Author:
McLeod Clay,Gout Alexander M.,Zhou Xin,Rahbarinia Delaram,Thrasher Andrew,Newman Scott,Birch Kirby,Macias Michael,Finkelstein David,Sunny Jobin,Mudunuri Rahul,Orr Brent A.,Treadway Madison,Davidson Bob,Ard Tracy,Swistak Andrew,Wiggins Stephanie,Foy Scott,Brady Samuel W.,Wang Jian,Sioson Edgar,Wang Shuoguo,Michael J. Robert,Liu Yu,Ma Xiaotu,Patel Aman,Edmonson Michael N.,Wilkinson Mark R.,Frantz Andrew,Chang Ti-Cheng,Tian Liqing,Lei Shaohua,Meyer Christopher,Thangaraj Naina,Tater Pamella,Kandali Vijay,Ma Singer,Nguyen Tuan,Serang Omar,McGuire Irina,Robison Nedra,Gentry Darrell,Tang Xing,Palmer Lance,Wu Gang,Suh Ed,Tanner Leigh,McMurry James,Lear Matthew,Wang Zhaoming,Wilson Carmen,Cheng Yong,Weiss Mitch,Armstrong Gregory T.,Robison Leslie L.,Yasui Yutaka,Nichols Kim E.,Ellison David W.,Bangur Chitanya,Mullighan Charles G.,Baker Suzanne J.,Dyer Michael,Miller Geralyn,Rusch Michael,Daly Richard,Perry Keith,Downing James R.,Zhang Jinghui
Abstract
ABSTRACTEffective data sharing is key to accelerating research that will improve the precision of diagnoses, efficacy of treatments and long-term survival of pediatric cancer and other childhood catastrophic diseases. We present St. Jude Cloud (https://www.stjude.cloud), a cloud-based data sharing ecosystem developed via collaboration between St. Jude Children’s Research Hospital, DNAnexus, and Microsoft, for accessing, analyzing and visualizing genomic data from >10,000 pediatric cancer patients, long-term survivors of pediatric cancer and >800 pediatric sickle cell patients. Harmonized genomic data totaling 1.25 petabyes on St. Jude Cloud include 12,104 whole genomes, 7,697 whole exomes and 2,202 transcriptomes, which are freely available to researchers worldwide. The resource is expanding rapidly with regular data uploads from St. Jude’s prospective clinical genomics programs, providing public access as soon as possible rather than holding data back until publication. Three interconnected apps within the St. Jude Cloud ecosystem—Genomics Platform, Pediatric Cancer Knowledgebase (PeCan) and Visualization Community—provide a unique experience for simultaneously performing advanced data analysis in the cloud and enhancing the pediatric cancer knowledgebase. We demonstrate the value of the St. Jude Cloud ecosystem through use cases that classify 48 pediatric cancer subtypes by gene expression profiling and map mutational signatures across 35 subtypes of pediatric cancer.
Publisher
Cold Spring Harbor Laboratory