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Cancer discovery
05, 2021;11 (5): 1082-1099.

St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem.

Clay McLeod, Alexander M Gout, Xin Zhou, Andrew Thrasher, Delaram Rahbarinia, Samuel W Brady, Michael Macias, Kirby Birch, David Finkelstein, Jobin Sunny, Rahul Mudunuri, Brent A Orr, Madison Treadway, Bob Davidson, Tracy K Ard, Arthur Chiao, Andrew Swistak, Stephanie Wiggins, Scott Foy, Jian Wang, Edgar Sioson, Shuoguo Wang, J Robert Michael, Yu Liu, Xiaotu Ma, Aman Patel, Michael N Edmonson, Mark R Wilkinson, Andrew M Frantz, Ti-Cheng Chang, Liqing Tian, Shaohua Lei, S M Ashiqul Islam, Christopher Meyer, Naina Thangaraj, Pamella Tater, Vijay Kandali, Singer Ma, Tuan Nguyen, Omar Serang, Irina McGuire, Nedra Robison, Darrell Gentry, Xing Tang, Lance E Palmer, Gang Wu, Ed Suh, Leigh Tanner, James McMurry, Matthew Lear, Alberto S Pappo, Zhaoming Wang, Carmen L Wilson, Yong Cheng, Soheil Meshinchi, Ludmil B Alexandrov, Mitchell J Weiss, Gregory T Armstrong, Leslie L Robison, Yutaka Yasui, Kim E Nichols, David W Ellison, Chaitanya Bangur, Charles G Mullighan, Suzanne J Baker, Michael A Dyer, Geralyn Miller, Scott Newman, Michael Rusch, Richard Daly, Keith Perry, James R Downing, Jinghui Zhang
Author Information
  1. Clay McLeod: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  2. Alexander M Gout: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  3. Xin Zhou: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  4. Andrew Thrasher: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  5. Delaram Rahbarinia: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  6. Samuel W Brady: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  7. Michael Macias: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  8. Kirby Birch: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  9. David Finkelstein: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  10. Jobin Sunny: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  11. Rahul Mudunuri: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  12. Brent A Orr: Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  13. Madison Treadway: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  14. Bob Davidson: Microsoft Research, Redmond, Washington.
  15. Tracy K Ard: Microsoft Research, Redmond, Washington.
  16. Arthur Chiao: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  17. Andrew Swistak: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  18. Stephanie Wiggins: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  19. Scott Foy: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  20. Jian Wang: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  21. Edgar Sioson: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  22. Shuoguo Wang: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  23. J Robert Michael: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  24. Yu Liu: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  25. Xiaotu Ma: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  26. Aman Patel: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  27. Michael N Edmonson: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  28. Mark R Wilkinson: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  29. Andrew M Frantz: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  30. Ti-Cheng Chang: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  31. Liqing Tian: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  32. Shaohua Lei: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  33. S M Ashiqul Islam: Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, California. ORCID
  34. Christopher Meyer: DNAnexus, Mountain View, California.
  35. Naina Thangaraj: DNAnexus, Mountain View, California.
  36. Pamella Tater: DNAnexus, Mountain View, California.
  37. Vijay Kandali: DNAnexus, Mountain View, California. ORCID
  38. Singer Ma: DNAnexus, Mountain View, California. ORCID
  39. Tuan Nguyen: DNAnexus, Mountain View, California.
  40. Omar Serang: DNAnexus, Mountain View, California. ORCID
  41. Irina McGuire: Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee.
  42. Nedra Robison: Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee.
  43. Darrell Gentry: Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  44. Xing Tang: Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  45. Lance E Palmer: Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  46. Gang Wu: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  47. Ed Suh: Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee.
  48. Leigh Tanner: Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee.
  49. James McMurry: Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee.
  50. Matthew Lear: Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  51. Alberto S Pappo: Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  52. Zhaoming Wang: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  53. Carmen L Wilson: Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  54. Yong Cheng: Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  55. Soheil Meshinchi: Fred Hutchinson Cancer Research Center Professor of Pediatrics, University of Washington School of Medicine, Seattle, Washington.
  56. Ludmil B Alexandrov: Department of Cellular and Molecular Medicine and Department of Bioengineering, Moores Cancer Center, University of California, San Diego, La Jolla, California. ORCID
  57. Mitchell J Weiss: Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  58. Gregory T Armstrong: Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee.
  59. Leslie L Robison: Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee.
  60. Yutaka Yasui: Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee.
  61. Kim E Nichols: Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  62. David W Ellison: Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  63. Chaitanya Bangur: Microsoft Research, Redmond, Washington.
  64. Charles G Mullighan: Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  65. Suzanne J Baker: Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  66. Michael A Dyer: Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  67. Geralyn Miller: Microsoft Research, Redmond, Washington.
  68. Scott Newman: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
  69. Michael Rusch: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. ORCID
  70. Richard Daly: DNAnexus, Mountain View, California.
  71. Keith Perry: Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee. jinghui.zhang@stjude.org keith.perry@stjude.org james.downing@stjude.org.
  72. James R Downing: Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee. jinghui.zhang@stjude.org keith.perry@stjude.org james.downing@stjude.org.
  73. Jinghui Zhang: Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee. jinghui.zhang@stjude.org keith.perry@stjude.org james.downing@stjude.org. ORCID
PMID: 33408242 DOI: 10.1158/2159-8290.CD-20-1230

Abstract

Effective data sharing is key to accelerating research to improve diagnostic precision, treatment efficacy, and long-term survival in pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.stjude.cloud), a cloud-based data-sharing ecosystem for accessing, analyzing, and visualizing genomic data from >10,000 pediatric patients with cancer and long-term survivors, and >800 pediatric sickle cell patients. Harmonized genomic data totaling 1.25 petabytes are freely available, including 12,104 whole genomes, 7,697 whole exomes, and 2,202 transcriptomes. The resource is expanding rapidly, with regular data uploads from St. Jude's prospective clinical genomics programs. Three interconnected apps within the ecosystem-Genomics Platform, Pediatric cancer Knowledgebase, and Visualization Community-enable simultaneously performing advanced data analysis in the cloud and enhancing the Pediatric cancer knowledgebase. We demonstrate the value of the ecosystem through use cases that classify 135 pediatric cancer subtypes by gene expression profiling and map mutational signatures across 35 pediatric cancer subtypes. SIGNIFICANCE: To advance research and treatment of pediatric cancer, we developed St. Jude Cloud, a data-sharing ecosystem for accessing >1.2 petabytes of raw genomic data from >10,000 pediatric patients and survivors, innovative analysis workflows, integrative multiomics visualizations, and a knowledgebase of published data contributed by the global pediatric cancer community..

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Grants

  1. R01 CA216391/NCI NIH HHS

MeSH Term

Anemia, Sickle Cell
Child
Cloud Computing
Ecosystem
Genomics
Hospitals, Pediatric
Humans
Information Dissemination
Neoplasms
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
Article has an altmetric score of 43

Word Cloud

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