Genetic Polymorphisms and Forensic Parameters of Thirteen X-Chromosome Markers in the Iraqi Kurdish Population

Development and validation of a 55-Plex X-STR NGS panel for forensic casework: Population genetics, mutation analysis, and kinship discrimination.

BackgroundX‐chromosome short tandem repeats (X‐STRs) with unique sex‐linkage inheritance models play a complementary role in forensic science. Guizhou is a multiethnic province located in southwest China and some genetic evidence focusing on X‐STRs for various minorities was reported. However, population data of Guizhou Tujia are scarce.MethodsA total of 507 Guizhou Tujia individuals were profiled using the AGCU X‐19 STR kit. Allele frequencies and forensic parameters were calculated. Additionally, population genetic relationships between Guizhou Tujia and other 19 populations were explored.ResultsA total of 257 alleles with the allele frequencies ranged from 0.0013 to 0.6098 were found. The combined power of discrimination in males and females and mean exclusion chances in all case scenarios were all greater than 0.99999. Population comparisons showed Guizhou Tujia had a homogeneity with all Han populations from different administrative regions, and other ethnic populations residing in Guizhou, while had obviously genetic heterogeneity with the Altaic family populations except Xibe.ConclusionNineteen X‐STRs can afford a reliable and informative database of Guizhou Tujia population for human identification and paternity testing, especially in complex biological relations. The genetic relationships of Chinese are significantly influenced by the geographic position and ethnolinguistic origin.

Population data for 12 X-STRs loci in Malaysian Malay and Chinese populations

As a supplementary tool in forensic cases, X chromosomal short tandem repeats (X-STRs) might bridge large pedigree gaps and bring inspiration to forensic practices for the special mode of inheritance. To standardize the application of X-STRs, the DNA Commission of the International Society for Forensic Genetics (ISFG) presented recommendations concentrating on biostatistical evaluations. Following this guideline, in this study, 1247 (655 females and 592 males) unrelated individuals and 770 families originating from a Han Chinese population of Beijing were investigated with 16 X-STRs. The combined PDF and PDM were 0.999999999999994 and 0.999999997, respectively. The combined MECKrüger, MECKishida, MECDesmarais, and MECDesmarais duo were 0.999972736708864, 0.999999975670766, 0.999999975720931, and 0.999993489709197, respectively. In addition, a population comparison demonstrated that genetic heterogeneity widely exists between the Han population of Beijing and other populations, especially southern Han Chinese, European, and West African populations. Additionally, the overall mutation rates of the paternal and maternal germlines of the 16 X-STRs were 0.0021 and 0.0003, respectively. Among them, HPRTB showed the highest paternal mutation rate of 0.0094. Finally, based on these forensic parameters, the likelihood ratios of four second-degree kinship cases were evaluated. Comparing with autosomal STR, X-STR showed significant advantages for hypothesis exclusion. Our study indicated that the 16 X-STR loci are highly polymorphic in the Han population of Beijing and could be a satisfactory complimentary tool for forensic applications.

The study describes the development of a new multiplex PCR system that simultaneously amplifies 16 X chromosome short tandem repeats (X-STRs) loci in a single PCR reaction and its applicability on a sample of 200 from the Sinhalese population in Sri Lanka. 13 X-STR loci located in four clusters are selected for the assay (DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074-DXS10075, DXS6801-DXS6809-DXS6789 and DXS7424-DXS101-DXS7133). In addition, three single loci were also selected (DXS9902, HPRTB and DXS7423). Genomic DNA extracted using the Chelex-100 method was amplified with modified published primers and subjected to capillary gel electrophoresis. Complete DNA profiles were obtained with 0.20 ng 9947A DNA and the band sizes ranged between 100 and 320 bp with 10 loci having sizes below 237 bp. A total of 160 alleles were observed among the sample with 5-23 alleles for each locus. The forensic efficiency evaluation showed high values for the combined power of discrimination in males (1 in 1 × 1010) and females (1 in 1 × 1017). Combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were equally high (> 0.99999). Application of the new multiplex system to two actual kinship cases of full sibling and deficient paternity suggested that these 16 short tandem repeat loci are highly appropriate for forensic and kinship testing among the Sinhalese population.

