This linkage map is based on the amount of the interaction or recombination taking place among nearly 3,000 genetic markers whose positions are known. The markers used for the map are single-nucleotide polymorphisms (SNPs) – the variations of a gene that people may carry at one point on their DNA.
A paper describing the linkage map will appear in the August 2003 issue of the American Journal of Human Genetics and is currently available online. Matise is first author on the paper, with Assistant Professor Steven Buyske and graduate student Chunsheng He, both from Rutgers, The State University of New Jersey, also among the authors.
Matise pointed out that SNPs provide a shortcut for pinpointing genes that may contribute to disease because the SNPs are both plentiful and easy to analyze. Many SNPs lie within genes associated with a disease, while others are near such genes, she added.
"Our challenge was to calculate the recombination distance – a measure of interaction – between the markers," said Matise, an associate research professor in the department of genetics. "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 Matise. "It turns out that our map is equivalent to or better than the other maps that are currently used."
Matise explained that without this kind of map, SNP-based linkage screening in humans – a procedure by which the entire genome is scanned for evidence of linkage to a disease – cannot be done. This screening is currently performed using specialized and customized high-throughput genotyping machines commercially available from companies including Applied Biosystems, Illumina and Amersham Biosciences.
But in the journal article, Matise and her co-authors wrote, "It is anticipated that the successful identification of a set of SNPs tailored for linkage analysis, such as that presented here, will stimulate development of mass-produced (i.e., less expensive) means for large-scale genotyping with this same marker set."
American Journal of Human Genetics