Genetic polymorphism investigation of 16 X-STR loci in the Bai ethnic minority in Yunnan Province,Southwest China

To investigate the genetic variation and forensic efficiency of 16 X-chromosomal short tandem repeat (X-STR) loci (DX6795, DXS9902, DXS8378, HPRTB, GATA165B12, DXS7132, DXS7424, DXS6807, DXS6803, GATA172D05, DXS6800, DXS10134, GATA31E08, DXS10159, DXS6789, and DXS6810) in the Bai minority, we calculated allele frequencies, forensic parameters, and haplotype frequencies in 424 (202 males and 222 females) unrelated, healthy Bai individuals from Dali Bai Autonomous Prefecture in Yunnan Province, China. We observed a total of 132 alleles; 5–19 alleles were detected in each locus, and the corresponding allele frequencies ranged from 0.0016 to 0.7589. All of the loci detected were highly polymorphic in the Bai population in Yunnan Province, except DXS6800. The values for the combined power of discrimination in females (PDf) and males (PDm) were 0.999999999999996 and 0.999999997487061, respectively. According to a phylogenetic tree, neighboring populations and different nationalities in the same area appeared to have relatively close evolutionary relationships. This study provides and complements X-chromosome genetic polymorphism data for the Bai people in Yunnan Province, Southwest China, and enriches the available reference materials for this Chinese minority population.

     

Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast

Twenty-one X-chromosomal short tandem repeat (STR) loci, including the six clusters of linked markers DXS10148–DXS10135–DXS8378 (Xp22), DXS7132–DXS10079–DXS10074 (Xq12), DXS6801–DXS6809–DXS6789 (Xq21), DXS7424–DXS101 (Xq22), DXS10103–HPRTB–DXS10101 (Xq26), DXS8377–DXS10146–DXS10134–DXS7423 (Xq28) and the loci DXS6800, GATA172D05 and DXS10011 were typed in a popula3tion sample from Ivory Coast (n = 125; 51 men and 74 women). Allele and haplotype frequencies as well as linkage disequilibrium data for kinship calculations are provided. On the whole, no significant differences in the genetic variability of X-STR markers were observed between Ivorians and other sub-Saharan African populations belonging to the Niger–Kordofanian linguistic group.     

Analysis of 21 X-chromosomal STRs in an Algerian population sample

Twenty-one X-chromosomal short tandem repeat loci, including the six clusters of linked markers DXS10148-DXS10135-DXS8378 (Xp22), DXS7132-DXS10074-DXS10079 (Xq12), DXS6801-DXS6809-DXS6789 (Xq21), DXS7424-DXS101 (Xq22), DXS10103-HPRTB-DXS10101 (Xq26), DXS8377-DXS10146-DXS10134-DXS7423-DXS10011 (Xq28), and the loci DXS6800 and GATA172D05 were typed in a northwestern Algerian population sample (n = 210; 104 men and 106 women). Allele and haplotype frequencies were calculated. No evidence of linkage disequilibrium was observed between pairs of loci within clusters of linked markers. At locus DXS10148, sequence analysis of a subset of alleles displaying unusual amplicon length (≥ 36 repeat units) and anomalous electrophoretic mobility showed that this marker has a complex molecular structure with different repeat variants within alleles of identical amplicon size.     

Genetic diversity study on 12 X-STR loci of investigator® Argus X STR kit in Bangladeshi population

