Human Variation Detection and Visualization on the DNAnexus Web 2.0 platform

DESCRIPTION (provided by applicant): DNAnexus proposes to develop a complete solution for the identification and stratification of personal genetic variation from ultra-high-throughput sequencing projects. The solution will be implemented as a Web 2.0 service and online browsing tool that will integrate public data sources such as the 1000 genomes project, comparative information, and the ENCODE II project data. Users will be able to browse and stratify the identified variation in the context of these genomic annotations, and according to the likely functional impact. In Phase I of our project, we will develop a basic browser for displaying sequence reads that are mapped to a reference genome with our state-of-the-art read mapper. The browser will support viewing mate paired reads as well as display of the variation between these reads and the reference genome. It will facilitate the algorithmic development that we will perform during Phase II, and it will be the foundation for the more sophisticated variation browser also proposed in Phase II. In Phase II, we will develop algorithms for detecting genomic variation, and a state-of-the-art browser for viewing variation in the context of existing genome annotations, functional genomic and comparative genomic data. Our algorithms for detecting variation will support all major types of genomic variation, including SNPs, microindels, larger insertions and deletions, duplications, copy number variations, inversions, and translocations. Our algorithms will be based on state-of-the-art statistical and machine learning methodology for human genome resequencing. The DNAnexus browser will have two components: a list browser that displays variation as a list filtered and stratified by criteria that a user chooses, and a powerful GUI whose navigation capabilities are inspired by modern online tools such as Google Maps. PUBLIC HEALTH RELEVANCE: DNAnexus proposes to develop a complete solution for identifying and analyzing personal genetic variation for individuals whose genomes are sequenced using new sequencing technologies. Users will be able to browse an individual genome in the context of public data sources such as the 1000 genomes project, comparative information to other mammalian species, and functional data from the ENCODE II project.