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Figure 1. Screen shots from GEYSIR (a, b, d) and BioCarta (c) illustrating the ability to identify candidate genetic loci. Likelihood surfaces, illustrated as "heat maps," of the 22 human chromosomes from two retrospective linkage disequilibrium (LD) studies of response to vaccines or infections in a sample of families from the Icelandic population. Selection of chromosome one results in a horizontal heat map of chromosome 1. This is depicted as a heat map from one of the LD studies and is shown in the top "track." Vertical hatch marks on linkage and physical maps depict mapped simple sequence repeat (SSR) markers in the second track. Also depicted are representations of the location of all annotated genes in the third track. The location of these genes on the LD track and linkage and physical maps are shown with the "slider" bars that are used for navigation across the chromosome. Candidate genetic loci known to be associated with immunological responses are color coded (blue). Selection of one candidate genetic locus (CGL), IL12Rβ2, with a "control click" results in a BioCarta view of the supporting information from the literature and known pathways in which the gene participates. Currently these literature citations are hyperlinked to Online Mendelian Inheritance in Man (OMIM) and Medline, while pathways are hyperlinked to Kyoto Encyclopedia of Genes and Genomes (KEGG) and BioCarta. A view of the structural annotation of the gene IL12Rβ2 and the positions of allelic variants, currently in the form of single nucleotide polymorphisms (SNPs), are displayed relative to the structural annotation. A slider placed over the annotation and SNP tracks enables a view of the canonical sequence with known sequence variants displayed as "bubbles."
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