X-chromosomal Short Tandem Repeat Loci Research Articles

Genetic polymorphisms of 12 X-STR for forensic purposes in Shanghai Han population from China

X-chromosomal short tandem repeats (X-STR) loci are used for forensic practice in recent years in some complex kinship cases. The commercially available kit of Investigator Argus X-12 (Qiagen, Hilden, Germany) makes it possible to examine the markers of DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074, DXS10103-HPRTB-DXS10101 and DXS10146-DXS10134-DXS7423, which belong to four linkage groups of X-chromosome. In this study, a total of 309 unrelated individuals (200 males and 109 females) from Shanghai Han population were successfully analyzed with this kit. Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (P>0.05) for all of the 12 X-STR loci in the Shanghai Han population. Linkage disequilibrium tests were performed for all pairs of loci by the Arlequin v3.1 software and only DXS10103-DXS10101 remained significant after adjustment for multiple testing (P<0.05/66). The combined power of discrimination in males (CDP(M)) was 0.999999996 while in females (CDP(F)) was 0.999999999999995, and the combined mean exclusion chance in duo cases (CMEC(D)) was 0.999998 while in trio cases (CMEC(T)) was 0.999999986. The results suggest that the twelve X-STR loci may provide high polymorphic information for paternity testing and forensic identification in Chinese Han population from Shanghai.

Development of a 12-plex X chromosomal STR loci typing system

X-chromosomal short tandem repeat (X-STR) loci can play increasingly important roles in some complex kinship cases. In our paper, 360 samples (191 males and 169 females) unrelated individuals from Guangdong province were successfully genotyped using a new multiplex PCR system which can co-amply 12 X-STR markers (GATA172D05, DXS6789, DXS10074, DXS10078, GATA165B12, DXS6797, DXS6803, DXS6804, GATA31E08, DXS7130, DXS9895 and DXS6810). 110 alleles were observed totally. Hardy–Weinberg equilibrium tests showed no significant deviation for all of the 12 X-STR loci. DXS6789–GATA165B12 and DXS7130–DXS9895 were found to be in linkage disequilibrium. The results show that the 12-plex X-STR multiplex system is highly polymorphic and sensitive. It may be useful for forensic personal identification, paternity testing, especially for the kinship testing.

Genetic analysis of the 11 X-STR loci in Uigur and Northern Han populations from China

X-chromosomal short tandem repeats (X-STRs) loci are used for forensic practice in recent years which play increasingly important roles in some complex kinship cases. In this paper, a total of 1250 samples obtained from 941 Northern Hans Chinese and 309 Uigur were successfully analyzed using a homemade new multiplex polymerase chain reaction (PCR) system which can analyze simultaneously11 X-STR markers including DXS8378, DXS6795, DXS7132, DXS6803, DXS9898, DXS6801, DXS7133, GATA165B12, HPRTB, DXS8377 and DXS7423. A total of 103 alleles for all the loci were observed. Hardy–Weinberg equilibrium tests demonstrated no significant deviation from expected values ( P > 0.05) for all of the 11 X-STR loci. The results show the 11 loci in the multiplex systems may provide high polymorphism information for kinship testing and relationship investigations, and it is useful for forensic analysis for the two nationality populations from China.

Structural polymorphisms at the X-chromosomal short tandem repeat loci DXS10134, DXS10135, DXS10146 and DXS10148

Sequence analyses for the X-chromosomal short tandem repeat loci DXS10134, DXS10135, DXS10146 and DXS10148 were performed in 140 unrelated Japanese males. For the DXS10134 locus, 12 different-sized alleles were identified; a structural polymorphism was found in 1 allele only. For the DXS10135 locus, 16 different-sized alleles were identified; structural polymorphisms were found in 8 different-sized alleles. For the DXS10146 locus, 14 different-sized alleles were identified; structural polymorphisms were found in 2 different-sized alleles. For the DXS10148 locus, 16 different-sized alleles were identified; structural polymorphisms were found in 7 different-sized alleles. Discrepancies between allele designations based on size and repeat number were observed in 2 samples each for DXS10146 and DXS10148. Therefore, sequencing is effective in identifying alleles of DXS10134, DXS10135, DXS10146 and DXS10148 where sequence polymorphisms are observed.

