X-chromosomal Short Tandem Repeats Research Articles

X-chromosome STRs analysis of Ewenke ethnic population

X-chromosome STR, known as microsatellite, is a kind of the most information genetic markers for specific biological materials. Because the size of X-chromosome STR alleles is small, generally including 100–350 nucleotides, it is relatively easy to be amplified and detected with high sensitivity. We have investigated 10 X-chromosome STR loci in an Ewenke ethnic population who live in Neimengu of northeast China. Allele frequencies of 10 X-chromosome STR loci, including DXS7133, DXS6799, DXS8378, DXS7423, DXS6804, HPRTB, DXS7424, DXS7132, DXS6789 and DXS101, were obtained from healthy unrelated individuals (45 females and 53 males) of Ewenke ethnic group.

Patterns of genetic polymorphism at the 10 X-chromosome STR loci in Mongol population

Genetic diversity at 10 X-chromosome STR loci has been approved and widely used for forensic science field. In this paper, we have studied this genetic diversity in various Mongol ethnic group with geographic backgrounds. Allele frequencies of 10 X-chromosome STR loci, including DXS7133, DXS6799, DXS8378, DXS7423, DXS6804, HPRTB, DXS7424, DXS7132, DXS6789 and DXS101, were obtained from healthy unrelated individuals (53 females and 47 males) of Mongol ethnic group lived in north China. Gene diversity analysis showed that the average heterozygosity was uniformly high (0.687) in the studied population. The coefficient of PIC was 0.99998.

Development of a heptaplex PCR system to analyse X-chromosome STR loci from five Italian population samples: A collaborative study

Many X-chromosome short tandem repeats (X-STRs) have been validated for forensic use even if further studies are needed on allele frequencies and mutation rates to evaluate the extent of polymorphism in different populations and to establish reference databases useful for forensic applications and for anthropological studies. A single multiplex reaction of seven X-STRs, which includes the DXS6789, HUMARA, DXS10011, DXS7423, HPRTB, DXS6807, DXS101 loci, is presented and their allele frequency distribution in a large population sample including 556 subjects (268 females and 288 males) analysed by five forensic laboratories of Central and Northern Italy is shown. Our results demonstrate the feasibility of a single amplification/detection reaction involving seven markers of the X chromosome, which can be fruitfully used in complex kinship analysis.

Population data of 10 X-chromosomal loci in Latvia

Ten X-chromosomal STRs from two multiplex PCR approaches (DXS9898, DXS6807, HPRTB, DXS101, and androgen receptor (ARA); DXS7133, DXS10011, DXS7424, DXS8377, and DXS8378) have been typed in a Latvian population sample.

X-chromosome STRs polymorphisms of Han ethnic group from Northwest China

Allele frequencies of 11 X-chromosome STRs loci, namely DXS7133, DXS6799, DXS8378, DXS7423, DXS6804, HPRTB, DXS7424, DXS7132, DXS6789, DXS101 and DXS1214, were determined from healthy unrelated individuals (110 female and 94 males) of Han ethnic group from Northwest China.

Development of two pentaplex systems with X-chromosomal STR loci and their allele frequencies in a northeast German population

In this study we present two new pentaplex systems for the coamplification of X-chromosomal short tandem repeats (STRs). X-penta-1 comprises DXS9898, DXS6807, HPRTB, DXS101, and androgen receptor (ARA); X-penta-2 consists of DXS7133, DXS10011, DXS7424, DXS8377, and DXS8378. In addition, allele frequencies for these loci in a northeast German population comprising 100 females and 105 males were shown. The applicability and usefulness of our two PCR pentaplex approaches in paternity deficiency cases is demonstrated by a combined power of discrimination (PD c) for both females and males with PD c > 0.999999.

Development of a pentaplex X-chromosomal short tandem repeat typing system and population genetic studies

Quadruplex and pentaplex systems for polymerase chain reaction amplification of X-chromosomal short tandem repeats DXS101, HPRTB, DXS8377, DXS981 (STRX1) and DXS6789 were developed for automated profiling of liquid and membrane-bound DNA samples. Chinese, Japanese and Thai populations were typed using a quadruplex system, while German and Philippine populations were analyzed using a five-locus system. Out of 88 meioses studied in Philippine family samples at each locus, a possible one repeat deletion (allele 51 to 50) at DXS8377 was observed in a father–daughter pair. Exact tests performed on genotype data from females in the Philippine, German and Thai populations indicated that these groups conform to Hardy–Weinberg equilibrium. Exact tests for population differentiation indicate significant variations in allele distributions, particularly at loci DXS101, DXS981 and DXS6789. Considered individually, DXS8377 was the most polymorphic and HPRTB the least polymorphic locus in these five populations. When the forensic efficiency of the quadruplex system was calculated, the combined power of discrimination among males (PD M) was no lower than 0.998, while among females the combined PD F was at least 0.9999 in all populations. The combined power of paternity exclusion was a minimum of 0.998 in trio cases and 0.98 in motherless cases. The addition of locus DXS6789 to the German and Philippine population databases using a pentaplex increased the forensic efficiency of the analysis system.

