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

Genetic polymorphisms of 17 X-STR loci in two Tunisian populations from Sousse and Makthar

BACKGROUND

Tunisia has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, only one population study based on X-STR markers has been reported so far.

AIM

To investigate the genetic polymorphisms of 17 X-STRs in two Tunisian populations from the cities of Sousse and Makthar, and to reveal the genetic relationships with other reference populations.

SUBJECTS AND METHODS

A total of 194 unrelated healthy individuals were analysed for 17 X-STR markers.

RESULTS

Our results indicate that DXS6809 is the most polymorphic locus, whereas DXS6807 is the least informative marker in the populations of Sousse and Makthar. In addition, forensic statistical parameters, such as the power of discrimination in males and females, as well as the mean of exclusion in duos and trios, reveal that the panel of 17 X-STRs is highly informative and useful in different forensic applications. Overall, pairwise genetic distances (Fst) and non-metric MDS plots demonstrate clustering of different populations according to their geographic locations and their historical relationships.

CONCLUSION

Overall, the study of X-STR markers of the Tunisian populations can help to promote the establishment of a forensic DNA reference database in Tunisia and provide reference for future anthropological research.

Study of 17 X-STRs in Native American and Mestizo populations of Central America for forensic and population purposes

In the present work, an extensive analysis of the X-chromosomal pool of Native American and Mestizo groups of Central America (Guatemala, El Salvador, Nicaragua, and Panama) has been carried out. Allele and haplotype frequency databases, as well as other forensic parameters for these populations, are presented. The admixture analysis supports the tri-hybrid composition in terms of ancestry in the Mestizo populations, with a predominant Native American contribution (54-69%), followed by European (19-28%) and African contributions (12-19%). Pairwise F_ST genetic distances highlight the genetic proximity between the northernmost Central American populations, especially among admixed populations. The unique and complex nature of this area, where populations from different origins intercrossed, as well as the informativity of X-STR data, highpoint the great interest of this genetic study. Furthermore, the X-chromosome databases for Central American populations here provided will be not only useful for forensic and population purposes not only in the target countries but also in the host countries.

Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population

Short tandem repeats (STRs) are widely used as DNA markers in paternity testing and criminal investigations because of their high genetic polymorphism among individuals in population. However, many factors influence genetic variations of STRs. Therefore, understanding STR information within individual populations could provide database and scientifically reliable STR genotyping for forensic genetic purposes. We aimed to examine allele frequencies of X-STRs, including some forensic parameters, in a northern Thai population. A retrospective descriptive study was conducted by collecting X-STR data from unrelated individuals living in a northern region of Thailand. The allele frequency and forensic parameters - for example polymorphism information content (PIC), power of discrimination in females and males (PD_f and PD_m), mean exclusion chance (MEC) and haplotype frequency - were calculated. The Hardy-Weinberg equilibrium was analysed. A total of 132 alleles were observed, with corresponding allele frequency ranging from 0.0064 to 0.4904. The PIC of all loci was >0.6, representing high genetic polymorphism, except DXS8378 and DXS7423. Notably, DXS10135 was the most diverse loci with the highest PD and MEC, while DXS7423 was the least polymorphic marker with the lowest PD and MEC. The highest haplotype diversity in male data was on linkage group III (DXS10101-DXS10103-HPRTB) by 0.9895. The genetic distance analysis demonstrated that the northern Thai population had a close relationship with Taiwanese (D_A = 0.023). There are no significant deviations among the Hardy-Weinberg equilibrium except DXS10148. This study has established a northern Thai X-STRs reference database to be used as a tool for forensic genetic purposes.

