Multi-Copy DNA More Common Than Thought

Each chromosome has a distinctive patterning of gains and losses of DNA. Yellow points show chromosomal segments with no copy number differences between people, whereas red and green points represent losses and gains of DNA respectively. The most structurally variable regions in the human genome are those with a high density of red and green points. [Credit: Matthew Hurles]


Multi-Copy DNA More Common Than Thought
By Steven Reinberg, HealthDay Reporter
posted: 22 November 2006 02:39 pm ET

(HealthDay News) -- It appears that many more genes than once thought have multiple copies of themselves, called "copy-number variants" -- some of which may contain disease-causing mutations, researchers report.
While scientists have long thought that genes appear in paired copies, researchers reporting in the Nov. 23 Nature say that many have three copies or as few as one. Moreover, these variations appear to occur in many more genes than was once thought.
This type of mutation has often been overlooked as a cause of genetic disease, the researchers add. What proportion of genetic disease is caused by copy-number variation isn't known but experts believe that it is significant.
To find out more, they have developed a DNA map of gene segments.
"This is the first-generation map of copy-number variation in the human genome," said co-researcher Stephen Scherer, from the Center for Applied Genomics at The Hospital for Sick Children, Toronto, Canada.
It has been known for about two years that a large number of copy-number variations existed, Scherer said. "Surprisingly, we found more than 1,400 copy-number variations in 270 samples. This was more than we would have expected," he said.
Scherer's group made the map by analyzing DNA from 270 individuals from four populations from Europe, Africa or Asia. The team found over 1,447 copy-number variants, covering 12 percent of the human genome. This means that copy-number variants are much more common than has been thought.
"The genes, instead of being present in the normal two copies, could be present in one or three or more copies," Scherer said. The map will make it easier for researchers to identify which genes are likely to have copy-number variations.
Copy-number variants can influence gene expression and phenotype (the way genes play out in appearance or behavior) and can cause disease. So, unless they are analyzed directly, they could be missed by the current strategies that experts use to identify DNA mutations in genetic diseases.
Based on this finding, researchers may need to go back and look again at genes involved in diseases, Scherer said. "We are going to find tens of thousands of these differences," he said.
In a related study published online in Nature Genetics, Scherer and colleagues posit that many new copy-number variants might be identified by contrasting the work of two groups -- the government-funded Human Genome Project and the private company Celera Genomics. Both groups have mapped the human genome separately, so a comparison of the two outcomes might turn up numerous copy-number discrepancies.
Such a comparison would probably be sensitive and cost-effective, according to Scherer. "You can use this comparison to build a more complete reference sequence," he said.
Another expert believes the findings will be important in understanding gene-based diseases.
"These findings should cause us to re-think how our genomes -- our 'books of life' -- differ between individuals," said Chris P. Ponting, a professor of bioinformatics at the University of Oxford.
"We now know that humans' genetic texts (DNA) differ more because of the large copy or delete changes, than because of single-letter changes." Ponting said. "This should now give us hope that these textual changes can be linked to larger numbers of rare or common diseases," he said.
More information
There's much more on the human genome at the U.S. National Genome Research Institute.
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