title: Haplotype reconstruction and estimation of haplotype frequencies from nuclear families with only one parent available.
abstract: Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families can be an alternative strategy in determining the linkage phase. In this paper, haplotype reconstruction and estimation of haplotype frequencies via expectation maximization (EM) algorithm including nuclear families with only one parent available is proposed. Parent and his (her) child are treated as parent-child pair with one shared haplotype. This reduces the number of potential haplotype pairs for both parent and child separately, resulting in a higher accuracy of the estimation. In a series of simulations, the comparisons of PHASE, GENEHUNTER, EM-based approach for complete nuclear families and our approach are carried out. In all situations, EM-based approach for trio data is comparable but slightly worse error rate than PHASE, our approach is slightly better and much faster than PHASE for incomplete trios, the performance of GENEHUNTER is very bad in simple nuclear family settings and dramatically decreased with the number of markers being increased. On the other hand, the comparison result of different sampling designs demonstrates that sampling trios is the most efficient design to estimate haplotype frequencies in populations under same genotyping cost.
authors.affiliation: Institute of Animal Breeding and Genetics, University of Goettingen, Goettingen, Germany. xding@gwdg.de
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Ding
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.forename: Christine
authors.initials: C
authors.lastname: Flury
authors.forename: Henner
authors.initials: H
authors.lastname: Simianer
mesh_terms: D002648:Child; D003198:Computer Simulation; D004526:Efficiency; D005787:Gene Frequency; D008040:Genetic Linkage; D005828:Genetics, Population / Q000379:methods*; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D009679:Nuclear Family; D010290:Parents; D010641:Phenotype; D018401:Sample Size