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.
Highlights
Autosomal short tandem repeats (AS-STR) and Y chromosomal STR (Y-STR) are powerful tools for human identification and kinship test
These results indicate that allele frequency distribution for most X chromosomal STR (X-STR) loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation
We developed two multiplex PCR system with twenty-six X-STR loci including DXS6800(Xq13), DXS6803(Xq21), DXS9898(Xq21), GATA165B12 (Xq25), DXS6854(Xq25), HPRTB(Xq26), GATA31E08 (Xq27), and six clusters of closely linked markers, cluster I: DXS6807-DXS8378DXS9902 (Xp22); II: DXS7132-DXS10079-DXS10074DXS10075-DXS981 (Xq12); III: DXS6801-DXS6809DXS6789-DXS6799 (Xq21); IV: DXS7424-DXS101-DXS7133 (Xq22); V: DXS6804- GATA172D05 (Xq23); and VI: DXS8377DXS7423 (Xq28). (Fig. 1 shows the physical localization of these markers)
Summary
Autosomal short tandem repeats (AS-STR) and Y chromosomal STR (Y-STR) are powerful tools for human identification and kinship test. Many multiplex PCR systems of autosomal STR (ASSTR) and Y chromosomal STR (Y-STR) have been reported, and many commercial kits of the AS-STR and the Y-STR are available. Considerable X-STR systems have been studied in the field of population genetics and forensics [1,2,3,4,5]. Haplotype 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. It is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific
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