German population data for 18 X-STRs: a hexaplex PCR adding two clusters of X-STRs to the Argus X-12 set and expanding t
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German population data for 18 X-STRs: a hexaplex PCR adding two clusters of X-STRs to the Argus X-12 set and expanding the German haplotype databases Sandra Hering 1 & Anna Klimova 2 & Jeanett Edelmann 3 Received: 18 March 2020 / Accepted: 20 April 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract In kinship analysis, large data sets with estimated haplotype frequencies for marker clusters are very important for the likelihood calculation. Practical use of the X-STRs demonstrated that in some complex kinship cases, the marker set of the Investigator Argus X-12 kit can be insufficient. This study aimed to extend the German data base of the Argus X-12 kit (1037 haplotypes) and for a cluster in Xq21 (806 haplotypes) with additional 700 male haplotypes and to include a further cluster in Xp22.3 to complete the X-STR marker set for complex kinship cases. Keywords X chromosome . STR markers . Haplotype frequencies . Linkage disequilibrium . Kinship analysis
Short tandem repeat markers located on the X chromosome (X-STRs) are widely used to solve complex kinship cases, especially when autosomal STRs are not informative [1]. Most of the analysis is performed using the commercial Investigator Argus X-12 kit amplifying four clusters (LG; linkage group) of three closely located markers. Further markers covering the whole X chromosome are reported, with most of them being scattered and genetically distant from each other without the assumption of linkage disequilibrium (LD) [2–6]. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00414-020-02306-z) contains supplementary material, which is available to authorized users. * Jeanett Edelmann [email protected] Sandra Hering [email protected] Anna Klimova [email protected] 1
Institute of Legal Medicine, University of Dresden, Dresden, Germany
2
Institute for Medical Informatics and Biometry, University of Dresden, Dresden, Germany
3
Institute of Legal Medicine, University of Leipzig, Leipzig, Germany
The current guidelines of using X-STRs in kinship analysis were published in 2017 [7], and the likelihood calculations accounting for linkage, LD, mutations, and recombination within or between the clusters can be implemented using a freely available software [8]. These calculations require large data sets with estimated haplotype frequencies for marker clusters that have an LD [9]. Data files for several populations are listed on the FamLinkX homepage (http://www.famlink. se/fx_index.html). However, since from a mathematical point of view, the number of haplotypes is small; larger data sets are preferred [7]. The practical application of X-STRs has shown that in some cases, the available data on 12 markers are not sufficient, especially when rare events such as mutations or recombinations occur within a linkage group [10]. Therefore, in this study, two additional clusters of X-STRs were analyzed in a new designed hexaplex PCR. The first cluste
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