Development of two multiplex PCR systems for the analysis of 14 X-chromosomal STR loci in a southern Brazilian population sample

We developed two multiplex systems for the coamplification of X-chromosomal short tandem repeats (STRs). X-Multiplex 1 consisted of DXS6807, DXS6800, DXS7424, DXS101, GATA172D05 and HPRTB and X-Multiplex 2 consisted of DXS8378, DXS9898, DXS6801, DXS6809, DXS6789, DXS7133, DXS8377 and DXS7423. In addition, we present allele frequencies for these loci in a south Brazilian population comprising 124 females and 141 males and haplotype frequencies of linked markers for males. Hardy-Weinberg equilibrium (HWE) was tested in the female sample and no significant deviations were found after applying Bonferroni's correction. Linkage disequilibrium (LD) tests were performed for all pairs of loci and three significant results, out of 91 pairwise comparisons, were obtained. We did not find any evidence of linkage disequilibrium between close or linked markers. The power of discrimination in females (PD(F)) varied between 0.832 for DXS6801 and 0.987 for DXS8377. DXS6801 was the least informative marker (PIC = 0.605), while DXS8377 was the most polymorphic (PIC = 0.911), followed by DXS101 (PIC = 0.872). Genetic distances were estimated for each STR marker applying the calculation of F (ST) between our total sample and other studies from Brazil, Europe, Asia and Africa. The most distant populations were Japan, Korea, China, Ghana and Uganda.

Development of 11 X-STR loci typing system and genetic analysis in Tibetan and Northern Han populations from China

X-chromosomal short tandem repeats (X-STRs) loci are used for forensic practice in recent years which play increasingly important roles in some complex kinship cases. In this paper, a new multiplex polymerase chain reaction (PCR) system which can simultaneously analyze 11 X-STR markers (DXS8378, DXS6795, DXS7132, DXS6803, DXS9898, DXS6801, DXS7133, GATA165B12, HPRTB, DXS8377 and DXS7423) was developed. The samples of 1,605 (742 males and 863 females) unrelated individuals from Tibetan and Northern Han population were successfully analyzed using this multiplex system. A total of 103 alleles for all the loci were observed. Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (P > 0.05) for all of the 11 X-STR loci in the two studied populations. Polymorphism information contents of the loci were 0.3864-0.9013, and powers of discrimination in females of the loci were 0.6317-0.9845. There were no statistically significant differences between Tibetan and Northern Han populations in allele distribution of the 11 X-STR loci, in line with analysis of molecular variance (AMOVA) results. Our work indicates that this multiplex system is useful for forensic analysis for the two populations in China.

Genetic polymorphisms of Investigator Argus X-12 amplification system in Guangdong Han population

To investigate the genetic polymorphisms of 12 X chromosome short tandem repeat (X-STR) loci of Investigator Argus X-12 amplification kit in Guangdong Han population. DNA samples from 200 unrelated individuals (100 males and 100 females) and 103 families (59 father-mother-daughter trios and 44 mother-son duos) were extracted and amplified with fluorescence labeled multiplex PCR system. PCR products were separated and genotyped with capillary array electrophoresis. One hundred and thirty-seven alleles,including 9 off ladder alleles (OL allele) were observed at the 12 X-STR loci in the population. Six mutations were observed in 162 meioses. The combined power of discrimination (DP) was 0.999 999 997 in males and 0.999 999 999 in females, and the combined mean exclusion chance (MEC) was 0.999 999 988 in the trio cases and 0.999 998 013 in the duo cases. Investigator-Argus X-12 amplification system is highly polymorphic in Guangdong Han population and it is powerful for personal identification and paternity testing.

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.

Genetic analysis of eight population groups living in Taiwan using a 13 X-chromosomal STR loci multiplex system

A 13 X-chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, and DXS7423) was tested on 1,037 DNA samples from eight population groups currently living in Taiwan. Different distributions of the allelic frequencies in different populations were presented. DXS8377 and DXS101 were the two most polymorphic loci in these eight populations, whereas DXS7423 was the least informative marker in most of the populations studied. The genetic distances between the populations and the constructed phylogenetic tree revealed a long genetic distance between Asian and Caucasian populations as well as isolation of the Tao population. The phylogenetic tree grouped populations into clusters compatible with their ethnogeographic relationships. This 13 X-chromosomal short tandem repeat multiplex system offers a considerable number of polymorphic patterns in different populations. This system can be useful in forensic identification casework and ethnogeographic research.

