Genomic studies, such as those for the Cancer Genome Atlas (TCGA) project, are poised to revolutionize the way we approach the study of cancer and chart the way to novel treatment regimens for the disease. They require the high-throughput generation and analysis of multiple types of genomic data. Key to this work is the ability to (1) Simultaneously view and interact with all the data types while anchoring them to the genome and highlighting the important relationships, (2) Handle terabytes of data, (3) Smoothly and rapidly zoom from base-pair to whole-genome scale just as Google Maps can zoom from street to city to country to the world, (4) Easily integrate new data types, views, and layouts. No current genome browser or other software tool fully meets this challenge. The goal of this proposal is to design and develop an Integrative Genomics Data Viewer (IGV) that meets all these key needs and to make it available to the cancer research community.
The specific aims of the proposal focus on:
Aim 1. Developing an integrative data viewer allowing rapid, simultaneous navigation of multiple data types, Aim 2. Providing data representations and tools to insure maximally responsive user interaction with very large (terabyte+) data sets, including real time zoom and pan from base-pair to whole-genome views, Aim 3. Software distribution and support. We are part of both a TCGA Genome Sequencing Center and TCGA Cancer Genome Characterization Center. We have extensive experience in software engineering, including the development and distribution of software used by over 5500 scientists world-wide. All this, together with our initial IGV prototype, makes us well poised to carry out the aims of this proposal. Project narrative: We propose to design and develop an Integrative Genomics Data Viewer (IGV) to support the TCGA project. The IGV will provide the ability to flexibly display multiple data types and analytic results against genomic coordinates with near-immediate response time from single base-pair to the whole-genome views and will scale to multi-terabyte data sets.
| Thorvaldsdóttir, Helga; Robinson, James T; Turner, Douglass et al. (2015) A genomic data viewer for iPad. Genome Biol 16:46 |
| Thorvaldsdóttir, Helga; Robinson, James T; Mesirov, Jill P (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178-92 |
| Robinson, James T; Thorvaldsdóttir, Helga; Winckler, Wendy et al. (2011) Integrative genomics viewer. Nat Biotechnol 29:24-6 |
