A very interesting paper is now online at Nature. It is entitled 'Global variation in copy number in the human genome' (
Redon et al., 2006). The full article is freely available online.
We have recently had a number of threads discussing human/chimp genetics and the significance of indels on measurements of divergence and their significance to evolution. This paper studied copy number variations which include indels as well as duplications and more complex genetic events.
This nature paper is a product of the haplotype mapping (HAPMAP) project which is being worked on by a number of HGP contributors such as the Sanger centre. The abstract is as follows...
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
They identified 1,447 regions (CNVRs) in the genome where there were variations in copy number amongst the sampled genomes of sequences greater than 1Kb in size. These regions covered 12% of the genome altogether.
They go on to show that copy number variations can be used to identify populations with putative common ancestry from european, asian and african populations.
It would be interesting to see how these CNVRs compare to the regions of indels associated with the increased estimates in human chimp divergence. If both human and chimps can have as much as 12% variation based on CNVR's with populations then how much distinct difference do such factors present between the 2 species.
This is really phenomenal work and as more organisms are studied at the same level of detail it opens up the possibility of identifying a vast area of functionally relevant variation both within and between mammalian species and throughout the animal kingdom. This also has major implications for the study of genetic differences affecting responses to medical treatments and to disease in general.
There are at least 2 other CNV papers out related to this one, one in nature genetics (
Khaja et al, 2006) and one in Genome Research which explains the technical methodology behind the comparisons in more detail(
Fiegler et al., 2006)
TTFN,
WK
Edited by Wounded King, : No reason given.
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