MI-GWAS: a SAS platform for the analysis of inherited and maternal genetic effects in genome-wide association studies using log-linear models.
MI-GWAS: a SAS platform for the analysis of inherited and maternal genetic effects in genome-wide association studies using log-linear models.
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DOI：
10.1186/1471-2105-12-117
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发表时间：
2011-04-22
影响因子：
3
通讯作者：
Mitchell LE
中科院分区：
文献类型：
--
作者：
Agopian AJ;Mitchell LE
有几个分析全基因组关联数据的平台可用。然而，这些平台侧重于对受影响个人(即病例)遗传的基因进行评估，而对于某些情况(如出生缺陷)，受影响个人的母亲的基因也可能导致风险。对于这样的情况，评估与母体和遗传(即病例)基因的相关性是至关重要的。当病例-双亲三联症的基因型数据可用时，使用对数线性建模的基于似然的方法可用于评估母系和遗传型。然而，可用于对数线性分析的软件包并不能很好地适用于典型的全基因组关联数据(例如，包括缺失数据)的分析。描述了一个用于全基因组关联研究的综合平台--母系和遗传分析(MI-GWAS)，用于对大型全基因组数据集中的母系和遗传遗传效应进行对数线性分析。MI-Gwas结合使用SAS和LEM软件对数据进行适当格式化，执行对数线性分析，并对结果进行汇总。该平台使用现有的全基因组数据进行了评估，并被证明执行准确和相对有效。MI-Gwas平台提供了一个宝贵的工具，用于使用来自病例-父母三系的全基因组数据来分析表型或疾病与母体和遗传的基因类型的关联。该平台的源代码可在http://www.sph.uth.tmc.edu/sbrr/mi-gwas.htm.上免费获得
Several platforms for the analysis of genome-wide association data are available. However, these platforms focus on the evaluation of the genotype inherited by affected (i.e. case) individuals, whereas for some conditions (e.g. birth defects) the genotype of the mothers of affected individuals may also contribute to risk. For such conditions, it is critical to evaluate associations with both the maternal and the inherited (i.e. case) genotype. When genotype data are available for case-parent triads, a likelihood-based approach using log-linear modeling can be used to assess both the maternal and inherited genotypes. However, available software packages for log-linear analyses are not well suited to the analysis of typical genome-wide association data (e.g. including missing data). An integrated platform, Maternal and Inherited Analyses for Genome-wide Association Studies (MI-GWAS) for log-linear analyses of maternal and inherited genetic effects in large, genome-wide datasets, is described. MI-GWAS uses SAS and LEM software in combination to appropriately format data, perform the log-linear analyses and summarize the results. This platform was evaluated using existing genome-wide data and was shown to perform accurately and relatively efficiently. The MI-GWAS platform provides a valuable tool for the analysis of association of a phenotype or condition with maternal and inherited genotypes using genome-wide data from case-parent triads. The source code for this platform is freely available at http://www.sph.uth.tmc.edu/sbrr/mi-gwas.htm.
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