Institute of Environmental Science and Research, Auckland, New Zealand.
Forensic Science SA, Adelaide, Australia; School of Biological Sciences, Flinders University, Adelaide, Australia.
Forensic Sci Int Genet. 2023 Jul;65:102876. doi: 10.1016/j.fsigen.2023.102876. Epub 2023 Apr 21.
The discrete Laplace method can be used to estimate the frequency of a Y-chromosomal STR haplotype using a random sample from the population. Two limitations of the method are the assumptions that each profile has exactly one allele at every locus and that this allele has an integer repeat number. We relax these assumptions to allow for multi-copy loci, partial repeats and null alleles. We show how the parameters to the extension of the model can be estimated by numerical optimisation using an off-the-shelf solver. Concordance with the discrete Laplace method is obtained when the data satisfy the more stringent assumptions of the original method. We also investigate the performance of the (extended) discrete Laplace method when used to assign match probabilities for haplotypes. A simulation study shows that as more loci are used, match probabilities are underestimated more severely. This is consistent with the hypothesis that the discrete Laplace method cannot model the matches that arise by being identical by descent (IBD). As the number of loci increases the fraction of matches that are IBD increases. Simulation provides support that the discrete Laplace can model those matches that arise from identity by state (IBS) only.
离散拉普拉斯方法可以用于从人群中随机抽样估计 Y 染色体 STR 单倍型的频率。该方法有两个局限性，即假设每个谱在每个位点只有一个等位基因，并且该等位基因具有整数重复数。我们放宽了这些假设，允许多拷贝位点、部分重复和无效等位基因。我们展示了如何通过使用现成的求解器进行数值优化来估计模型扩展的参数。当数据满足原始方法更严格的假设时，与离散拉普拉斯方法是一致的。我们还研究了当用于分配单倍型匹配概率时扩展的离散拉普拉斯方法的性能。一项模拟研究表明，随着使用的基因座数量的增加，匹配概率的低估程度更加严重。这与离散拉普拉斯方法不能模拟因同源（IBD）而产生的匹配的假设是一致的。随着基因座数量的增加，因同源而产生的匹配比例增加。模拟提供了支持，即离散拉普拉斯只能模拟那些因状态相同（IBS）而产生的匹配。
