Rapid haplotype reconstruction in pedigrees with dense marker maps

Summary Reconstruction of marker phases is not straightforward when parents are untyped. In these cases information from other relatives has to be used. In dense marker maps, however, the space of possible haplotype configurations tends to be too large for procedures such as Monte Carlo Markov chains (MCMC) to be finished within a reasonable time. We developed an algorithm that is fast and generally finds the most probable haplotype. The basic idea is to use, the smallest informative marker brackets in offspring, for each marker interval. By using only information from the offspring and analysing each marker interval separately, the lengthy analysis of large numbers of different haplotype configurations is avoided. Nevertheless the most probable haplotype can be found quickly provided the marker map is dense and enough offspring are available. Simulations are provided to indicate how well the algorithm works at different combinations of marker density, number of offspring and number of alleles per marker. In situations where the algorithm reconstruction of the most probable haplotype is not guaranteed, the algorithm may still provide a haplotype close to the optimum, i.e. a suitable starting point for numeric optimization algorithms.