Researchers Unveil New SNP Genetic Linkage Map

Researchers have produced a high-resolution genetic linkage map based on more than 3,000 single-nucleotide polymorphisms (SNPs), points in a gene where there are variations due to the replacement of a single nucleotide.

Investigators at Rutgers University (Piscataway, NJ, USA) evaluated 6,297 SNPs in a diversity panel composed of European Americans, African Americans, and Asians. The markers were assessed for assay robustness, suitable allele frequencies, and informativeness of multi-SNP clusters. Extensive genotyping-error analysis was performed, and the resulting SNP linkage map has an average map resolution of 3.9 cM, with map positions containing either a single SNP or several tightly linked SNPs. The map was published in the August 2003 issue of the American Journal of Human Genetics.

"Our challenge was to calculate the recombination distance--a measure of interaction-- between the markers,” explained first author Dr. Tara Matise, associate research professor in the department of genetics at Rutgers University. "This is the first map of its kind, a genomewide SNP linkage map, and it provides the kind of data we need to conduct our analyses in the search for disease genes. Since our map is much more dense and has more markers than other kinds of maps, we wanted to see how good it really is. We did some calculations to compare the information content of our SNP map versus some existing maps commonly used for genome screening,” said Dr. Matise. "It turns out that our map is equivalent to or better than the other maps that are currently used.”



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