Pong-Wong R, George A W, Woolliams J A, Haley C S
Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK.
Genet Sel Evol. 2001 Sep-Oct;33(5):453-71. doi: 10.1186/1297-9686-33-5-453.
A fast, partly recursive deterministic method for calculating Identity-by-Descent (IBD) probabilities was developed with the objective of using IBD in Quantitative Trait Locus (QTL) mapping. The method combined a recursive method for a single marker locus with a method to estimate IBD between sibs using multiple markers. Simulated data was used to compare the deterministic method developed in the present paper with a stochastic method (LOKI) for precision in estimating IBD probabilities and performance in the task of QTL detection with the variance component approach. This comparison was made in a variety of situations by varying family size and degree of polymorphism among marker loci. The following were observed for the deterministic method relative to MCMC: (i) it was an order of magnitude faster; (ii) its estimates of IBD probabilities were found to agree closely, even though it does not extract information when haplotypes are not known with certainty; (iii) the shape of the profile for the QTL test statistic as a function of location was similar, although the magnitude of the test statistic was slightly smaller; and (iv) the estimates of QTL variance was similar. It was concluded that the method proposed provided a rapid means of calculating the IBD matrix with only a small loss in precision, making it an attractive alternative to the use of stochastic MCMC methods. Furthermore, developments in marker technology providing denser maps would enhance the relative advantage of this method.
为了在数量性状基因座（QTL）定位中使用同源相同（IBD），开发了一种快速、部分递归的确定性方法来计算IBD概率。该方法将单个标记位点的递归方法与使用多个标记估计同胞之间IBD的方法相结合。使用模拟数据将本文开发的确定性方法与一种随机方法（LOKI）进行比较，以评估估计IBD概率的精度以及在使用方差分量方法进行QTL检测任务中的性能。通过改变家系大小和标记位点间的多态性程度，在各种情况下进行了这种比较。相对于马尔可夫链蒙特卡罗（MCMC）方法，确定性方法具有以下特点：（i）速度快一个数量级；（ii）尽管在单倍型不确定时不提取信息，但发现其IBD概率估计值非常接近；（iii）QTL检验统计量随位置变化的轮廓形状相似，尽管检验统计量的大小略小；（iv）QTL方差估计值相似。得出的结论是，所提出的方法提供了一种快速计算IBD矩阵的方法，精度损失很小，使其成为使用随机MCMC方法的有吸引力的替代方法。此外，标记技术的发展提供了更密集的图谱，将增强该方法的相对优势。