Polymorphism of four X-chromosomal STRs in a Polish population sample

Allele frequencies for four X-chromosomal STR were determined in a population sample of 240 unrelated males and females from the northeastern Poland by multiplex PCR and subsequent automated fluorescent detection (ABI 310) using a commercially available multiplex PCR kit (Mentype Argus X-UL). Kinship tests revealed a typical X-linked inheritance with no mutation. The analysed quadruplex is a potential extension to a battery of autosomal systems in forensic applications, especially in the investigation of kinship analysis and deficiency cases.

DXS10011: studies on structure, allele distribution in three populations and genetic linkage to further q-telomeric chromosome X markers.

The hypervariable tetranucleotide STR polymorphism DXS10011 is a powerful marker for forensic purposes. Investigation of this STR led to an allele nomenclature which is in consensus with the ISFG recommendations. DXS10011 is located at Xq28 and genetically closely linked to DXS7423 and DXS8377 but is unlinked to HPRTB and more distant X-chromosomal STRs. DXS10011 is a very complex marker exhibiting some structural variants within alleles of identical length. Two types of repeat structure (regular and inter-alleles) are known and described as types A and B. Two SNPs which are in strong linkage disequilibrium to the different sequence types were found in the repeat flanking region. The type A sequence consists of a long stretch of uninterrupted homogenous repeats which is highly susceptible to slippage mutation during male meiosis.

Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898.

The four X-chromosomal short tandem repeats (STRs), DXS9898, DXS6809, DXS7424 and DXS10011 were analyzed by single multiplex PCR in 150 male and 150 female Koreans. The loss of an allele at DXS9898 was observed in 13 out of 450 chromosomes (2.9%) and the PCR analysis showed that the X-chromosome with a null allele at DXS9898 has more than 1 kb deletion at the DXS9898 locus. Statistical analyses for these four X-STRs showed that they are highly informative for forensic application in Koreans. No linkage disequilibrium was observed among these four STRs and the previously reported five polymorphic STRs, HumARA, DXS101, GATA172D05, HPRTB and DXS8377 in Koreans. The test of homogeneity between allele frequencies revealed that there are some discrepancies in allele distributions between Koreans and Germans.

Genetic analysis of 18 X-linked short tandem repeat markers in Korean population

The population genetic data of 18 X-chromosomal short tandem repeat (STR) markers DXS6807, DXS8378, DXS9895, DXS9902, DXS6810, DXS7132, DXS981, DXS6800, DXS9898, DXS6789, DXS101, DXS6797, GATA172D05, GATA165B12, HPRTB, GATA31E08, DXS8377, and DXS7423 were analyzed in samples of unrelated 220 males and 181 females from Korean population. The exact test for genotype distribution of the markers showed no significant deviation from the Hardy–Weinberg equilibrium. Allele frequencies between male and female samples were not significantly different in all examined markers. All examined males and females showed different hemizygotic haplotype and combined genotypes, respectively. Four cases of mutation were found in GATA172D05, GATA31E08, DXS7132, and HPRTB from the analysis of 95 father–child–mother trios. Details of X chromosomal STRs in Koreans would be useful in paternity tests and forensic purposes as well as whole X-chromosomal mapping studies.

Allele frequency distribution of two X-chromosomal STR loci in the Han population in China

Background: X-chromosome (ChrX) STR loci have been proven to be a useful tool for paternity testing, especially in some cases. In paternity testing, genetic markers on ChrX are only applicable when the disputed child is female. Methods: The author investigated allele frequency distribution of ChrX STR loci DXS6789 and HumSTRX1 in a sample of unrelated individuals (males and females) in Han population living in Chengdu, China, by using PCR and PAGE followed by silver staining. Results: Ten and six different alleles of DXS6789 and HumSTRX1 loci were detected, respectively. The genotype frequencies of DXS6789 and HumSTRX1 loci were in good agreement with the Hardy–Weinberg equilibrium. The observed heterozygosity of DXS6789 and HumSTRX1 loci were 0.795 and 0.748 in females, respectively. Conclusions: It is suggested that these ChrX markers are appropriate for the purposes of forensic analyses.

