drexler
  18. Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
    Ross A Dickins
  19. Department of Biostatistics, College of Medicine, University of Florida, Gainesville, Florida, USA
    Meenakshi Devidas
  20. Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
    Andrew J Carroll
  21. Department of Pathology, College of Medicine, Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
    Nyla A Heerema
  22. Department of Laboratory Medicine, Seattle Children's Hospital, Seattle, Washington, USA
    Brent Wood
  23. Division of Hematologic Pathology, Johns Hopkins Hospital, Baltimore, Maryland, USA
    Michael J Borowitz
  24. Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
    Julie M Gastier-Foster
  25. Department of Pediatrics, Ohio State University, Columbus, Ohio, USA
    Julie M Gastier-Foster
  26. Siteman Cancer Center, Washington University, St. Louis, Missouri, USA
    Elaine R Mardis & Richard K Wilson
  27. Section of Pediatric Hematology/Oncology/Bone Marrow Transplantation and Center for Cancer and Blood Disorders, University of Colorado Denver School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
    Stephen P Hunger

Authors

  1. Linda Holmfeldt
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  2. Lei Wei
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  3. Ernesto Diaz-Flores
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  4. Michael Walsh
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  5. Jinghui Zhang
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  6. Li Ding
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  7. Debbie Payne-Turner
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  8. Michelle Churchman
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  9. Anna Andersson
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  10. Shann-Ching Chen
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  11. Kelly McCastlain
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  12. Jared Becksfort
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  13. Jing Ma
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  14. Gang Wu
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  15. Samir N Patel
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  16. Susan L Heatley
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  17. Letha A Phillips
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  18. Guangchun Song
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  19. John Easton
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  20. Matthew Parker
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  21. Xiang Chen
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  22. Michael Rusch
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  23. Kristy Boggs
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  24. Bhavin Vadodaria
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  25. Erin Hedlund
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  26. Christina Drenberg
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  27. Sharyn Baker
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  28. Deqing Pei
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  29. Cheng Cheng
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  30. Robert Huether
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  31. Charles Lu
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  32. Robert S Fulton
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  33. Lucinda L Fulton
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  34. Yashodhan Tabib
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  35. David J Dooling
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  36. Kerri Ochoa
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  37. Mark Minden
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  38. Ian D Lewis
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  39. L Bik To
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  40. Paula Marlton
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  41. Andrew W Roberts
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  42. Gordana Raca
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  43. Wendy Stock
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  44. Geoffrey Neale
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  45. Hans G Drexler
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  46. Ross A Dickins
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  47. David W Ellison
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  48. Sheila A Shurtleff
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  49. Ching-Hon Pui
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  50. Raul C Ribeiro
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  51. Meenakshi Devidas
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  52. Andrew J Carroll
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  53. Nyla A Heerema
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  54. Brent Wood
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  55. Michael J Borowitz
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  56. Julie M Gastier-Foster
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  57. Susana C Raimondi
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  58. Elaine R Mardis
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  59. Richard K Wilson
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  60. James R Downing
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  61. Stephen P Hunger
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  62. Mignon L Loh
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  63. Charles G Mullighan
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L.H., C.G.M., M.L.L. and S.P.H. designed the experiments. L.H. and D.P.-T. prepared patient samples and generated xenografts. L.H., E.D.-F., M.C., K.M., S.N.P., L.A.P. and S.L.H. performed biochemical analyses. C.D. and S.B. performed ex vivo drug studies. L.H. and J.M. analyzed SNP array data. L.H. and J.E. performed transcriptome sequencing. K.B. performed exome sequencing. L.H., D.P.-T. and B.V. performed sequencing validation. L.W., J.Z., L.D., J.B., Y.T., X.C. and C.L. analyzed sequence data. S.-C.C., A.A., G.N. and L.H. analyzed expression microarray data. M.R., E.H., M.P., G.W., R.H. and G.S. provided bioinformatic support. D.P., C.C. and M.D. performed statistical analyses. R.S.F. and L.L.F. supervised whole-genome sequencing data generation. D.J.D. supervised the automated analysis pipeline. S.C.R., A.J.C. and N.A.H. performed cytogenetic analyses. M.W., C.-H.P., M.M., I.D.L., L.B.T., P.M., A.W.R., G.R., W.S., M.L.L., J.M.G.-F., R.C.R., B.W., M.J.B. and S.P.H. provided clinical samples and data. D.W.E. performed pathological analyses. R.A.D. and H.G.D. provided important reagents. L.H. and C.G.M. wrote the manuscript. L.H., L.W., J.Z., L.D., D.P.-T., M.C., A.A., S.-C.C., K.M., J.B., J.M., G.W., G.S., J.E., M.P., X.C., M.R., E.H., C.L., R.S.F., L.L.F., D.J.D., K.O., S.A.S., C.-H.P., E.R.M., R.K.W., J.R.D. and C.G.M. are part of the St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project.

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Correspondence toCharles G Mullighan.

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The authors declare no competing financial interests.

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Holmfeldt, L., Wei, L., Diaz-Flores, E. et al. The genomic landscape of hypodiploid acute lymphoblastic leukemia.Nat Genet 45, 242–252 (2013). https://doi.org/10.1038/ng.2532

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