Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK.
BMC Bioinformatics. 2012 Jun 27;13:149. doi: 10.1186/1471-2105-13-149.
Here we present two new computer tools, PREMIM and EMIM, for the estimation of parental and child genetic effects, based on genotype data from a variety of different child-parent configurations. PREMIM allows the extraction of child-parent genotype data from standard-format pedigree data files, while EMIM uses the extracted genotype data to perform subsequent statistical analysis. The use of genotype data from the parents as well as from the child in question allows the estimation of complex genetic effects such as maternal genotype effects, maternal-foetal interactions and parent-of-origin (imprinting) effects. These effects are estimated by EMIM, incorporating chosen assumptions such as Hardy-Weinberg equilibrium or exchangeability of parental matings as required.
In application to simulated data, we show that the inference provided by EMIM is essentially equivalent to that provided by alternative (competing) software packages such as MENDEL and LEM. However, PREMIM and EMIM (used in combination) considerably outperform MENDEL and LEM in terms of speed and ease of execution.
Together, EMIM and PREMIM provide easy-to-use command-line tools for the analysis of pedigree data, giving unbiased estimates of parental and child genotype relative risks.
在这里，我们提出了两个新的计算机工具，PREMIM 和 EMIM，用于根据来自各种不同亲子配置的基因型数据来估计父母和子女的遗传效应。PREMIM 允许从标准格式的系谱数据文件中提取亲子基因型数据，而 EMIM 则使用提取的基因型数据来进行后续的统计分析。使用来自父母和有关子女的基因型数据可以估计复杂的遗传效应，例如母性基因型效应、母胎相互作用和亲源效应（印迹）。这些效应由 EMIM 估计，根据需要纳入诸如哈迪-温伯格平衡或父母交配的可交换性等选定假设。
在应用于模拟数据时，我们表明 EMIM 提供的推断实质上等同于 MENDEL 和 LEM 等替代（竞争）软件包提供的推断。然而，PREMIM 和 EMIM（组合使用）在速度和执行的简便性方面明显优于 MENDEL 和 LEM。
EMIM 和 PREMIM 一起为分析系谱数据提供了易于使用的命令行工具，可提供亲子基因型相对风险的无偏估计。