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.

The establishment of a nine X-chromosome short tandem repeat loci multiplex PCR and detection of the polymorphism of these loci

To establish a nine X-chromosome short tandem repeats (X-STR) loci multiplex PCR method and study the polymorphism of the 9 X-STR loci,and to determine its application in kinship tests for forensic medicine. A fluorescent multiplex PCR that simultaneously amplifies 9 X-STR loci, i.e. DXS7133, DXS981, DXS7424, DXS6789, DXS7132, GATA165B12, DXS101, GATA31E08 and DXS10011, were set up. PCR products were analyzed using capillary electrophoresis and ABI prism 3100 Genetic Analyzer with GeneMapper ID 3.1 analysis software. When 251 unrelated male and 112 unrelated female individuals from southern China were tested, 111 alleles were detected. The power of discrimination in females was 0.5837-0.9959. Mean exclusion chance for X-STR in standard trios with daughters was 0.4072-0.9511. Polymorphism information content was 0.4481-0.9531. The results demonstrate that the 9 loci in the multiplex system provide high polymorphism information, and the multiplex system provides a fast technology for forensic identification and paternity testing. The X-STR multiplex system can complement the analysis of AS-STR and Y-STR efficiently.

Genetic polymorphisms of eight X-chromosomal STR loci in the population of Japanese

The genetic polymorphisms of eight X-chromosomal short tandem repeats (STR) DXS10135, DXS8378, DXS7132, DXS10074, HPRTB, DXS10101, DXS10134 and DXS7423 were analyzed in a sample of 492 unrelated males (283) and females (209) from the Japanese population. Multiplex PCR amplification was performed using the Mentype ® Argus X-8 PCR amplification kit. The haplotype frequencies within the four linkage groups were studied for the 283 examined Japanese males. Allele frequencies of eight X-STR loci were calculated separately for males and females, and exact tests demonstrated no significant deviations from Hardy–Weinberg equilibrium. Several microvariant and rare alleles were observed, and forensic efficiency parameters were calculated. The combined powers of discrimination of the loci in men and women were 0.999995 and 0.9999999999988, respectively.

Evaluation of seven X-chromosomal short tandem repeat loci located within the Xq26 region

In this study a set of 29 X-chromosomal short tandem repeats (STRs) located within the Xq26 region was evaluated. These STRs were found within the 133.14–133.45 Mb region around the HPRTB locus. Evaluation of the microsatellites was performed with regard to polymorphism, reliable amplification, and low stutter artefacts. DXS10101, DXS10102, and DXS10103 were identified as those X-STRs with highest diversity; i.e. PIC values of 0.7174–0.8933. The locus DXS10101 was the optimal candidate for the integration in the commercial available test system Mentype Argus X-8 PCR amplification kit.

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.

Allele frequency distribution of 13 X-chromosomal STR loci in Pakistani population

Short tandem repeat (STR) markers are extensively being used for human identification as well as paternity and forensic case work. X-chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. Many X-linked microsatellites have been evaluated but further studies are required to determine population specific statistics. Here, we report allele frequencies of 13 X-linked microsatellites (DXS8378, DXS9902, DXS6810, DXS7132, DXS981, DXS6793, DXS6801, DXS6789, GATA172D05, HPRTB, GATA31E08, DXS8377, and DXS7423) in the Pakistani population. Blood samples were collected from individuals representing all major ethnic groups of the Pakistan population. A total of 5-18 alleles were observed for each locus and altogether 109 alleles for all 13 X-STR loci. Heterozygosity in females ranged from 0.524 to 0.884. No significant deviation was observed from Hardy-Weinberg equilibrium for all 13 microsatellites. In addition, there was no evidence of linkage disequilibrium in any pairs of these markers. These results strongly suggest that the X-linked microsatellites described here can potentially serve as an extension to autosomal systems currently used in parentage analysis and forensic case work.