The X-chromosome short tandem repeat (STR) loci are of particular interest for solving complex kinship and paternity cases. Here, we report the genetic data from 209 unrelated Bangladeshi individuals (102 males and 107 females) that were genotyped using the 12 X-chromosomal STR markers included in the Investigator® Argus X-12 kit (Qiagen). The 12 X-STR markers are located in four linkage groups (linkage group I: DXS10135, DXS10148, and DXS8378; linkage group II: DXS7132, DXS10079, and DXS10074; linkage group III: DXS10103, HPRTB, and DXS10101; and linkage group IV: DXS10146, DXS10134, and DXS7423). Allelic frequencies of the 12 X-STR loci and haplotype frequencies of the four linkage groups were investigated. No significant difference was observed in the allele frequencies of males and females. Distributions of heterozygosity were observed from 64.5 to 92.5% among the studied 12 X STR loci. DXS10135 and DXS10101 loci were found to be most polymorphic. For all the four linkage groups, the haplotype diversity was found to be greater than 0.986. A total of 95, 73, 66, and 74 haplotypes were observed in linkage groups I, II, III, and IV, respectively. Hardy–Weinberg equilibrium tests showed no significant deviation from expected values for all 12 loci (p > 0.05). The exact test for pairwise linkage disequilibrium for the 12 loci in the male samples did not show any significant linkage disequilibrium except the DXS10103 and DXS10101 loci after the p values were corrected by Bonferroni’s correction for multiple testing (p > 0.05/66). A combined power of discrimination in male and female individuals were 0.999999998159791 and 0.999999999999993, respectively. The combined mean exclusion chance were 0.999997635 in deficiency cases, 0.999999996 in normal trio cases, and 0.999999178 in duo cases. The currently investigated Bangladeshi population showed significant differences when compared with previously reported X-STR data from other 12 populations. The results of the data analysis indicated that all the loci in the Investigator® Argus X 12 kit were fairly informative and might be useful in forensic application and kinship analysis in Bangladeshi population.

     

Allele frequencies of 11 X-chromosomal loci in a population sample from Ghana

Eleven X-chromosomal short tandem repeats (STRs) from two multiplex PCR approaches (DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377, and DXS7423), located in four different X-chromosomal linkage groups, were typed in a population sample from Ghana, Africa. After genotyping unrelated men (129) and women (114) from the Ashanti population, forensic efficiency parameters such as polymorphism information content and mean exclusion chance were calculated. A deviation from the Hardy–Weinberg equilibrium could not be found. The investigation of 11 father–daughter and seven mother–son meioses revealed no mutations in any STR analyzed. Our data were compared with European, African-American, and Asian populations from the literature. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Characterisation of the STR markers DXS10146, DXS10134 and DXS10147 located within a 79.1 kb region at Xq28

Three polymorphic X-chromosomal STR markers within a 79 kb region at Xq28 were studied and registered in the GDB as DXS10146, DXS10134 and DXS10147. These markers were molecular characterised and evaluated for their forensic usage. As a result DXS10134 was recently integrated in the commercial available test kit Mentype Argus X-8. At locus DXS10146 we found 23 alleles with PIC and HET values of 0.878 and 0.887. Locus DXS10134 showed 17 alleles with PIC and HET values of 0.844 and 0.858. At locus DXS10147 only 5 alleles with some lower PIC and HET values of 0.636 and 0.692 were found. Additionally, the already known and closely linked STR DXS7423 was included into the haplotyping and recombination studies. Testing this cluster a German population of 404 males revealed the presence of 311 haplotypes. Recombination analysis was performed in 109 father–daughter–grandson trios in which two crossing over events were observed located in the 65.8 kb region between DXS10146 and DXS10134. By using this STR complex for haplotyping in kinship testing further genetic analyses are required to establish an exact recombination rate.     

Phylogenic analysis and forensic genetic characterization of Guizhou Miao tribes from 58 microareas via autosomal STR

Genetic polymorphism of 17 autosomal short tandem repeat (STR) loci, included in the PowerPlex®18D amplification kit, were analyzed in Miao tribes from 58 different sampling microareas (N = 5255) of Guizhou as well as two cities (N = 151) of Hunan, China. Allele frequencies and forensic efficiency parameters were calculated. Moreover, comprehensive population genetic comparisons among 91 nationwide populations and 174 Asian populations were conducted based on raw genotype data and allele frequency data, respectively. Our results of forensic efficiency parameters showed that the panel was a robust tool in forensic individual identification and paternity cases for this population. Genetic affinities were observed among most of the Miao tribes revealed by multidimensional scaling plot, principal component analysis, and neighboring-joining tree. The genetic distance between Miao tribes and Han nationalities were varies by different geographical positions. Some of the Miao tribes were genetically closer to the Hmong-Mien populations living in southeastern contiguous regions and even the Indochina. The result coincided with the migration or reverse migration routes for Miao nationality in modern history. This study of the Miao tribes from plenty of microareas in Guizhou would be useful in reconstructing the population history and establishing a more comprehensive forensic reference database.     

