The incorporation of prior genomic information does not necessarily improve the performance of Bayesian linkage methods: an example involving sex-specific recombination and the two-point PPL.
The incorporation of prior genomic information does not necessarily improve the performance of Bayesian linkage methods: an example involving sex-specific recombination and the two-point PPL.
复制标题
先前基因组信息的合并并不一定会提高贝叶斯连锁方法的性能：涉及性别特异性重组和两点 PPL 的示例。
DOI：
10.1159/000090543
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发表时间：
2005
期刊：
影响因子：
--
通讯作者：
Vieland,VeronicaJ
中科院分区：
文献类型：
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作者：
Logue,MarkW;Vieland,VeronicaJ
目的：我们继续统计发展的后验连锁概率（PPL）。我们提出了一个两点PPL，允许不相等的男性和女性重组分数，Θ M和ΘF，并考虑替代先验的ΘM，ΘF。方法：我们比较性别平均PPL（PPLSA），假设ΘM= ΘF，性别特异性PPL（PPLSS）（ΘM，ΘF），在一系列的模拟;我们还计算PPLSS使用替代先验（ΘM，θF）。结果：PPLSS基于先验，忽略性别特异性重组率的基因组信息，执行基本相同的PPLSA，即使在大的ΘM，Θ F差异的存在下。此外，自适应地偏斜先验，以将（正确的）基因组信息并入关于ΘM、Θ F差异，实际上降低了PPLSS的性能。我们证明，这与PPLSS本身没有什么关系，而是由于在现实的datasets.Conclusions的最大似然估计（ΘM，ΘF）的位置非常高的变异性水平：验证（正确）的基因组信息并不总是有帮助的。我们建议将PPLSA作为PPL的标准形式，而不考虑所讨论的标记区域的性别特异性重组率。
Objective:We continue statistical development of the posterior probability of linkage (PPL). We present a two-point PPL allowing for unequal male and female recombination fractions, ΘMand ΘF, and consider alternative priors on ΘM, ΘF.Methods:We compare the sex-averaged PPL (PPLSA), assuming ΘM= ΘF, to the sex-specific PPL (PPLSS) in (ΘM, ΘF), in a series of simulations; we also compute the PPLSSusing alternative priors on (ΘM, ΘF).Results:The PPLSSbased on a prior that ignores prior genomic information on sex specific recombination rates performs essentially identically to the PPLSA, even in the presence of large ΘM, ΘFdifferences. Moreover, adaptively skewing the prior, to incorporate (correct) genomic information on ΘM, ΘFdifferences, actually worsens performance of the PPLSS. We demonstrate that this has little to do with the PPLSSper se, but is rather due to extremely high levels of variability in the location of the maximum likelihood estimates of (ΘM, ΘF) in realistic data sets.Conclusions:Incorporating (correct) prior genomic information is not always helpful. We recommend that the PPLSAbe used as the standard form of the PPL regardless of the sex-specific recombination rates in the region of the marker in question.