Combining Structural-Equation Modeling with Genomic-Relatedness-Matrix Restricted Maximum Likelihood in OpenMx.

Combining Structural-Equation Modeling with Genomic-Relatedness-Matrix Restricted Maximum Likelihood in OpenMx.
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DOI:
10.1007/s10519-020-10037-5
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发表时间:
2021-05
期刊:
影响因子:
2.6
通讯作者:
Neale MC
Neale MC
中科院分区:
医学3区
文献类型:
--
作者:
Kirkpatrick RM;Pritikin JN;Hunter MD;Neale MC

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在双胞胎、家庭和收养研究的前基因组行为遗传学文献中,拟合生物统计结构方程模型(SEM)有很长的历史。最近,已经出现了一种方法,用于估计生物统计方差-协方差分量的基础上,而不是预期程度的遗传相似性亲属之间,但在观察到的程度的遗传相似性无关的个人之间的全基因组基因型是可用的基因组相关矩阵限制最大似然(GREML)。然而,大多数现有的GREML软件关注的是快速和有效地估计遗传力系数,遗传相关性,等等,而不是允许用户适合SEM的基因型参与者的多性状样本。因此,我们在OpenMx包中引入了一个功能,“mxGREML”,旨在适应当今基因组研究设计中的前基因组时代的生物统计SEM。我们将解释这个新特性为OpenMx带来的额外功能,以及新功能的工作原理。我们提供了一个说明性的例子,它的使用。我们讨论了该功能目前的局限性,以及我们对其进一步发展的计划。
There is a long history of fitting biometrical structural-equation models (SEMs) in the pregenomic behavioral-genetics literature of twin, family, and adoption studies. Recently, a method has emerged for estimating biometrical variance-covariance components based not upon the expected degree of genetic resemblance among relatives, but upon the observed degree of genetic resemblance among unrelated individuals for whom genome-wide genotypes are available—genomic-relatedness-matrix restricted maximum-likelihood (GREML). However, most existing GREML software is concerned with quickly and efficiently estimating heritability coefficients, genetic correlations, and so on, rather than with allowing the user to fit SEMs to multitrait samples of genotyped participants. We therefore introduce a feature in the OpenMx package, “mxGREML”, designed to fit the biometrical SEMs from the pregenomic era in present-day genomic study designs. We explain the additional functionality this new feature has brought to OpenMx, and how the new functionality works. We provide an illustrative example of its use. We discuss the feature’s current limitations, and our plans for its further development.
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影响因子: 2.6
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