Abstract
Single nucleotide polymorphisms in the human genome have become an increasingly popular topic in that their analyses promise to be a key step toward personalized medicine. We investigate two related questions, how much the haplotype information contributes to linkage disequilibrium (LD) mapping and whether an in silico haplotype construction preceding the LD analysis can help. For disease gene mapping, using both simulated and real data sets on cystic fibrosis and the Alzheimer disease, we reached the following conclusions: (1) for simple Mendelian diseases, in which case a tractable full statistical model can be developed, the loss of haplotype information for either control or disease data do not have a great impact on LD fine mapping, and haplotype inference should be carried out jointly with LD mapping; (2) for complex diseases, inferring haplotype phases for individuals prior to LD mapping helps achieve a better accuracy. An improved version of the linkage disequilibrium mapping program, BLADE v2, is available at http://www.fas.harvard.edu/junliu/TechRept/03folder/bladev2.tgz.