Dodds Ken G, McEwan John C, Brauning Rudiger, Clarke Shannon M
AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
J R Soc N Z. 2025 May 21;55(6):2677-2688. doi: 10.1080/03036758.2025.2500999. eCollection 2025.
Sequencing-based methods are increasingly being used for genetic studies. Genotypes derived from the sequence data are sometimes assigned incorrectly, due to having no reads for one of the alleles. This is particularly the case when the data has low sequencing depth. Here, we develop a correction that can be applied to both a measure and a test for the population differentiation metric when considering populations as a fixed effect, to account for this incomplete genotyping. It is shown that the measure of differentiation is not influenced much by this correction in reasonably sized studies but that significance testing is too liberal without the correction. This correction will allow appropriate inference in population studies.
基于测序的方法越来越多地用于基因研究。由于其中一个等位基因没有读数，从序列数据得出的基因型有时会被错误分配。当数据的测序深度较低时，情况尤其如此。在这里，我们开发了一种校正方法，当将群体视为固定效应时，该方法可应用于群体分化指标的测量和检验，以解决这种不完全基因分型的问题。结果表明，在规模合理的研究中，这种校正对分化测量的影响不大，但如果不进行校正，显著性检验就会过于宽松。这种校正将有助于在群体研究中进行适当的推断。
