Department of Mathematics and Statistics, American University, Washington, District of Columbia, USA.
Biometrics. 2023 Sep;79(3):2143-2156. doi: 10.1111/biom.13722. Epub 2022 Jul 26.
Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. We validate our methods on both simulated and real data.
许多生物信息学管道都包含平衡测试。二倍体的测试研究得很好，也广泛可用，但将这些方法扩展到同源多倍体时，会受到减数分裂过程中同源染色单体片段双减数的阻碍。虽然这对平衡测试构成了障碍，但双减数率本身就是人们感兴趣的数量，因为它们提供了同源多倍体生物减数行为的见解。在这里，我们开发了一些程序来（i）在考虑双减数的情况下进行平衡测试，（ii）在给定平衡的情况下估计双减数率。为此，我们采用了两种方法：一种是似然方法，另一种是新颖的 U 统计量最小化方法，我们证明该方法在二倍体中推广了经典的平衡 χ 检验。对于小样本量和不确定的基因型，我们进一步开发了基于我们的 U 统计量的自举程序来进行平衡测试。我们在模拟和真实数据上验证了我们的方法。
