应用鼻咽癌家系资料评估HLA三座位单倍型软件推算方法的研究  

Evaluation of computational methods for HLA three loci haplotype by compare with family-based data

作　　者：汤敏中[1] 李军[2] 蔡永林[2] 郑裕明[2] 廖建 曾洪[2] O'BRIEN Stephen 曾毅[5] 

机构地区：[1]北京工业大学生命科学与生物工程学院,100022 [2]广西梧州市红十字会医院梧州市卫生系统鼻咽癌病因学及分子机理重点实验室 [3]广西苍梧县鼻咽癌防治所 [4]Laboratory of Genomic Diversity, National Cancer Institute Frederick, Maryland 21702, USA [5]中国疾病预防控制中心病毒病所传染病预防控制国家重点实验室

出　　处：《中华实验和临床病毒学杂志》2012年第4期288-290,共3页Chinese Journal of Experimental and Clinical Virology

基　　金：广西科技计划项目（114003A--49）;美国国立卫生院国立癌症研究所资助项目（N01-CO-12400）;梧州市科技计划项目（201102062）

摘　　要：目的通过家系资料，对比分析不同统计学单倍型推算方法在HLA-A—B—C三基因座位单倍型推算运用中的准确性及有效性。方法选择558例有完整家系资料的个体，通过SAS／Genetics、Arlequin遗传学分析软件的EM算法、ELB算法分别进行单倍体确认，计算个体单倍型频率，并与家系分析结果相比较。结果558例研究个体中，SAS／Genetics、Adequin遗传学分析软件的EM算法、ELB算法分别估算得到248、247和238种单倍型，推算准确率分别为88．5％、89．1％，90．3％。3种软件推算方法得到的单倍型推算准确性、最常见单倍型分布差异无统计学意义。结论运用统计学推算软件进行群体数据的单倍型推算可获得较高的准确性，3种算法得到的常见单倍型频率差异无统计学意义。但总体来说，ELB算法更加准确。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.

关 键 词：白细胞抗原 鼻肿瘤 单倍性 统计学 

分 类 号：R739.63[医药卫生—肿瘤]