January 12-16, 2008
Town & Country Convention Center
San Diego, CA
Faye D. Schilkey , Neil A. Miller , Joann Mudge , Andrew Farmer , Selene Virk , C. Forrest Black , M. Kathy Myers , Lar C. Mader , Dan C. Weems , Melodie Rice , Terri Gomez , Linda Julien , Sharon Lewis , Steven Day , Kamal Gajendran , Susan M. Baxter , Gregory D. May , Stephen F. Kingsmore
Non-synonymous genetic variations (nsVariants) that cause an amino acid change are key to understanding both traits and the response to various diseases in plants. These variations include non-synonymous (ns) single nucleotide polymorphisms (SNPs), insertions / deletions (indels), premature stop codons, and splice isoforms, We have developed an analysis pipeline and visualization software for genetic variation detection using high-throughput, “next-generation” DNA sequencing technologies, specifically Illumina-Solexa Genome Analyzer (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystems SOLiD (sequencing-by-ligation). These technologies feature gigabase-scale throughput with characteristic short reads that are problematic for conventional assembly and analysis pipelines. Alpheus identifies variants within short DNA sequence reads and filters these reads based on consistent variant calls, allele frequency, quality, coverage, and variant type, thus dramatically reducing false positive variants. Researchers performing candidate gene studies for example, can reduce their candidate gene list from tens of thousands to tens. Alpheus features automated data handling, a computational analysis pipeline, a results database and a web-based query and visualization interface. The system allows clients to view and analyze sequence alignments, nucleotide variants and splice isoforms, as well as cross-sample comparisons via a secure web-browser. We demonstrate the facility of the software applied to variant detection in a soybean resequencing project.