The Genom of Homo sapiens.pdf

HUMAN SEQUENCE VARIATION 59Figure 2. Linkage disequilibrium (LD) and meiotic recombination: Chromosome 22. The LD profile is based on average D´ valuesin sliding windows (see text). LD and cumulative recombination frequency are plotted relative to physical distance along the chromosome,with the telomere of the long arm on the right of the figure.where pair-wise LD values (based on D´) between threeor more adjacent SNPs exceeded a defined threshold (seeFig. 3a–c). Within regions of high LD, it was possible todefine a limited number of common haplotypes that representedmost of the chromosomes in the study (Fig. 3d).These regions were termed “haplotype blocks” (Gabrielet al. 2002). They were separated by regions where LDhad not been detected, either because LD was low or becausethere were too few markers available. The blockmethod did not fully take into account LD between blocksand did not provide a continuous view of the pattern ofLD. Nevertheless, it would be possible to use it as a simpleand reliable indicator of regions where data frommore SNPs was needed. As expected from previous workFigure 3. SNPs, linkage disequilibrium, and haplotypes. The schematic diagram depicts the course of an experiment carried out intwo tiers as follows. First tier: From the SNP map of the genome, SNPs are selected (blue vertical bars in a) and used to genotypeDNA samples. The results are used to calculate pair-wise LD (curved arrows in b), and the results are compiled to define regions ofhigh LD (diagonally shaded boxes in c, drawn over the SNP map). At this point, overall progress in characterizing LD is assessed,and additional SNPs are selected where more data are needed (red vertical bars in a and c). Common haplotypes (colored bars in d)are determined from the LD data. A subset of the SNPs (“tag” SNPs; arrows in e) is selected that captures most or all of the commonvariation in the region (see text for details).