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

• Published in: Cancer discovery Vol. 11; no. 5; p. 1082
• Main Authors: McLeod, Clay, Gout, Alexander M, Zhou, Xin, Thrasher, Andrew, Rahbarinia, Delaram, Brady, Samuel W, Macias, Michael, Birch, Kirby, Finkelstein, David, Sunny, Jobin, Mudunuri, Rahul, Orr, Brent A, Treadway, Madison, Davidson, Bob, Ard, Tracy K, Chiao, Arthur, Swistak, Andrew, Wiggins, Stephanie, Foy, Scott, Wang, Jian, Sioson, Edgar, Wang, Shuoguo, Michael, J Robert, Liu, Yu, Ma, Xiaotu, Patel, Aman, Edmonson, Michael N, Wilkinson, Mark R, Frantz, Andrew M, Chang, Ti-Cheng, Tian, Liqing, Lei, Shaohua, Islam, S M Ashiqul, Meyer, Christopher, Thangaraj, Naina, Tater, Pamella, Kandali, Vijay, Ma, Singer, Nguyen, Tuan, Serang, Omar, McGuire, Irina, Robison, Nedra, Gentry, Darrell, Tang, Xing, Palmer, Lance E, Wu, Gang, Suh, Ed, Tanner, Leigh, McMurry, James, Lear, Matthew, Pappo, Alberto S, Wang, Zhaoming, Wilson, Carmen L, Cheng, Yong, Meshinchi, Soheil, Alexandrov, Ludmil B, Weiss, Mitchell J, Armstrong, Gregory T, Robison, Leslie L, Yasui, Yutaka, Nichols, Kim E, Ellison, David W, Bangur, Chaitanya, Mullighan, Charles G, Baker, Suzanne J, Dyer, Michael A, Miller, Geralyn, Newman, Scott, Rusch, Michael, Daly, Richard, Perry, Keith, Downing, James R, Zhang, Jinghui
• Format: Journal Article
• Language: English
• Published: United States 01-05-2021
• Subjects: Anemia, Sickle Cell - genetics; Child; Cloud Computing; Ecosystem; Genomics; Hospitals, Pediatric; Humans; Information Dissemination; Neoplasms - genetics
• DOI: 10.1158/2159-8290.cd-20-1230
• EISSN: 2159-8290

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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