A novel algorithm for minimum recombinant haplotyping on pedigrees by zero recombinant block partition

Abstract

Haplotype inference based on pedigree data under the Mendelian law of inheritance and the minimum recombination principle is imperative for the construction of haplotype maps and the study of disease genes. But this problem has been proven to be NP-hard, exact algorithms previously known can't be applied to handle large-scale genotype datasets while heuristic algorithms can't gain high accuracy. This paper presents an algorithm named zero recombinant block algorithm (ZRBA) based on a new strategy using zero recombinant blocks (ZRB) as intermediate structure to reconstruct the haplotype configurations, theoretical analysis shows that this strategy can reduce the possible haplotype configurations exponentially, and following experiments demonstrate that our algorithm runs much faster than existing exact haplotyping algorithms with comparable accuracy.