Since my last report on Nature‘s copy number polymorphism (CNP) papers, a couple other journals have published studies of human structural polymorphisms:
Genome Research has two papers on detecting CNPs using oligonucleotide microarrays. The strategy here is to develop a microarray that contains all the unique regions of the genome (divided into ~20 nucleotide pieces). You can quantify the amount of DNA hybridized to the array. So, when you test genomic DNA, regions of single copy DNA will have a certain intensity, whereas regions that are present at multiple copies will have higher intensities. By screening for high intensity regions present in some individuals, but missing in others, CNPs can be identified. This tool can be used to identify CNPs de novo or to screen individuals for known CNPs. And the applications for disease detection (or, rather, a predisposition for disease) are pretty obvious. I’ve been meaning to write about this type of research for a while, and I hope to have more at a later date.
The American Journal of Human Genetics has published a study that used the microarray technique described above to search for CNPs in a panel of 95 individuals. They identified over 600 novel CNPs present at frequencies above 3%, many of which contain known genes. Evan Eichler is one of the senior authors on the study, and, given his role in getting the CNP game started, it’s nice to see him still contributing to this research.