Fragment length distributions and collision probabilities for AFLP markers
Fragment length distributions and collision probabilities for AFLP markers
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DOI：
10.1111/j.1541-0420.2006.00613.x
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发表时间：
2006-12-01
期刊：
影响因子：
1.9
通讯作者：
Stein, Alfred
中科院分区：
文献类型：
--
作者：
Gort, Gerrit;Koopman, Wirn J. M.;Stein, Alfred
AFLP是一种DNA指纹技术，经常用于植物和动物科学。该技术的一个缺点是在单个AFLP通道中出现相同长度的多个DNA片段，我们称之为碰撞。在本文中，我们量化了这个问题。众所周知的生日问题起了作用。碰撞概率的计算需要一个碎片长度分布（field）。我们讨论了三种估计田间的方法：基于理论考虑，利用拟南芥DNA序列数据进行计算机测定，或直接从AFLP数据进行估计。在后一种情况下，我们使用具有片段长度概率单调平滑的广义线性模型。碰撞概率从两个角度计算，假设已知碎片计数和假设已知频带计数。我们比较了许多领域的结果，范围从均匀到高度倾斜。结论是碰撞经常发生，频带数量越多，分布越偏，在较小程度上，得分范围越小，碰撞概率越高。对于一个典型的植物基因组，一个有19个条带的AFLP可能包含第一次碰撞。讨论了碰撞的实际意义。生菜和菊苣的AFLP例子用于说明。
AFLP is a DNA fingerprinting technique frequently used in plant and animal sciences. A drawback of the technique is the occurrence of multiple DNA fragments of the same length in a single AFLP lane, which we name a collision. In this article we quantify the problem. The well-known birthday problem plays a role. Calculation of collision probabilities requires a fragment length distribution (fld). We discuss three ways to estimate the fld: based on theoretical considerations, on in-silico determination using DNA sequence data from Arabidopsis thaliana, or on direct estimation from AFLP data. In the latter case we use a generalized linear model with monotone smoothing of the fragment length probabilities. Collision probabilities are calculated from two perspectives, assuming known fragment counts and assuming known band counts. We compare results for a number of fld's, ranging from uniform to highly skewed. The conclusion is that collisions occur often, with higher probabilities for higher numbers of bands, for more skewed distributions, and, to a lesser extent, for smaller scoring ranges. For a typical plant genome an AFLP with 19 bands is likely to contain the first collision. Practical implications of collisions are discussed. AFLP examples from lettuce and chicory are used for illustration.