| Literature DB >> 33408242 |
Clay McLeod1, Alexander M Gout1, Xin Zhou1, Andrew Thrasher1, Delaram Rahbarinia1, Samuel W Brady1, Michael Macias1, Kirby Birch1, David Finkelstein1, Jobin Sunny1, Rahul Mudunuri1, Brent A Orr2, Madison Treadway1, Bob Davidson3, Tracy K Ard3, Arthur Chiao1, Andrew Swistak1, Stephanie Wiggins1, Scott Foy1, Jian Wang1, Edgar Sioson1, Shuoguo Wang1, J Robert Michael1, Yu Liu1, Xiaotu Ma1, Aman Patel1, Michael N Edmonson1, Mark R Wilkinson1, Andrew M Frantz1, Ti-Cheng Chang1, Liqing Tian1, Shaohua Lei1, S M Ashiqul Islam4, Christopher Meyer5, Naina Thangaraj5, Pamella Tater5, Vijay Kandali5, Singer Ma5, Tuan Nguyen5, Omar Serang5, Irina McGuire6, Nedra Robison6, Darrell Gentry6, Xing Tang7, Lance E Palmer7, Gang Wu1, Ed Suh6, Leigh Tanner6, James McMurry6, Matthew Lear2, Alberto S Pappo8, Zhaoming Wang1,9, Carmen L Wilson9, Yong Cheng7, Soheil Meshinchi10, Ludmil B Alexandrov4, Mitchell J Weiss7, Gregory T Armstrong9, Leslie L Robison9, Yutaka Yasui9, Kim E Nichols8, David W Ellison2, Chaitanya Bangur3, Charles G Mullighan2, Suzanne J Baker11, Michael A Dyer11, Geralyn Miller3, Scott Newman1, Michael Rusch1, Richard Daly5, Keith Perry12, James R Downing13, Jinghui Zhang14.
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.This article is highlighted in the In This Issue feature, p. 995. ©2021 American Association for Cancer Research.Entities:
Mesh：
Year: 2021 PMID： 33408242 PMCID： PMC8102307 DOI： 10.1158/2159-8290.CD-20-1230
Source DB: PubMed Journal: Cancer Discov ISSN： 2159-8274 Impact factor: 39.397