Driven by new and emerging technologies for data acquisition, integrative genomic studies are revolutionizing the way we approach the study of cancer and other diseases, and charting the way to novel treatment regimens. They require the high-throughput generation and analysis of multiple, and often complex, types of genomic data. To address this challenge, and in active collaboration with end users, we developed a broadly applicable Integrative Genomics Viewer (IGV). IGV is a high-performance, user-friendly tool used by over 100,000 investigators and clinicians worldwide for the interactive exploration of large, integrated genomic datasets. The goal of this project is to ensure that IGV continues to track and respond to advances in genomics technology and changing user needs, and maintains its high level of utility for the cancer research community. We will accomplish this through our three specific aims as described below.
Aim 1. To ensure that the IGV continues to keep pace with new and emerging technologies and the changing cancer research environment we will develop new and improved IGV views of, e.g., long range genomic events, physical proximity data, and more. In recognition of the biomedical community's increasing use of the cloud, we will ensure efficient and accessible visualization of cloud data and seamless integration with analysis workflows. An IGV Advisory Board will ensure we are best tracking technologies and user needs.
Aim 2. To enhance, refine, and maintain IGV to best support cancer researchers in their work we will develop new features and updates based on feedback and suggestions from the IGV user community. We will also take advantage of external resources that are valuable for cancer research, as well as development in support of other projects that use IGV in their own applications and resources. Special attention will be paid to collaborations and initiatives within the Informatics Technology for Cancer Research (ITCR) family of tools.
Aim 3. To provide training, support, and outreach activities for the cancer research community we will continue to provide our email help desk, workshops and documentation to help both the user and developer communities take best advantage of IGV. Importantly, we will develop a new collection of focused IGV ?sketches? to walk users through visualization tasks with high utility. We have extensive experience in software engineering, including the development and distribution of IGV and other software tools used by hundreds of thousands of biomedical researchers and clinicians worldwide. We will continue our user-driven development approach working closely with large genomics projects like The Cancer Genome Atlas, NCI supported software projects like the Cancer Genomics Cloud Pilots and the ITCR program, as well as numerous single-investigator studies. IGV's current success, flexible architecture, and our plan to support external development make us well poised to accomplish our aims to further transform data visualization and accelerate the pace of biomedical discovery.

Public Health Relevance

Given the enormous amount of data generated by research studies and in the clinic today, visualization is often a key element in gaining insight into the genomic basis and mechanisms of disease. These insights will help to develop hypotheses for further study, guide treatment, and point the way to new therapeutic targets. We propose to ensure that the Integrative Genomics Viewer (IGV) continues to track and respond to advances in genomics technology and changing user needs, and maintains its high level of utility for the cancer research community.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Resource-Related Research Projects--Cooperative Agreements (U24)
Project #
1U24CA210004-01
Application #
9186440
Study Section
Special Emphasis Panel (ZCA1-TCRB-W (M2))
Program Officer
Li, Jerry
Project Start
2016-09-01
Project End
2021-08-31
Budget Start
2016-09-01
Budget End
2017-08-31
Support Year
1
Fiscal Year
2016
Total Cost
$776,012
Indirect Cost
$232,423
Name
University of California San Diego
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Archer, Tenley C; Ehrenberger, Tobias; Mundt, Filip et al. (2018) Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell 34:396-410.e8
Robinson, James T; Turner, Douglass; Durand, Neva C et al. (2018) Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst 6:256-258.e1
Rao, Suhas S P; Huang, Su-Chen; Glenn St Hilaire, Brian et al. (2017) Cohesin Loss Eliminates All Loop Domains. Cell 171:305-320.e24
C Yuen, Ryan K; Merico, Daniele; Bookman, Matt et al. (2017) Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat Neurosci 20:602-611
Robinson, James T; Thorvaldsdóttir, Helga; Wenger, Aaron M et al. (2017) Variant Review with the Integrative Genomics Viewer. Cancer Res 77:e31-e34