Comparisons of methods for linkage analysis and haplotype reconstruction using extended pedigree data

We compare and contrast the performance of SIMPLE, a Monte Carlo based software, with that of several other methods for linkage and haplotype analyses, focusing on the simulated data from the New York City population. First, a whole-genome scan study based on the microsatellite markers was performed using GENEHUNTER. Because GENEHUNTER had to drop individuals for many of the pedigrees, we performed a follow-up study focusing on several regions of interest using SIMPLE, which can handle all pedigrees in their entirety. Second, 3 haplotyping programs, including that in SIMPLE, were used to reconstruct haplotypic configurations in pedigrees. SIMPLE emerges clearly as a preferred tool, as it can handle large pedigrees and produces haplotypic configurations without double recombinant haplotypes. For this study, we had knowledge of the simulating models at the time we performed the analysis.