Evaluation of computational methods for HLA three loci haplotype by compare with family-based data / 中华实验和临床病毒学杂志

ABSTRACT

<p><b>OBJECTIVE</b>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.</p><p><b>METHODS</b>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.</p><p><b>RESULTS</b>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.</p><p><b>CONCLUSION</b>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.</p>