Allele and Haplotype Diversity of 26 X-STR Loci in Four Nationality Populations from China

Abstract

BackgroundHaplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis, especially when short tandem repeats (STR) fail to resolve uncertainty in relationship analysis. STR located on the X chromosome show stronger linkage disequilibrium compared with autosomal STR. So, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific.Methodology and FindingsTwenty-six X-STR loci including six clusters of linked markers DXS6807-DXS8378-DXS9902(Xp22), DXS7132-DXS10079-DXS10074-DXS10075-DXS981 (Xq12), DXS6801-DXS6809-DXS6789-DXS6799(Xq21), DXS7424-DXS101-DXS7133(Xq22), DXS6804-GATA172D05(Xq23), DXS8377-DXS7423 (Xq28) and the loci DXS6800, DXS6803, DXS9898, GATA165B12, DXS6854, HPRTB and GATA31E08 were typed in four nationality (Han, Uigur, Kazakh and Mongol) samples from China (n = 1522, 876 males and 646 females). Allele and haplotype frequency as well as linkage disequilibrium data for kinship calculation were observed. The allele frequency distribution among different populations was compared. A total of 5–20 alleles for each locus were observed and altogether 289 alleles for all the selected loci were found. Allele frequency distribution for most X-STR loci is different in different populations. A total of 876 male samples were investigated by haplotype analysis and for linkage disequilibrium. A total of 89, 703, 335, 147, 39 and 63 haplotypes were observed. Haplotype diversity was 0.9584, 0.9994, 0.9935, 0.9736, 0.9427 and 0.9571 for cluster I, II, III, IV, V and VI, respectively. Eighty-two percent of the haplotype of cluster IIwas found only once. And 94% of the haplotype of cluster III show a frequency of <1%.ConclusionsThese results indicate that allele frequency distribution for most X-STR loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation. So it is necessary to obtain allele frequency and haplotypes data of the linked loci for forensic application.

Genetic analysis of 19 X chromosome STR loci for forensic purposes in four Chinese ethnic groups

“…Meanwhile, the PIC values for the DXS10164 and DXS7423 markers were less than 0.5, which is consistent with the results of Liu et al . 9 . We found that DXS10134, DXS10079, DXS10135, and DXS10101 were the most polymorphic loci.…”

Forensic Spanish allele and haplotype database for a 17 X-STR panel

“…The markers included in the 17 X-STR panel [13] have been gathered into different clusters according to the literature, such as the cluster DXS6807-DXS8378-DXS9902 in the region Xp22 [14]. In the region Xq21, the markers DXS6801, DXS6809, and DXS6789 have been considered linked by the majority of the authors [3,21,22] and additionally, DXS6799 has also been included in this cluster [14].…”

“…In the region Xq21, the markers DXS6801, DXS6809, and DXS6789 have been considered linked by the majority of the authors [3,21,22] and additionally, DXS6799 has also been included in this cluster [14]. Finally, the markers DXS7132, DXS10079, and DXS10074 have typically been considered as a haplotype in the Xq12 region [21,22,23] and some authors have also considered the locus DXS10075 [14,24] as part of it.…”

“…The use of X-STRs for forensic purposes requires a precise knowledge of the genetic linkage among the X chromosome markers [14] in order to avoid the application of the product rule that is invalid for calculating the forensic parameters when markers are linked [2]. Typically, the X chromosome has been divided into the linkage groups 1-4 located at the following regions Xp22.2, Xq12, Xq26, and Xq28 [4].…”

Twenty Years Later: A Comprehensive Review of the X Chromosome Use in Forensic Genetics

“…In Figure 2B, it is possible to observe that the number of X-STRs analyzed is highly variable among publications with some studies genotyping a high number of X-STRs (e.g., Liu et al, 2013;Fukuta et al, 2019) and others genotyping a reduced number of loci (e.g., Watanabe et al, 2000;Koyama et al, 2002;Carvalho and Pinheiro, 2011). The number of markers included in each study varied from 1 to 27.…”