title: [Evaluation of computational methods for HLA three loci haplotype by compare with family-based data].
abstract: OBJECTIVE
  We evaluated the accuracy and efficiency of computational inference methods for haplotype on estimate HLA-A-B-C haplotype frequencies by compared with the haplotypes manually defined in a family-base dataset.
  
  
  METHODS
  558 individuals with pedigree information were selected, and their haplotyps were compared with the data obtained by the following three method: the Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB)algorithms using the AELEQUIN software, and the SAS/Genetics PROC HAPLOTYPE method.
  
  
  RESULTS
  After performing the SAS/Genetics method, and the Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB) algorithms using the AELEQUIN software, 248, 247, and 238 different haplotypes were obtained respectively. The accuracy rates of these three methods were 88.5%, 89.1%, and 90.3% respectively. There are no significant different in the accuracy and estimated haplotype frequency comparisons among any two of these computational inference methods.
  
  
  CONCLUSIONS
  High accuracy haplotype frequency estimate rates could be obtained by these three computational inference methods, and there are no significant difference in the comparison of haplotypes estimated by SAS/Genetics, the EM and ELB algorithms using the AELEQUIN software. However, ELB algorithm shows better performance than EM algorithm and SAS/Genetics PROC HAPLOTYPE method for haplotype frequencies estimation in general.
authors.affiliation: College of Life Science and Bio-engineering, Beijing University of Technology, Beijing 100022, China.
authors.forename: Min-Zhong
authors.initials: MZ
authors.lastname: Tang
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Yong-Lin
authors.initials: YL
authors.lastname: Cai
authors.forename: Yu-Ming
authors.initials: YM
authors.lastname: Zheng
authors.forename: Jian
authors.initials: J
authors.lastname: Liao
authors.forename: Hong
authors.initials: H
authors.lastname: Zeng
authors.forename: Stephen
authors.initials: S
authors.lastname: O'Brien
authors.forename: Yi
authors.initials: Y
authors.lastname: Zeng
mesh_terms: D000328:Adult; D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D005260:Female; D006239:Haplotypes; D015395:Histocompatibility Antigens Class I / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009669:Nose Neoplasms / Q000175:diagnosis / Q000235:genetics*; D010375:Pedigree; D012984:Software; D055815:Young Adult
chemical_list: D015395:Histocompatibility Antigens Class I