Effect of copy number variation on mammalian gene expression

Project Start Date: Summer/Fall 2011
Project Title: Effect of copy number variation on mammalian gene expression
Project Contact: Mete Civelek (mcivelek@mednet.ucla.edu) (Jake Lusis’ laboratory)

Project Description:
Structural variation occurs in roughly 2-3% of the genome and can range in size from several kilobases to several megabases. These variations, termed Copy Number Variation (CNV), have been associated with disease, such as autism and schizophrenia. Human aortic endothelial cells (HAECs) that line inside the blood vessels play key roles in the initiation and progression of atherosclerosis. Our lab has been studying the effects of oxidized phospholipids on endothelial cell gene expression. We have recently cultured HAECs from approximately 150 human donors in control media or media containing oxidized phospholipids. We have genotyped the donors using

Affymetrix SNP 6.0 arrays and measured the gene expression levels using Affymetrix Human HT-HG133A arrays. Previous publication from our lab (Romanoski et al. Am J Hum Genet. 86(3):399-410) identified single nucleotide polymorphisms that control gene expression locally and distally.
For this project, we want to understand how CNVs affect gene expression and gene-by-environment interactions by performing an association study using the CNV information of the ~150 donors. This will be the first study that looks at affect of CNVs on a molecular phenotype in mammalian cells. CNV information and expression data have already been collected.

Required Experience: Interested student will use an association algorithm, such as PLINK, R and/or python for downstream analysis.

Possibility of Funding : No

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