LD between markers is a concern when using multipoint linkage analysis, and our results show there is strong LD among SNPs on chromosome 7 which were found to be associated with maximum drinks. As an additional analysis we studied global LD structure using an algorithm we have previously described [10] to produce a non-overlapping set of blocks across all the chromosomes in the Illumina and Affymetrix SNP sets and found a significant amount of LD and variable block coverage on the different chromosomes, as expected. We are developing techniques for selecting "tag" SNPs from LD blocks which should be useful in this context by allowing maps to be thinned for multipoint linkage analysis, or by targeting "tag" SNPs for priority genotyping.
