Chukhryaeva M I, Ivanov I O, Frolova S A, Koshel S M, Utevska O M, Skhalyakho R A, Agdzhoyan A T, Bogunov Yu V, Balanovska E V, Balanovsky O P
Genetika. 2016 May;52(5):595-604.
STR haplotypes of the Y chromosome are widely used as effective genetic markers in studies of human populations and in forensic DNA analysis. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. Performing this task manually is too laborious and thus unrealistic. We propose an algorithm for counting similarity between STR haplotypes. This algorithm is suitable for massive analyses of samples. It is implemented in the computer program Haplomatch, which makes it possible to find haplotypes that differ from the target haplotype by 0, 1, 2, 3, or more mutational steps. The program may operate in two modes: comparison of individuals and comparison of populations. Flexibility of the program (the possibility of using any external database), its usability (MS Excel spreadsheets are used), and the capability of being applied to other chromosomes and other species could make this software a new useful tool in population genetics and forensic and genealogical studies. The Haplomatch software is freely available on our website www.genofond.ru. The program is applied to studying the gene pool of Cossacks. Experimental analysis of Y-chromosomal diversity in a representative set (N = 131) of Upper Don Cossacks is performed. Analysis of the STR haplotypes detects genetic proximity of Cossacks to East Slavic populations (in particular, to Southern and Central Russians, as well as to Ukrainians), which confirms the hypothesis of the origin of the Cossacks mainly due to immigration from Russia and Ukraine. Also, a small genetic influence of Turkicspeaking Nogais is found, probably caused by their occurrence in the Don Voisko as part of the Tatar layer. No similarities between haplotype spectra of Cossacks and Caucasus populations are found. This case study demonstrates the effectiveness of the Haplomatch software in analyzing large sets of STR haplotypes.
Y染色体的STR单倍型在人类群体研究和法医DNA分析中被广泛用作有效的遗传标记。经常会出现比较个体或整个人群中单倍型谱的任务。手动执行此任务过于费力，因此不切实际。我们提出了一种计算STR单倍型之间相似度的算法。该算法适用于样本的大规模分析。它在计算机程序Haplomatch中实现，这使得能够找到与目标单倍型相差0、1、2、3个或更多突变步骤的单倍型。该程序可以在两种模式下运行：个体比较和群体比较。该程序的灵活性（使用任何外部数据库的可能性）、可用性（使用MS Excel电子表格）以及应用于其他染色体和其他物种的能力，可能使该软件成为群体遗传学、法医和家谱研究中的一种新的有用工具。Haplomatch软件可在我们的网站www.genofond.ru上免费获取。该程序用于研究哥萨克人的基因库。对顿河上游哥萨克人的一组代表性样本（N = 131）进行了Y染色体多样性的实验分析。对STR单倍型的分析检测到哥萨克人与东斯拉夫群体（特别是与俄罗斯南部和中部以及乌克兰人）的遗传接近性，这证实了哥萨克人主要起源于从俄罗斯和乌克兰移民的假设。此外，还发现了说突厥语的诺盖人的少量遗传影响，这可能是由于他们作为鞑靼层的一部分出现在顿河军区。未发现哥萨克人和高加索群体的单倍型谱之间有相似之处。这个案例研究证明了Haplomatch软件在分析大量STR单倍型方面的有效性。
