家系数据紧密连锁位点的单体型频率估计

Haplotype Frequency Estimation for Tightly Linked Loci from Family Data

在对单体型进行重构或进行连锁不平衡分析时,往往首先要估计单体型频率。针对家系数据,提出了紧密连锁位点的单体型频率估计方法。利用子代信息减少亲代单体型的不确定性,构建家系数据的似然函数,把家系中的个体潜在的单体型看成缺失数据,采用EM迭代算法,给出了家系数据单体型频率的极大似然估计。其结果表明,家系数据紧密连锁位点的单体型频率估计可通过简单的递归迭代进行,后一步的单体型的频率估计即为前一步的加权单体型频率。

Haplotype frequencies must be estimated first when haplotypes are reconstructed or linkage disequilibrium is tested. From nuclear family data, Haplotype frequency estimation for tightly linked loci is given. The information supported by offspring is used to reduce the uncertainty of parents' haplotype. The likelihood function is given for family data. The underlying haplotypes are regarded as missing data, and then the MLE (Maximum Likelihood Estimate) of the haplotype frequencies for the family data via an EM algorithm is given. The results show that haplotype frequency for tightly linked loci from family data could be estimated by a simple recursion. The successive haplotype frequency estimation is the weighted haplotype frequency of the preceding step.