Allele distribution of three X-chromosome STR loci in an antioquian population sample

The X-linked short tandem repeats (STR) markers have proven to be very useful tools for paternity testing when the disputed child is female. The aim of this study was to describe the polymorphism of three X-chromosomal STR loci (DXS6797, DXS6800 and HPRTB) in an Antioquian (Colombian) population sample. PCR products were separated in 4% acrylamide-bis-acrylamide denaturing gels followed by silver staining. Allele size determination and genotyping were performed according to recommendations of the DNA Commission of the International Society of Forensic Genetic using the allelic ladder manufactured at home and based on DNA controls including K562 and 9947A (Promega). Gene frequencies were calculated using ARLEQUIN version 3.11. Population genetic data were obtained by analyzing 127–400 unrelated males and 135 unrelated females from Antioquian (Colombian) population. Distribution of the allele frequencies of these systems for Antioquia population is similar to the European populations.

Genetic Polymorphisms of four X-STR Loci: DXS6797, DXS6800, HPRTB and GATA172D05 in a Peruvian population sample

The X linked short tandem repeats (STR) markers have proven to be very useful tools for paternity testing when the disputed child is female. The purpose of this study was to describe the genetic polymorphism of four X-chromosomal STR loci (DXS6797, DXS6800, HPRTB and GATA172D05) in a Peruvian population sample and evaluate their efficiency in forensic practice and paternity testing.

Mother-child double incompatibility at vWA and D5S818 loci in paternity testing

In a paternity dispute case, 17 autosomal short tandem repeats (STR) were examined and signified a possible paternal mismatch at vWA locus and a maternal mismatch at D5S818 locus in the child under investigation. Seventeen autosomal, 17 Y-chromosome and six X-chromosome repeat loci were used in parentage analysis. The mutated vWA and D5S818 alleles were amplified, cloned and sequenced to analyze the repeat structure. The vWA locus genotype in the mother, questioned child and suspected father were 18/19, 16/18 and 14/18, and were 13/15, 11/12 and 11/14, respectively, for the D5S818 locus. A complete match with the mother at six X-chromosome STR loci and with the father at 17 Y-chromosome STR loci was observed. Nucleotide sequence analysis of the family at vWA alleles indicated the maternal loss of the repeat motif TCTA by two repeat units and a loss of AGAT repeat by one unit in the D5S818 locus leading to an allele mismatch in the child. The probability of maternity and paternity were 0.999999 and 0.999999, respectively. This is the first study of a maternally transmitted microsatellite mutation in the loci D5S818 and vWA in paternity DNA testing. The results convincingly established that the mother and suspected father are the biological parents of the questioned child.

Development of two multiplex PCR systems for the analysis of 12 X-chromosomal STR loci in a northwestern Italian population sample

Two multiplex polymerase chain reaction systems for the automated profiling of 12 X-chromosomal short tandem repeat (STR) markers were developed. Multiplex A consisted of DXS6789, DXS6809, GATA172D05, DXS101, DXS8378, and DXS8377. Multiplex B consisted of DXS7132, DXS6800, DXS6801, DXS7424, HPRTB, and DXS10011. The set of amplified X-STRs was designed to include groups of closely linked markers (DXS101-DXS7424 and DXS6789-DXS6801-DXS6809) to generate highly informative haplotypes for kinship testing. A population genetics study of the 12 X-STRs was conducted in a northwestern Italian population sample (n=160, 80 women and 80 men). A diallelic pattern at locus DXS6789 was observed in one man.

Japanese population data for eight X-STR loci using two new quadruplex systems

Using two new X-chromosome short tandem repeats (X-STR) multiplex (quadruplex) systems, we investigated Japanese population data (drawn from 401 individuals) for eight X-STR loci (DXS10011, DXS9898, DXS8377, HPRTB, DXS7132, DXS6797, GATA172D05, and DXS6807). Allele typing with the systems was successful for all loci. The combined powers of discrimination of the eight loci in men and women were 0.999997 and 0.9999999996, respectively. We conclude that combined analyses of the eight X-STR loci using these two quadruplex polymerase chain reaction systems represent a powerful tool for Japanese forensic practice.