PRELIMINARY ORDERING OF MULTIPLE LINKED LOCI USING PAIRWISE LINKAGE DATA
PRELIMINARY ORDERING OF MULTIPLE LINKED LOCI USING PAIRWISE LINKAGE DATA
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DOI：
10.1002/gepi.1370090507
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发表时间：
1992-01-01
影响因子：
2.1
通讯作者：
FALK, CT
中科院分区：
文献类型：
--
作者：
FALK, CT
提出了一种利用成对连锁数据对染色体上的基因座进行初步排序的方法。该方法基于生物学上合理的假设，即一组连锁基因座的“真实”顺序将是使染色体片段的总长度最小化的顺序。这里，“长度”被定义为相邻重组分数的总和。该方法搜索最佳顺序，由最小距离图（MDMAP）表示，即使当它是不可能检查的n！/ n个基因座的2个可能的不同顺序。使用柯克帕特里克等人[1983]的模拟退火算法的计算机化方法形成了该方法的基础。它可以应用于从辐射杂种实验以及从传统的家庭连锁研究的数据。该技术应用于几组已发布的数据，以说明它在实践中的表现。的优点和缺点的方法进行了讨论，以便它将是清楚的，在什么条件下，它可能会工作得很好。当数据集是“完整的”，在这个意义上说，所有可能的成对重组分数有估计，当没有非常紧密连锁的基因座的大集群是存在的，该方法产生的基因座，以及同意与其他更复杂的方法所产生的有序集。出现的任何差异都可能是关于最近邻基因座的方向，其中相对顺序不能通过任何方法可靠地建立。因此，该方法提供了一种简单、快速的手段，用于获得已知在同一连锁群中的一组基因座的初步顺序。
A method is presented for the preliminary ordering of loci on a chromosome using pairwise linkage data. The method is based on the biologically reasonable assumption that the "true" order of a set of linked loci will be the one that minimizes the total length of the chromosome segment. Here the "length" is defined as the sum of adjacent recombination fractions. The method searches for the optimal order, represented by a minimum distance map (MDMAP), even when it is not possible to examine the n!/2 possible distinct orders for n loci. A computerized approach, using the simulated annealing algorithm of Kirkpatrick et al. [1983], forms the basis of the method. It can be applied to data from radiation hybrid experiments as well as that from conventional family linkage studies. The technique is applied to several sets of published data to illustrate how it performs in practice. The advantages and the disadvantages of the method are discussed so that it will be clear under what conditions it is likely to work well. When data sets are "complete," in the sense that all possible pairwise recombination fractions have estimates, and when no large clusters of extremely tightly linked loci are present, the method produces ordered sets of loci that agree well with those generated by other, more complex methods. Any discrepancies that occur are likely to be with respect to the orientation of nearest-neighbor loci, where relative order cannot be reliably established by any method. The method thus provides a simple, rapid means of obtaining a preliminary order for a set of loci known to be in the same linkage group.