Patterns of genetic variation in humans and mice

Positional cloning of genes underlying the heritability of autoimmune disease, as in many complex diseases, has largely been a frustrating exercise with few replicated positive findings despite enormous efforts at linkage and association mapping over the past ten years. Similar difficulties have been encountered by researchers attempting to identify such genes in murine models of autoimmunity. One reason is the lack of primary knowledge of genetic variation patterns that would enable the more efficient design and interpretation of comprehensive genetic association studies. We here describe progress towards haplotype maps of both the human and mouse genomes including their current application in the search for genes underlying autoimmune and inflammatory disorders.