Lin Chen-Pang, Fann Cathy S J
Institute of Public Health, National Yang-Ming University, Taipei, Taiwan.
J Biomed Sci. 2009 Jun 2;16(1):52. doi: 10.1186/1423-0127-16-52.
In many studies, researchers may recruit samples consisting of independent trios and unrelated individuals. However, most of the currently available haplotype inference methods do not cope well with these kinds of mixed data sets.
We propose a general and simple methodology using a mixture of weighted multinomial (MIXMUL) approach that combines separate haplotype information from unrelated individuals and independent trios for haplotype inference to the individual level.
The new MIXMUL procedure improves over existing methods in that it can accurately estimate haplotype frequencies from mixed data sets and output probable haplotype pairs in optimized reconstruction outcomes for all subjects that have contributed to estimation. Simulation results showed that this new MIXMUL procedure competes well with the EM-based method, i.e. FAMHAP, under a few assumed scenarios.
The results showed that MIXMUL can provide accurate estimates similar to those haplotype frequencies obtained from FAMHAP and output the probable haplotype pairs in the most optimal reconstruction outcome for all subjects that have contributed to estimation. If available data consist of combinations of unrelated individuals and independent trios, the MIXMUL procedure can be used to estimate the haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.
在许多研究中，研究人员可能会招募由独立三人组和无关个体组成的样本。然而，目前大多数可用的单倍型推断方法并不能很好地处理这类混合数据集。
我们提出了一种通用且简单的方法，即使用加权多项混合（MIXMUL）方法，该方法将来自无关个体和独立三人组的单独单倍型信息结合起来，用于将单倍型推断到个体水平。
新的MIXMUL程序优于现有方法，因为它可以从混合数据集中准确估计单倍型频率，并在为所有参与估计的受试者优化重建结果中输出可能的单倍型对。模拟结果表明，在一些假设情况下，这种新的MIXMUL程序与基于期望最大化（EM）的方法FAMHAP竞争良好。
结果表明，MIXMUL可以提供与从FAMHAP获得的单倍型频率相似的准确估计，并在为所有参与估计的受试者的最优重建结果中输出可能的单倍型对。如果可用数据由无关个体和独立三人组的组合组成，则MIXMUL程序可用于准确估计单倍型频率，并在估计中输出每个受试者最可能重建的单倍型对。
