by dbking
Copy Number Variation Detection:
[Via Bench Marks]
With the sequencing of the human genome came the startling revelation that the number of copies of a given gene 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. Like all of our monthly featured protocols, it’s freely accessible for subscribers and non-subscribers alike.
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. More information on PennCNV can be found in this Genome Research article, PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.
I took the liberty of showing the entire post from David’s blog because, in contrast to my story below, this demonstrates a very good approach for publishing scientific work online.
It highlights a useful new protocol that can be downloaded for free. It also links to a Genome Research article that I can also download for free. Nice. I can quickly get up to speed on a novel protocol.
Protocols, particularly new ones are very useful to have. Making a small number available for free is a nice way to get people to check out the journal. I have it in my newsfeed. I like CSHP and enjoy David’s blog tremendously. Now I just need to find a way to become an adjunct professor at some research organization with an institutional license so I can read all the articles.
Technorati Tags: Open Access, Science, Web 2.0
Do older father’s sperm and spermatogonia have more CNVs? Is that an interesting hypothesis of where de novo CNVs come from?
I’m not an expert but I believe that the difference in copy number is between parent and children, not between different sperm in a single human. However, it is an interesting question and the tools might be available to see if it could be possible.