Characteristics of eight X-STR loci for forensic purposes in the Chinese population

X-chromosomal short tandem repeats (ChrX STRs) loci are used for forensic practice in recent years. Considering the unique heredity characteristics of ChrX, recombination and linkage disequilibrium (LD) among ChrX STR loci vary between male and female and different populations as well. However, there is a lack of data for analysis of recombination and linkage disequilibrium on ChrX STR loci in the Chinese population. In this work, a total of 303 unrelated individuals (203 males and 100 females) in the Chinese Han population were analyzed with Mentype Argus X-8 PCR amplification kit (DXS10135-DXS8378, DXS7132-DXS10074, HPRTB-DXS10101, and DXS10134-DXS7423). The recombination and linkage disequilibrium of the eight ChrX STR loci were investigated with HapMap LD plots and software ARLEQUIN 3.1. Allele frequencies of the eight loci and further population forensic genetic parameters were obtained. Our results revealed hotspots for recombination, and there was no obvious evidence for LD among the eight loci in the Chinese population. Our work implied that single locus frequencies rather than haplotype frequencies should be applied for forensic practice in the Chinese population.     

Population genetic evaluation of eight X-chromosomal short tandem repeat loci using Mentype Argus X-8 PCR amplification kit

The evaluation of four pairs of X-chromosomal short tandem repeats (STRs), i.e. DXS10135–DXS8378, DXS7132–DXS10074, HPRTB-DXS10101 and DXS7423–DXS10134 was carried out using the Argus X-8 Multiplex amplification kit. These eight STRs are distributed as four closely linked pairs over the entire X-chromosome (ChrX), and for practical reasons they are assigned to four linkage groups 1–4. The genetic distance within the STR pairs is assumed to be <1 cM, whereas the pair to pair space is about 50 cM or more. Here, we present single STR allele frequencies, haplotype frequencies of the respective STR pairs and further population genetic parameters of forensic interest. Most data refer to a German population, however small samples from Ghana and Japan were also investigated. Furthermore, sequencing of all STR loci displayed the presence of microvariant alleles and variations in the repeat flanking region. A total of 350 meioses investigated here revealed only one sperm DXS7132 mutation. For analysis of linkages within the STR pairs a study involving 104 female meiosis with respect to recombination events was performed. The STR panel presented here provides a powerful tool for solving complex kinship in the case that X-chromosomal lineages can be taken under investigation.     

Allele frequencies of 11 X-chromosomal loci of two population samples from Africa

Eleven X-chromosomal STRs from two multiplex PCR approaches (DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377, and DXS7423), located in four different X-chromosomal linkage groups, were typed in two population samples from Africa, Morocco, and Madagascar. Forensic efficiency parameters such as polymorphism information content and mean exclusion chance were calculated. A deviation from the Hardy–Weinberg equilibrium could not be found. The investigation of four father–daughter and five mother–son meioses (from Morocco) revealed no mutations in any STR analyzed. Our data were compared with European, African-American, and Asian populations from the literature.     

Development and population study of the 12 X-STR loci multiplexes PCR systems

To develop a multiplex polymerase chain reaction (PCR) system with 12 X-chromosomal short-tandem repeat (X-STR) loci and to investigate their polymorphism and linkage and/or independence, the 12 loci (DXS6807, DXS8378, DXS9902, DXS6800, DXS6803, DXS6799, DXS6804, GATA172D05, DXS6854, HPRTB, DXS8377, and DXS7423) were simultaneously analyzed in 1,005 unrelated individuals (574 males and 431 females) from Guangdong Han individuals and Kazakh populations living in China. The allele frequencies and mutation rates were investigated. Allele frequency distribution among different populations was compared. Haplotypes of linkage disequilibrium markers (DXS6807-DXS8378-DXS9902) and linked markers (DXS6804-GATA172D05 and DXS8377-DXS7423) were also reported. A total of 117 alleles, ranging from five to 20 for each locus, were observed in our selected populations. Eight cases with mutation of the selected loci were detected in 9,480 meioses. Pairwise comparisons of allele frequencies distribution showed statistically significant differences at most loci among different populations. Haplotype diversity of linked markers was 0.9404-0.9694. The results indicated that this multiplex system is very useful for forensic analysis and may be complementarities for X-12 kits or X-8 kits in forensic case.     

