IPEDX: An exact algorithm for pedigree reconstruction using genotype data

Abstract

The problem of inference of family trees, or pedigree reconstruction, for a group of individuals has attracted lots of attentions recently. Various methods have been proposed to automate the process of pedigree reconstruction given the genotypes or haplotypes of a set of individuals. The state-of-the-art method IPED is able to reconstruct large pedigrees with reasonable accuracy. However, the algorithm is shown to be an approximate algorithm. In this work, we proposed an exact method IPEDX, where two dynamic programming algorithms are developed to compute inheritance paths between ancestors and descendants as well as exact paths between extant individuals, respectively. Then IPEDX reconstructs the pedigrees utilizing the outputs of the two algorithms. Experiments show that as an exact algorithm, IPEDX generally achieves better results than IPED does. It does require longer computation time but is still very efficient for pedigrees which have a large number of generations. © 2013 IEEE.