Riester Markus, Stadler Peter F, Klemm Konstantin
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
Theor Popul Biol. 2010 Sep;78(2):109-17. doi: 10.1016/j.tpb.2010.05.002. Epub 2010 May 23.
We present a Bayesian method for the reconstruction of pedigrees in clonal populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). The accuracy of the algorithm is demonstrated for simulated data. We show that the joint estimation of parameters of interest such as the rate of self-fertilization is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.
我们提出了一种贝叶斯方法，用于使用共显性基因组标记（如微卫星和单核苷酸多态性（SNP））重建克隆群体中的谱系。该算法的准确性在模拟数据中得到了验证。我们表明，即使使用中等效力的标记面板，也能够高精度地联合估计诸如自交率等感兴趣的参数。在这种情况下，经典方法只能确定数量非常有限的具有统计学意义的亲子关系，因此会失败。统计置信度通过马尔可夫链蒙特卡罗（MCMC）抽样进行估计。该方法在一个快速且易于使用的开源软件中实现，该软件可扩展到包含数千个体的大型数据集。