Genetic polymorphisms of 10 X-chromosome STR loci in Chinese Daur ethnic minority group

The population genetic data of 10 X-chromosomal short tandem repeats (STR) loci DXS101, DXS7130, DXS6804, DXS7133, DXS7132, DXS6799, DXS8378, DXS6789, DXS7423 and HPRTB were analyzed in samples of unrelated individuals from Chinese Daur population. Average heterozygosity of above 10 STR loci was 0.6489 and the DXS6789 was the most polymorphic. The exact test for female data showed no significant deviation from the Hardy–Weinberg equilibrium (P > 0.05). Allele frequencies between male and female samples were not significantly different in all examined loci. Further, the allelic frequencies of Daur ethnic population were compared with those of other populations, and most of loci were significantly different from each other (P = 0.05). Presented study is potential extension to a battery of autosomal systems in forensic application in the region, and enriches Chinese ethnical genetic informational resources.     

Population genetic data for 11 X-STR loci in eleven populations of India

Allele frequencies and forensic parameters were estimated for 11 X chromosome STRs (DXS9898, DXS7424, DXS981, DXS8377, DXS9895, DXS10161, DXS10164, DXS6800, DXS6801, DXS9902 and DXS7423) from 749 samples of unrelated male individuals belonging to eleven populations of India.     

Genetic analysis of 20 autosomal STR loci in the Miao ethnic group from Yunnan Province,Southwest China

The genetic polymorphisms of 20 autosomal short tandem repeat (STR) loci included in the PowerPlex^® 21 kit were evaluated from 748 unrelated healthy individuals of the Miao ethnic minority living in the Yunnan province in southwestern China. All of the loci reached Hardy–Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. The genetic relationship between the Miao population and other Chinese populations were also estimated. The combined discrimination power and probability of excluding paternity of the 20 STR loci were 0.999 999 999 999 999 999 999 991 26 and 0.999 999 975, respectively. The results suggested that the 20 STR loci were highly polymorphic, which makes them suitable for forensic personal identification and paternity testing.     

Allele frequencies for 11 X chromosomal short tandem repeats in a population from Turkey

X chromosomal STRs are nowadays an important part of forensic genetic analysis, especially in complex kinship cases. In this study, allele frequencies and forensic efficiency parameters of the 11 X chromosomal STRs DXS6807, DXS8378, DXS7132, DXS6800, DXS9898, DXS7424, DXS101, DXS7133, HPRTB, DXS8377 and DXS7423 in an admixed population from Turkey are presented.     

An X-STR meiosis study in Kurds and Germans: allele frequencies and mutation rates

X-linked short tandem repeats (X-STRs) play an important supplementary role in the field of forensic genetics, especially in deficiency cases. This paper presents population genetic data for the microsatellite markers DXS8378, DXS6800, DXS101, HPRTB, and DXS8377 in a German and a Kurdish population sample. Buccal swabs were obtained from 217 unrelated healthy German individuals (107 women and 110 men) from the area of Münster and 208 unrelated Kurdish individuals (103 women and 105 men), immigrants mainly from Northern Iraq. Additionally, more than 1,200 meiotic transfers (419 paternal and 819 maternal meioses) were investigated in the systems DXS6800, DXS101, and DXS8377. Five mutations were found in the system DXS8377. With the power of discrimination in females [PD(F)] ranging from 0.81 (DXS8378 in Kurds) to 0.99 (DXS8377 in Germans), the investigated X-STRs systems turned out to be highly informative in the two populations.     

Linkage and linkage disequilibrium analysis of X-STRs in Italian families

Twenty X-chromosomal short tandem repeat (STR) loci were typed in 80 families of Italian descent, composed by mother and two or more sons, for a total of 93 meiosis. The analyzed X-STR panel included six clusters of closely linked markers (each spanning<3cM): DXS10135-DXS10148-DXS8378 (Xp22); DXS7132-DXS10074-DXS10079 (Xq12); DXS6801-DXS6809-DXS6789 (Xq21); DXS7424-DXS101 (Xq22); DXS10103-HPRTB-DXS10101 (Xq26); DXS8377-DXS10134-DXS7423-DXS10146 (Xq28). Recombination fractions between pairs of markers calculated by pedigree analysis were compared with those obtained from the second-generation Rutgers combined linkage-physical map of the human genome. The observed differences confirm that recombination is not homogeneous along the X chromosome and that the conventional subdivision of X-STRs in four groups of completely unlinked markers cannot be regarded as true. Significant linkage disequilibrium was found between markers DXS6801 and DXS6809 (p=0.017). The effect on likelihood calculations of inferring haplotype frequencies from allele distributions rather than haplotype count in the relevant population was evaluated.     

