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  • Title: [Evaluation of computational methods for HLA three loci haplotype by compare with family-based data].
    Author: Tang MZ, Li J, Cai YL, Zheng YM, Liao J, Zeng H, O'Brien S, Zeng Y.
    Journal: Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi; 2012 Aug; 26(4):288-90. PubMed ID: 23189847.
    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. CONCLUSION: 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.
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