Population genetic comparisons of three X-chromosomal STRs (DXS7132, DXS7133 and GATA172D05) in North and South Italy

Population genetic data of three tetranucleotide X-chromosomal STRs, DXS7132, DXS7133 and GATA172D05, were obtained by analyzing 295 unrelated healthy individuals living in North and South Italy (160 females and 135 males), and 40 family trios with female children. PCR primers for the loci DXS7132 and DXS7133 were redesigned in order to reduce the length of the amplification products compared with conventional design so that improved typing success rate when highly degraded DNA is used as a template. The comparison of the allele frequencies of these three ChrX markers gave similar distributions for North and South Italy although minor variations were found for some alleles. Additionally, some differences were found when comparing the allele frequencies of the male and female samples independently. Based on the investigated meiotic events, mutations were not found.

Development of a heptaplex PCR system to analyse X-chromosome STR loci from five Italian population samples. A collaborative study

A heptaplex PCR has been developed to amplify DXS6789, HUMARA, DXS10011, DXS7423, HPRTB, DXS6807 and DXS101 on Italian samples from Bologna, Modena, Padova, Ancona and Pisa. Statistical analyses were performed for all the loci.

Allele distribution of five X-chromosome STR loci in an Italian population sample

Population genetic data for five X-chromosomal STR loci (DXS7423, DXS6789, DXS6795, DXS9898 and DXS8377) were generated by analysing a population sample from Northwest Italy. Intensive stutter bands were observed for the DXS8377 locus. The analysis of the 40 family trios segregation showed no new mutation.

Five highly informative X-chromosomal STRs in Koreans.

The five X-chromosomal short tandem repeats (STRs) GATA172D05, HPRTB, DXS8377, DXS101 and HumARA were analyzed in 150 males and 150 females from Korea. Markers were amplified in a quadruplex and a monoplex PCR reaction with fluorescently labeled primers. For accurate and reproducible STR typing, sequenced allelic ladders were constructed and a Genotyper macro was programmed. Some differences were found on comparing the allele frequencies of Koreans with those of other populations in DXS8377, DXS101 and HumARA. The forensic efficiency parameters showed that the five X-linked STRs are highly informative for forensic application in Koreans.

Population Data of Three X-Chromosomal STRs: DXS7132, DXS7133 and GATA172D05 in North Italy

Abstract The samples for database studies were obtained from 175 unrelated healthy individuals (85 women and 90 men) living and born in North Italy. The DNA from blood samples was extracted using a GenomicPrep Blood DNA Isolation Kit (APB, Milano, Italy), according to the manufacturer's instructions. The quantity of human DNA was determined by spectrophotometry. Aliquots of 2-5 ng of target DNA were amplified in singlepex with the primers reported by Edelmann (1) for DXS7133, GATA172D05 and newly designed forward primer for DXS7132.

The X-linked STRs DXS7130 and DXS6803

This paper presents sequence and population genetic data of two new X-linked microsatellite markers, suitable for forensic purposes. Data were obtained from a sample of unrelated German individuals (male and female). Two highly informative markers could be added to the panel of ChrX STRs [J. Edelmann, S. Hering, M. Michael, R. Lessig, D. Deichsel, G. Meier-Sundhausen, L. Roewer, I. Plate, R. Szibor, 16 X-chromosome STR loci frequency data from a German population, For. Sci. Int. 124 (2001) 215–218; J. Edelmann, D. Deichsel, S. Hering, I. Plate, R. Szibor, Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377, For. Sci. Int. 129 (2002) 99–103].

Two X-Chromosome STR Loci DXS6804 and DXS9896 Frequency Data in Chinese Population

Abstract Blood samples were collected from unrelated individuals of the Chinese Han ethnic group in Chengdu, China. DNA was extracted using the Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/DXS6804.htm. The volume of PCR reaction for each locus was 37.5 µL. The PCR products were analyzed by horizontal nondenaturing polyacrylamide gel electrophoresis with a discontinuous buffer system and visualized by silver staining (2). Data of female population genetics and forensic science were analyzed using the POWERSTATS program (3). The complete dataset can be accessed at http://www.legalmed. org/dna/DXS6804.htm

Two X-Chromosome STR Loci DXS6807 and DXS7133 Frequency Data in Chinese Population

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/DXS6807.htm. The volume of PCR reaction for each locus was 37.5 L. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data of female population genetics and forensic science were analyzed using POWERSTATS program (3).