In northeast Argentina, different Amerindian communities share territory and history with settlers, mainly Europeans. Due to miscegenation, the current Argentinean population has a particular structure that can be described through X chromosome variation. The objectives of this study were to describe the variation of 10 X-chromosome short tandem repeats (X-STRs) in urban populations of the Argentinean regions known as Gran Chaco and Mesopotamia, report the forensic parameters of these STRs, and estimate the European and indigenous genetic components in these regions. Population and forensic parameters were estimated for 419 individuals from the analyzed populations, including two indigenous groups, Wichí and Mocoví, previously reported. Population structure was estimated through FST and RST distances and analysis of molecular variance. The indigenous American and European components were assessed with STRUCTURE. X-STRs showed a high level of genetic variability in urban and indigenous populations. Indigenous people of the Gran Chaco region showed significant differentiation from the urban samples (FST = 5.5%) and among themselves (FST = 5.3%). Genetic differentiation among urban groups was almost negligible, except that the population from Misión Nueva Pompeya differed from the rest of the city populations. Forensic parameters indicate that these X-STRs are useful as a complement to paternity tests. The set of 10 STRs could be a good tool for examining population differences.

Background: X-chromosomal short tandem repeats (X-STRs) are crucial in forensic applications, particularly in complex kinship cases, and play an important role in population genetics. However, there is limited data on X-STR variation in Pakistani populations, especially among ethnic groups like Kashmiri and Punjabi. Methodology: This study investigates the forensic and genetic properties of 12 X-STRs from the Investigator Argus X-12 Kit (QIAGEN, Hilden, Germany) in 125 families (75 Kashmiri, 50 Punjabi) from Azad Jammu and Kashmir and Punjab, Pakistan. Results: In both populations, a total of 222 alleles were identified across the 12 X-STR loci (Punjabi 171 alleles, Kashmiri 161 alleles), with allele frequencies ranging from 0.0056 to 0.3033. DXS10148 was the most polymorphic locus with 28 alleles, while DXS7132 was the least polymorphic with 9 alleles. Most loci were in linkage equilibrium, except for the DXS10135/DXS10148 pair in males, with no loci exhibiting significant linkage disequilibrium in females. The combined power of discrimination was 0.999 999 9977 for Kashmiri males, 0.999 999 999 999 9746 for Kashmiri females, and 0.999 999 999 999 9781 for Punjabi females. In Kashmiri males, 34, 31, 28, and 32 haplotypes were observed across the four linkage groups (LG1, LG2, LG3, and LG4), though these groups did not form stable haplotypes, as indicated by Linkage Equilibrium within and significant Linkage Disequilibrium between groups. Conclusions: Genetic structure analysis using Principal Component Analysis and STRUCTURE revealed distinct clustering patterns for the Kashmiri and Punjabi populations, indicating unique genetic backgrounds and ancestry influences, particularly distinguishing them from East Asian populations. This study provides a comprehensive analysis of X-STR variation in Punjabi and Kashmiri populations, offering valuable insights for forensic and population genetic studies.

Back ground: X-chromosomal short tandem repeats (X-STRs) have assured to be informative and particular role in complex relationship testing. DXS6807 known as tetra nucleotides polymorphism representing eight alleles of 251-275 bp in length. DXS6807 is located in, at XP 22.2, at a genetic distance of more than 87 and 151 Cm of X-chromosome. DXS101 is located104.9–121 cM from the Xp-telomere (Xp-tel) corresponding to cytogenetic position in Xq21.33–Xq22.3. 
 Objective: The aim of this present study investigates the allele frequency of two markers DXS101, DXS6807 and forensic efficiency parameters for sample of Arabic Iraqi males.
 Material and methods: The population of this study includes 200 males apparently healthy unrelated participants from different region of Baghdad city, their ages ranged between (20-50) years. The Genomic DNA extracted and purified successfully from blood samples. 
 Results: The forensic efficiency parameters result for these markers were following: polymorphism information content (PIC) of 0.834708, power of discrimination (PD) in male 0.851750, Power of exclusion (PE) 0.698316, MEC Krüger0.511679, MEC Kishida 0.694890. The forensic efficiency parameters analyzing from Arabic population were Power of discrimination (PD) = 0.73405, Polymorphism information content (PIC) =0.69489, Power of exclusion (PE) =0.482879.MEC Krüger =0.511679, MEC Kishida = 0.694890.
 Conclusions: The information provided establish this X-linked microsatellite marker as a valuable strategy for forensic application. DXS101is and DXS6807 recently consider more stable and suitable forensic markers for forensic application.