Extensive survey of 12 X-STRs reveals genetic heterogeneity among Brazilian populations

The admixed Brazilian population shows high levels of genetic variability, which resulted from the contribution of three main ethnicities, Amerindian, European, and African. However, due to its huge territory, admixing has been asymmetrical, i.e., the relative contribution from each ethnicity has been unequal in the five geopolitical regions of the country. The aim of this study was to describe genetic variability using a panel of short-tandem repeats on the X chromosome (X-STR) in order to perform a comprehensive evaluation of the usefulness of such markers for forensic purposes in Brazil. Twelve X-STR (DXS9895, DXS7132, DXS6800, DXS9898, DXS6789, DXS7133, GATA172D05, DXS7130, HPRTB, GATA31E08, DXS7423, and DXS10011) were chosen and tested in a sample of 2,234 individuals belonging to 16 out of the 27 Brazilian States, representing all of its five geopolitical regions. No markers showed significant deviation from the Hardy–Weinberg equilibrium, even when analyses were partitioned to represent geopolitical regions. Genetic diversity per locus ranged from 67% (DSX7133) to 95% (DXS10011), and the State of Ceará showed the highest average genetic diversity (79% for all 12 X-STR markers). Considering the Brazilian population as a whole, the power of discrimination of the 12 X-STR panel in females (PDF) was 0.999999999999994, while the power of discrimination in males (PDM) was 0.9999999969. Such high values suggest the potential of that panel to be used in forensic applications and relatedness tests among individuals. Comparisons among the Brazilian populations investigated revealed significant differences when they were compared among each other, a pattern that was maintained when additional populations from Europe and Latin America were compared to Brazilians. Our results highlight the need and usefulness of specific genetic database for forensic purposes in Brazilian populations.     

Population data for DXS6800, DXS101 and DXS8377 loci from Buenos Aires (Argentina)

The X-chromosomal short tandem repeats (X-STRs) DXS6800, DXS101 and DXS8377 were analysed in a population sample from Buenos Aires (Argentina) using a polymerase chain reaction (PCR) multiplex approach with fluorescent detection. We present allele frequencies for these loci in a population comprising 113 women and 99 men. The Hardy–Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were observed. The homogeneity of allele frequencies of men and women was compared by the Fisher's exact test and showed similar distributions. Linkage disequilibrium (LD) tests were performed in males for all pairs of loci and no significant associations were detected. Parameters of forensic interest were also estimated.     

Development of the nine X-STR loci typing system and genetic analysis in three nationality populations from China

This study is to develop a new multiplex polymerase chain reaction (PCR) system that simultaneously amplifies the nine X-chromosome short tandem repeats loci in the same PCR reaction, and to explore their polymorphism and mutation rate among three nationality populations from China. These loci included DXS6854, DXS9902, DXS6809, GATA172D05, HPRTB, DXS7423, DXS6807, DXS8378, and DXS8377. The samples of 890 (484 males and 406 females) unrelated individuals from Guangdong Han population, Xinjiang Uigur, and Inner-Mongolia Mongol were successfully analyzed using this multiplex system. The allele frequencies and mutation rates of the nine loci were investigated, and the comparison of allele frequency distribution among different populations was performed. There were 87 alleles for all the loci, and six to 18 alleles for each locus observed by our new multiplex PCR system. Polymorphism information content was 0.4998–0.9101, and power of discrimination in females was 0.6518–0.9846. Five cases with mutation of above loci were detected in 5,310 meioses. Pair-wise comparisons of allele frequencies distribution showed significant differences for most loci among different populations. Our results indicate that this multiplex system is very useful for identification analysis, and that the information about polymorphism and mutation rate is necessary for forensic application in three nationality populations from China.