Computational Tools for Genomic Cancer Research (306431)Lisa McShane, National Cancer Institute (NIH), DCTD Division of Cancer Treatment and Diagnosis
*Alida Palmisano, National Cancer Institute (NIH), DCTD Division of Cancer Treatment and Diagnosis
Yingdong Zhao, National Cancer Institute (NIH), DCTD Division of Cancer Treatment and Diagnosis
Keywords: cancer research, computational tools, bioinformatics, genomics
In the era of personalized medicine big datasets are collected for many biomedical purposes. Computational tools are crucial to address the challenges of processing and analyzing this complex information. We develop software for various aspects biomedical research. For clinical trial management, we developed GeneMed, an informatic system to coordinate patient registration, genomic sequencing, and treatment assignment for the NCI-MPACT trial. GeneMed streamlines clinical trial management and implements support tools for complex tasks like assigning treatment based on tumor mutations and treatment eligibilities. A customizable version of the system was developed to serve as communication hub between teams of clinicians, lab personnel and statisticians. For the interactive exploration of genomic datasets, we developed D3Oncoprint, a standalone application to visualize annotated genomic mutation files. In support of the research community effort of understanding drug sensitivity and resistance, we released a database with measured gene-expression changes across cell lines exposed to anticancer agents (the NCI Transcriptional Pharmacodynamics Workbench, NCI TPW).