High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System

Population genetic data for 12 X-STR loci in the Northern Han Chinese and StatsX package as tools for population statistics on X-STR

Study of DXS9895 and DXS7130: Population data from North of Portugal

StatsX (Statistics for X-STR) v2.0 is developed to facilitate the workflow for analysis of population data on X-chromosomal short tandem repeat (X-STR) marker. The interactive graphical and installable software can estimate allele/haplotype frequencies from female, male, and pooled samples and calculate forensic parameters by importing a single file. In addition, it is able to filter out the invalid raw data and export a series of pre-formatted Arlequin input files that are directly used for testing the significance of the Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and gender differentiation. As expected, all results of frequencies and forensic parameters can be saved as EXCEL workbooks and also plotted as bar or line graphs. Further, full concordance was obtained by recalculating frequencies and forensic parameters with other established software from a published Han Chinese population.

In this study, three drinking water treatment plant supply springs were selected within different sites in Sulaymaniyah province- Kurdistan region of Iraq. Samples were collected over period of eight months from May to the end of December 2015. Five stations were selected, Stations 1, 2 and 3 were located at Bestan Sowr drinking water project in Sharazur district, station 4 was located at Saray Subhan Agha drinking water project in Said sadiq district and station 5 was located at Khurmal drinking water project in Khurmal district within Halabja district. The study involved a qualitative (identification) and quantitative (Density and Total count) study of phytoplankton in water for selected stations. A total of 155 algal species were identified belong to 9 classes in all studied stations, 80 species belonged to Bacillariophyceae (diatoms), 35 species to chlorophyceae, 30 species to Cyanophyceae, 3 species to Euglenophyceae, 2 species for each of Crptophyceae and Pyrophyceae and 1 species for each of Chrysophyceae, Dinophyceae and Xanthophyceae. Diatoms were dominated (according to the total count of taxa) over all other phytoplankton in all sites, Chlorophyceae formed the second most algal group at the selected sites and Cyanophyceae formed the third most algal group of phytoplankton at the selected sites. The results of phytoplankton quantitative study in the studying stations recorded the highest total density of phytoplankton during the study period was at Station1 (18377.28 ind×103/l), followed by (12513.34 ind×103/l) at Station 2 and (4779.45 ind×103/l) at Station 3. The results of total Count of phytoplankton at all stations ranged between 5913×103 cell/l and 29×103 cell/l.

Genetic analysis of 12 X-STRs for forensic purposes in Liaoning Manchu population from China

To investigate genetic polymorphisms of 12 X chromosome short tandem repeat (X-STR) loci in ethnic Hebei Han population using an Investigator Argus X-12 amplification kit. DNA was extracted for 198 unrelated individuals (96 males and 102 females) and amplified with a fluorescence labeled multiplex PCR system. PCR products were separated and genotyped with capillary array electrophoresis. Only DXS10103 and DXS10101 showed significant linkage disequilibrium at the 12 X-STR loci. One hundred and forty-eight alleles, including 22 off-ladder (OL) alleles, were observed at the 12 X-STR loci in the population. The heterozygosity and polymorphic information content (PIC) were 0.5074-0.9143 and 0.4377-0.9079, respectively. The power of discrimination (PD) was 0.5074-0.9143 in males and 0.6876-0.9863 in females. The mean exclusion chance was 0.4377-0.9079 in the trios cases and 0.2984-0.8373 in the duo cases, respectively. The Investigator Argus X12 amplification system is highly polymorphic in ethnic Han population from Hebei and is useful for personal identification and paternity testing.