Emerging Genome Technologies
Baxter, Ivan , Williams, Rick , Emerson, JJ , Okamoto, Ken , Salt, David , Borevitz, Justin .
Deletion and Duplication Detection in Arabidopsis using Tiling Arrays.
Duplications and deletions are a common source of genetic variation and are likely to contribute to phenotypic diversity within and between species. Methods to globally identify these polymorphisms will allow researchers to quickly identify candidate mutations and novel markers. Advances in microarray technology have produced arrays with millions of 25mer features. Whole genome tiling arrays cover the non-repetitive part of the Arabidopsis genome at ~35bp resolution and thus can comprehensively interrogate copy number polymorphisms > 100-200 bp when adjacent probes show increased or decreased hybridization intensity relative to a reference strain. We have improved the sensitivity of deletion /duplication prediction using the following method. 1) Probes are binned based on their thermodynamic properties and reference hybridization intensity. 2) Training data is used to calibrate insertion and deletion states and make state predictions for each probe. 3) A three state Hidden Markov Model is applied along the chromosome in the forward and backward direction. 4) Posterior Odds thresholds are applied to make state calls and provide confidence intervals around insertions and deletions. We have used this method to identify deletions and duplications in wild accessions and fast neutron induced deletions. We will present several of these examples and discuss how altering the experimental setup (for ex. by varying the number of hybridizations for each line) will alter the detection sensitivity of the method.
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1 - Purdue University, Bindley Bioscience Center, 625 Agriculture Mall Rd, HORT 305, West Lafayette, IN, 47905, USA
2 - University Of Chicago, Department of Evolution and Ecology
3 - Academia Sinica, Taiwan
4 - UCLA
5 - Purdue University, Bindley Bioscience Center, Horticulture and Landscape Architecture Department
Presentation Type: ASPB Minisymposium
Location: Continental A/Hilton
Date: Sunday, July 8th, 2007
Time: 2:50 PM