RT Journal Article
SR Electronic
T1 Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 089631
DO 10.1101/089631
A1 Marco A. Albuquerque
A1 Bruno M. Grande
A1 Elie J. Ritch
A1 Selin Jessa
A1 Martin Krzywinski
A1 Jasleen K. Grewal
A1 Sohrab P. Shah
A1 Paul C. Boutros
A1 Ryan D. Morin
YR 2016
UL http://biorxiv.org/content/early/2016/11/26/089631.abstract
AB We present a collection of Galaxy tools representing many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We implemented methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability on cloud-based infrastructure and commodity hardware. Some tools represents extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate several of these to perform some standard data integration and visualization tasks are demonstrated on a cohort of 96 diffuse large B-cell lymphomas, enabling the discovery of multiple candidate lymphoma-related genes that have not been reported previously.