Identifying functional elements in the genome is our ultimate objective. These elements are not just confined to protein coding portions, but also RNA coding genes and the regulatory elements that dictate the pattern of expression. Evidence indicates some of these non-protein coding regions have distinct patterns of substitution (see Wakefield, Maxwell and Huttley, 2005). For instance, cytosine residues that are subject to methylation can be functional but prone to mutation. We seek to establish how this mutation selection balance plays out within the genome.
Biological processes arise from networks of interacting molecules. These networks underlie the important genetic phenomenon epistasis, a dependence of the genotype to phenotype map at a locus on the genotypes present at other loci. Such effects underlie the genetic etiology of complex diseases. We have projects underway to assess the potential utility of comparative genomic analyses to revealing these dependencies.
One of the most successful approaches to-date for establishing associations between genetic variation and human phenotype has been using candidate genes, genes that from external evidence such as molecular biology research, contribute to a suspected process. We are involved in assessing the contribution to human lupus of candidate genes identified from a genome wide ENU mouse mutagenesis.