The Integrative Genomics Viewer (IGV) for Cancer Research

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Project Summary/Abstract Driven by new and emerging technologies for data acquisition, integrative genomic studies are revolutionizing the way we approach the study of cancer 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, and released in 2008, a broadly applicable Integrative Genomics Viewer (IGV). IGV is an interactive, high-performance, user-friendly tool launched millions of times a year by investigators and clinicians worldwide. 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. Aim 1. Evolve IGV to keep pace with the needs of the cancer genomics community. We will continue to evolve IGV to leverage recent and future advances in genomics technologies and methods that are key to moving cancer research and treatment forward. We will add new visualizations and features to better enable interpretation and validation of complex variants from both short and long read data. Through collaborations with other projects we will add new capabilities to better assess and interpret single nucleotide and structural variants. Responding to IGV’s increased use for review of variants in patient tumors, we will enhance support for this task. Aim 2. Maintain IGV to ensure continued high levels of utility, usability, and reliability. We will continue to provide frequent software releases to address feature requests, bug reports, and other suggestions from IGV’s community of both users and developers. Based on community input, we will review the IGV user interface to improve usability. We will address the challenges and opportunities presented by the evolving computing and software technology environment. We will continue to maintain the code base and downloadable installers and update them for new releases of Java, JavaScript, external libraries, browsers, and operating systems. Aim 3. Support the IGV user and open-source developer communities. We will continue to provide a high level of support including rapid responses to help requests; in-depth documentation on software use; short videos to walk users through tasks with high utility; training materials and exercises. For our vibrant, open-source developer community that contributes to the IGV code base and uses IGV in their own applications or resources, support includes: documentation and code examples for integrating and extending IGV; guidance on new development through our GitHub forums; prompt review of contributions; and acknowledgement of their work. We have extensive software engineering experience, developing and distributing IGV and other software tools used by hundreds of thousands of biomedical researchers and clinicians worldwide. IGV’s success, user-driven development approach, collaborative tradition, and flexible architecture make us well poised to accomplish our aims to further transform data visualization and accelerate the pace of biomedical discovery.