Cloud computing for clinical nanopore fusion detection

Abstract

Fusion genes identification is integral in management and diagnosis of leukemia patients; however, current techniques are limited by sensitivity and range. Despite lower accuracy, fusion gene identification is suitable for nanopore sequencing as the main analytical requirement is to find reads with gene segments that do not belong together. The lack of packaged software with easy user interface for nanopore is a deterrent. Bwb is a graphical tool that allows users to link Docker container enclosed software, build, and execute workflows to be run on GPU and cloud enabled servers that accelerates analysis speed and reduces costs.

Bio

Dr. Cecilia Yeung is an Associate Professor at the Fred Hutchinson Cancer Research Center and the University of Washington, Department of Laboratory Medicine and Pathology.  She serves as the medical director of the Fred Hutch CLIA Laboratories that focus on translational and exploratory testing for cooperative group heme malignancy and immunotherapy clinical trials. Her research interest focuses on engineering innovative devices and assays using pathology and molecular technology to assist decision making for patient management and therapy guidance.

Dr. Olga Sala-Torra is a staff scientist in the Radich/Yeung laboratory at the Fred Hutchinson Cancer Research Center in Seattle, WA. Her main research interests are the application of gene expression and sequencing techniques to the diagnosis and detection of minimal residual disease in leukaemias, and the development of low-cost diagnostic methods for hematologic malignancies that can be useful in low-income countries.