A new method to estimate relatedness from molecular markers
A new method to estimate relatedness from molecular markers
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DOI：
10.1111/j.1365-294x.2006.02873.x
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发表时间：
2006-05-01
影响因子：
4.9
通讯作者：
Toro, MA
中科院分区：
文献类型：
--
作者：
Fernández, J;Toro, MA
四个主要问题会影响从分子标记信息估计个体间亲缘关系的方法的效率：(i)其中一些方法依赖于对基础群体中真实等位基因频率的了解；（ii）假设所有基因座均为非连锁且处于Hardy-Weinberg和连锁平衡；（iii）成对方法可能导致不协调的分配，因为它们一次只考虑两个个体；（iv）大多数通常是为特定的结构化人群构建的（只考虑少数关系类别，例如，全兄妹与非亲属）。我们开发了一种新的方法来估计相关性，它不受上述限制。该方法使用“盲搜索算法”（实际上是模拟退火）来寻找产生与使用标记计算的分子共祖矩阵相关性最高的共祖矩阵的谱系。因此（i和ii）它没有直接假设等位基因频率或Hardy-Weinberg和连锁平衡；（iii）它总是提供一致的关系，因为它同时考虑所有个体；（iv）只要增加所提议的家谱的“深度”（即世代数），亲缘关系的程度就可以像期望的那样复杂。计算机模拟表明，在特定情况下，这种新方法对基因分型错误的准确性和稳健性与其他提出的方法相当，但它更灵活，可以应对更复杂的情况。
Four major problems can affect the efficiency of methods developed to estimate relatedness between individuals from information of molecular markers: (i) some of them are dependent on the knowledge of the true allelic frequencies in the base population; (ii) they assume that all loci are unlinked and in Hardy-Weinberg and linkage equilibrium; (iii) pairwise methods can lead to incongruous assignations because they take into account only two individuals at a time; (iv) most are usually constructed for particular structured populations (only consider a few relationship classes, e.g. full-sibs vs. unrelated). We have developed a new approach to estimate relatedness that is free from the above limitations. The method uses a 'blind search algorithm' (actually simulated annealing) to find the genealogy that yield a co-ancestry matrix with the highest correlation with the molecular co-ancestry matrix calculated using the markers. Thus (i and ii) it makes no direct assumptions about allelic frequencies or Hardy-Weinberg and linkage equilibrium; (iii) it always provide congruent relationships, as it considers all individuals at a time; (iv) degrees of relatedness can be as complex as desired just increasing the 'depth' (i.e. number of generations) of the proposed genealogies. Computer simulations have shown that the accuracy and robustness against genotyping errors of this new approach is comparable to that of other proposed methods in those particular situations they were developed for, but it is more flexible and can cope with more complex situations.