Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees
Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees
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DOI：
10.1159/000053366
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发表时间：
2001-01-01
期刊：
影响因子：
1.8
通讯作者：
Weeks, DE
中科院分区：
文献类型：
--
作者：
Sobel, E;Sengul, H;Weeks, DE
目标：描述、实现和测试一种有效的算法，以获得一般谱系标记基因座中任意位置的多点同一血统 (IBD) 概率。与现有程序不同，我们的算法可以分析包含大量人员和标记的数据集。该算法已在 SimWalk2 计算机包中实现。方法：使用包含五个不同大小的谱系和真实标记数据的严格测试方案，我们比较了几种广泛使用的 IBD 计算程序：Allegro、Aspex、GeneHunter、MapMaker/Sibs、Mendel、Sage、SimWalk2 和 Solar。结果：测试显示出一些差异，特别是在近亲血统方面，但确定性多点包的总体结果非常出色。 SimWalk2 还被发现与确定性多点程序非常一致，通常将 0 到 1 范围内的亲属关系系数匹配到小数点后两位。然而，基于单点 IBD 估计的程序包虽然彼此一致，但往往显示出较差的结果，与多点亲属关系结果不一致高达 0.5。结论：我们的测试清楚地表明多点 IBD 估计比单点估计要好得多。此外，我们的测试验证了我们用于估计一般谱系中任意位置的 IBD 概率的算法。版权所有 (C) 2001 S. Karger AG，巴塞尔。
Objectives:To describe, implement, and test an efficient algorithm to obtain multipoint identity-by-descent (IBD) probabilities at arbitrary positions among marker loci for general pedigrees. Unlike existing programs, our algorithm can analyze data sets with large numbers of people and markers. The algorithm has been implemented in the SimWalk2 computer package. Methods: Using a rigorous testing regimen containing five pedigrees of various sizes with realistic marker data, we compared several widely used IBD computation programs: Allegro, Aspex, GeneHunter, MapMaker/Sibs, Mendel, Sage, SimWalk2, and Solar. Results:The testing revealed a few discrepancies, particularly on consanguineous pedigrees, but overall excellent results in the deterministic multipoint packages. SimWalk2 was also found to be in good agreement with the deterministic multipoint programs, usually matching to two decimal places the kinship coefficient that ranges from 0 to 1. However, the packages based on single-point IBD estimation, while consistent with each other, often showed poor results, disagreeing with the multipoint kinship results by as much as 0.5. Conclusions: Our testing has clearly shown that multipoint IBD estimation is much better than single-point estimation. In addition, our testing has validated our algorithm for estimating IBD probabilities at arbitrary positions on general pedigrees. Copyright (C) 2001 S. Karger AG, Basel.