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New Map for Gene Hunters
Midsize DNA variations could aid in search for disease genes

Results: Researchers led by Evan Eichler of the University of Washington have made a map of specific types of variation in the human genome, many of which had never been documented before: insertions, deletions, and inversions of pieces of DNA, the majority of which ranged from 8,000 to 40,000 letters long. By comparing the genomes of two people, they found 297 sites of such variations, including 139 insertions, 102 deletions, and 44 inversions. When they compared these sites to 16 that had been previously documented, they found that their map had identified seven of them, most of which were associated with disease risk or drug sensitivity. This suggests that more of these newly discovered variations may play a role in disease or drug response.

Why It Matters: To find disease-causing genes, researchers need maps showing the locations of genetic variations between individuals. In the last few years, researchers have been mapping single-nucleotide polymorphisms (SNPs), one-letter changes in the DNA sequence, both individually and in sets of thousands that occur together. Researchers have also identified much-larger-scale genomic differences between individuals but hadn’t yet mapped intermediate-size variations such as insertions, deletions, and inversions. To do a comprehensive search for disease genes, researchers need to look at all types of variation. This new map can help them do that.

Methods: The researchers compared the reference human genome decoded in draft form in 2001 with the genome of a second person. This second genome was in the form of a library of one million pieces of DNA, each 40,000 letters long. The researchers sequenced 500 letters on each end of each piece and looked for matching sequences in the reference genome using bioinformatics software. By looking at the distance between two 500-letter-long sections of DNA in the reference genome, which corresponded to the two ends of one piece from the second genome, the researchers could tell whether an insertion or deletion had occurred between them. If the two 500-letter-long sections were in reverse order, that indicated an inversion.

Next Step: The researchers would like to make their map more complete by comparing not just two genomes but 10. They are also developing tests that can quickly identify which variations occur in particular patients. Other researchers could then use these tests to compare the genomic variations of thousands of healthy and diseased individuals to find genes that may be contributing to the disease.

Source: Tuzun, E., et al. 2005. Fine-scale structural variation of the human genome. Nature Genetics 37:727-732.

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Tagged: Biomedicine

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