Genetic polymorphisms in 16 X-STR loci analyzed in the She population from Zhejiang Province, China

Allele frequencies for 16 X-chromosomal STR (X-STR) loci (DXS6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS6810, DXS6789, and DXS10159) were obtained from a sample set of 296 unrelated individuals from the Zhejiang She population in China. We observed a total of 117 alleles in the group, with allele frequencies ranging from 0.0022 to 0.8143. The most informative marker for the studied population was DXS10134, with a polymorphism information content (PIC) of 0.8547, and the least polymorphic locus was DXS6800 (PIC = 0.3071). The power of discrimination (PD) varied from 0.3244 (DXS6800) to 0.8680 (DXS10134) in males and from 0.5263 (DXS6800) to 0.9693 (DXS10134) in females. The combined PD_M and PD_F was 0.999999996987156 and 0.999999999999993, respectively. The combined MEC_D and MEC_T was 0.999993100252466 and 0.999999973583357, respectively. In the population comparisons, a close relationship between the Zhejiang She and Eastern Han populations was observed. In general, the present findings indicate that the 16 X-STR loci examined are highly genetically polymorphic in the She population of Zhejiang, providing useful information on She for forensic science and population genetic studies.

Genetic variation of 17 X-chromosome STR loci in Tunisian population of Nabeul

In the present study, the genetic variations of 17 X-STR markers (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801, DXS7423, DXS6809, DXS6799, DXS7132, DXS9902, DXS6800, DXS6789, DXS10075, DXS10079, DXS6807, and DXS6803) were analyzed in 139 unrelated individuals in Nabeul, aiming to perform an X-STR database for anthropological and forensic purposes. Our results indicate that DXS6809 was the most polymorphic locus, whereas DXS6807 was the least informative marker. In addition, the obtained values for the statistical parameters of forensic interest, i.e., the power of discrimination in males (PD_M) and females (PD_F), as well as the mean exclusion chance in duos (MEC_D) and trios (MEC_T) have demonstrated that this panel of 17 X-STRs is highly informative and useful for forensic application and anthropological research. Additionally, pairwise genetic distances based on F_ST were calculated between Nabeul population and other populations extracted from the literature. Genetic distances were represented in a non-metric MDS plot and clustering of populations according to their geographic locations and their historical relationship was detected.

Establishment of 11 linked X-STR loci within 1.1 Mb to assist with kinship testing

This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci. The distance between each pair of loci ranged from 24,998 to 244,701 bp with an average of approximately 110.8 kb. The number of observed alleles ranged from 7 to 30 for these 10 loci with a polymorphic information content ranging from 0.593 to 0.930. The LOD score from a pairwise linkage study ranged from 4.40 to 23.73, indicating that these 11 loci were highly linked, as expected. In line with standard forensic practice, all 11 loci can be amplified in one multiplex reaction, and comprehensive allelic ladders for all the loci have been constructed. These newly established 11 linked STR loci on the human X chromosome were found to be highly polymorphic and have the potential to aid in kinship testing where the X chromosome loci currently plays a role.

A genetic overview of Atlantic coastal populations from Europe and North-West Africa based on a 17 X-STR panel

The forensic use of X-STRs requires the creation of allele and haplotype frequency databases in the populations where they are going to be used. Recently, an updated Spanish allele and haplotype frequency database for the new 17 X-STR panel has been created, being the only database available up to now for this new multiplex. In order to broaden the forensic applicability of the 17 X-STR panel, 513 individuals from four different populations located on the Atlantic Coast of Europe and North-West Africa have been studied, i.e. Brittany (France), Ireland, northern Portugal, and Casablanca (Morocco). Allele and haplotype frequency databases, as well as parameters of forensic interest for these populations are presented. The obtained results showed that the 17 X-STR panel constitutes a highly discriminative tool for forensic identification and kinship testing in the studied populations. Furthermore, we aimed to study if these populations located on the Atlantic coast actually share alike allele and haplotype frequency distributions since they have experienced genetic exchanges throughout history. This would allow creating larger forensic databases that include several genetically similar populations for its use in forensic casework. For this purpose, pairwise F_ST genetic distances between the analyzed populations and others from the Atlantic Coast previously studied with the 17 X-STR panel or the ten coincident markers included in the decaplex of the GHEP-ISFG were estimated. Our results suggest that certain nearby populations located on the European Atlantic coast could have underwent episodes of genetic interchange as they have not shown statistically significant differentiation between them. However, the population of Casablanca showed significant differentiation with the majority of the European populations. Likewise, the autochthonous Basque Country and Brittany populations have shown distinctive allele frequency distributions between them. Therefore, these findings seem to support that the use of independent allele and haplotype frequency databases for each population instead of a global database would be more appropriate for forensic purposes.