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Cold Spring Harbor Protocols features methods for analyzing genomes and plant cells

COLD SPRING HARBOR, N.Y. (Monday, June 2, 2008) With the sequencing of the human genome came the startling revelation that the number of copies of a genes and other DNA sequences can vary widely between individuals. This copy number variation (or CNV), contributes to our species' genetic diversity but it has also been linked to genetic diseases. This month's issue of Cold Spring Harbor Protocols ( features a new method for detecting copy number variation.

"Copy Number Variation Detection Via High-Density SNP Genotyping" describes the use of PennCNV, a new computational tool for CNV detection in data from genomic arrays. Developed in the laboratory of Maja Bucan ( at the University of Pennsylvania, the software is freely available for download ( Analysis with PennCNV will provide a more comprehensive understanding of genome variation and will aid in studies seeking the causes of genetic diseases. The protocol is freely accessible on the website for Cold Spring Harbor Protocols (

The second featured method for June, "Isolation and Whole-Cell Patch Clamping of Arabidopsis Guard Cell Protoplasts," provides a method for analyzing ion differences across membranes, a vital step in understanding cellular responses to internal and external stimuli. This is particularly difficult to study in plant cells because they are surrounded by cell walls that make traditional techniques impossible. Pennsylvania State University's Sarah Assmann (, provides a protocol that describes the isolation of plant cells without cell walls and the patch clamp method of measuring electrical differences inside and outside of these cells. This method is freely accessible on the website for Cold Spring Harbor Protocols (


Contact: David Crotty
Cold Spring Harbor Laboratory

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