Graphical tests for Hardy-Weinberg equilibrium based on the ternary plot
Graphical tests for Hardy-Weinberg equilibrium based on the ternary plot
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DOI：
10.1159/000108939
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发表时间：
2008-01-01
期刊：
影响因子：
1.8
通讯作者：
Morales Camarena, Jair
中科院分区：
文献类型：
--
作者：
Graffelman, Jan;Morales Camarena, Jair
目的：设计Hardy-Weinberg均衡的图解检验。这可以绕过p值的计算，并且可以从它们在图中的位置来推断大量双等位标记的统计(非)意义。方法：用杂合子频率改写X(2)统计量(有无连续性校正)的表达式，得到可用三元图描述的Hardy-Weinberg平衡的接受区域。结果：我们得到了三元曲线图中的曲线方程，该曲线图将超出Hardy-Weinberg平衡的标记与处于平衡的标记分开。曲线取决于所选的重要程度、样本大小和连续性校正参数。描述了使用人类22号染色体长臂上的一组106个SNPs进行图形测试的一些例子。显著标记和有大量缺失值的较差标记很容易在所建议的地块中被识别。提供了用于绘制图表的软件。结论：提出的图谱可作为大规模基因分型研究中发现有问题的标记的控制图，并为双等位基因标记数据的图形化探索提供了一个很好的工具。版权所有(C)2007 S.Karger AG，巴塞尔。
Objective: We design a graphical test for Hardy- Weinberg equilibrium. This can circumvent the calculation of p values and the statistical (non)significance of a large number of bi-allelic markers can be inferred from their position in a graph. Method: By rewriting expressions for the chi(2) statistic ( with and without continuity correction) in terms of the heterozygote frequency an acceptance region for Hardy- Weinberg equilibrium is obtained that can be depicted in a ternary plot. Results: We obtain equations for curves in the ternary plot that separate markers that are out of Hardy- Weinberg equilibrium from those that are in equilibrium. The curves depend on the chosen significance level, the sample size and on a continuity correction parameter. Some examples of graphical tests using a set of 106 SNPs on the long arm of human chromosome 22 are described. Significant markers and poor markers with a lot of missing values are easily identified in the proposed plots. R software for making the diagrams is provided. Conclusion: The proposed graphs can be used as control charts for spotting problematic markers in large scale genotyping studies, and constitute an excellent tool for the graphical exploration of bi-allelic marker data. Copyright (C) 2007 S. Karger AG, Basel.