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United States Department of Agriculture

Agricultural Research Service

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Research Project: Structural and Functional Impacts of Copy Number Variations on the Cattle Genome

Location: Animal Genomics and Improvement Laboratory

Project Number: 8042-31000-104-02
Project Type: Reimbursable

Start Date: Feb 01, 2011
End Date: Apr 30, 2015

Objective:
Our project will produce a bioinformatics tool to study copy number variation by combining sequence-based and array-based approaches. This framework can easily re-purposed for other species and other purposes such as functional genomics studies using RNA-seq. Our project will provide the next generation cattle CNV map (many events at base resolution) - a crucial resource for developing CNV genotyping platforms and a cattle 1000 genomes project. It will also significantly improve the cattle reference genome and its annotation by filling in novel sequence information.

Approach:
1. Develop a general integrated framework to detect, classify and compare copy number variation by jointly using existing next generation sequencing, aCGH and SNP genotyping data; 2. Apply these pipelines to human and cattle datasets and evaluate their performances through computational comparison and experimental validation; 3. Test functional impacts of cattle CNVs by associating them with animal production and health traits.

Last Modified: 11/21/2014
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