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Y-SNP analysis versus Y-Haplogroup Predictor in the Slovak population

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Human Y-chromosome haplogroups are important markers used mainly in population genetic studies. The haplogroups are defined by several SNPs according to the phylogeny and international nomenclature. The alternative method to estimate the Y-chromosome haplogroups is to predict Y-chromosome haplotypes from a set of Y-STR markers using software for Y-haplogroup prediction. The purpose of this study was to compare the accuracy of three types of Y-haplogroup prediction software and to determine the structure of Slovak population revealed by the Y-chromosome haplogroups. We used a sample of 166 Slovak males in which 12 Y-STR markers were genotyped in our previous study. These results were analyzed by three different software products that predict Y-haplogroups. To estimate the accuracy of these prediction software, Y-haplogroups were determined in the same sample by genotyping Y-chromosome SNPs. Haplogroups were correctly predicted in 98.80 % (Whit Athey's Haplogroup Predictor), 97.59 % (Jim Cullen's Haplogroup Predictor) and 98.19 % (YPredictor by Vadim Urasin 1.5.0) of individuals. The occurrence of errors in Y-chromosome haplogroup prediction suggests that the validation using SNP analysis is appropriate when high accuracy is required. The results of SNP based haplotype determination indicate that 39.15 % of the Slovak population belongs to R1a-M198 lineage, which is one of the main European lineages.
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Keywords: HAPLOGROUP; PREDICTION; SLOVAK POPULATION; SNP ANALYSIS; Y-CHROMOSOMAL POLYMORPHISMS

Document Type: Research Article

Publication date: 2014-06-01

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  • Anthropologischer Anzeiger is an international journal of human biology. It publishes original research papers on all fields of human biological research, that is, on all aspects, theoretical and practical of studies of human variability, including application of molecular methods and their tangents to cultural and social anthropology.

    Other than research papers, Anthropologischer Anzeiger invites the submission of case studies, reviews, technical notes and short reports.
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