X-chromosomal Short Tandem Repeat Markers Research Articles

How often have X- and autosomal-STRs mutations equivocal parental origin been assigned?

Short tandem repeat markers (STRs) are widely applied in population, evolutionary, and forensic genetics, due to extensive polymorphism in the number of repetitive motifs. The primary mutational mechanism leading to changes in the length of STRs is thought to be polymerase template slippage. Mutation rates in STRs and corresponding parental assignment are usually assessed through the number of Mendelian incompatibilities observed in one-generational, parent(s)-child, pedigrees, and paternal mutations have been assumed to be preponderant over maternal ones. Notwithstanding, diploid and haplodiploid modes of genetic transmission may not allow for the unequivocal assigning of the mutation to the correct parental origin (either paternal or maternal), especially when genotyping methodologies of fragment length determination are employed. In this work, the frequency under which a mutation might be assigned to the wrong parental origin or be interpreted as having an ambiguous origin is analyzed for both diploid and haplodiploid modes of genetic transmission. Genotypic configurations were generated with Python™ programming language, considering parents-child trios for autosomal transmission, and parents-daughter trios for the X chromosomal one. One single-, one two- or one three-step mutation was simulated in each familial constellation, and the resulting genotypic configuration was analyzed regarding the parental assignment of the mutation. When considering autosomal transmission, the meiosis suffering mutation was randomly selected. Contrarily, differential analyses were performed for paternal and maternal mutations for X-chromosomal transmission. In this work, we show that the biases in the rates between paternal and maternal mutations differ for autosomal and X-chromosomal modes of transmission. In the differential analysis performed for the X-chromosomal STRs, it is possible to ascertain that the maternal and paternal meioses are subject to different biases, the latter being better estimated than the first. This work shows that simulated data, along with reliable and properly communicated real one, may be crucial for the correct modeling of biological processes, such as the mutation in STRs.

Genetic analysis of X-chromosomal short tandem repeat (X-STR) frequencies in Arab Iraqi male population

BackgroundThe X-chromosome short tandem repeat (STR) polymorphisms are a particular tool in the fields of human population genetics and personal identification. It was necessary in investigating complex kinship or deficiency cases in conditions where information on mitochondrial DNA (mtDNA) or Y chromosome polymorphisms have been used to explore their direct paternal line. This study aimed to investigate the allele frequency of (12X-STR) of 200 unrelated males from different region of Baghdad City to serve as a reference data base for individual identification in Iraqi population. ResultsTwelve X-STR loci (DXS7424, HPRTB, DXS8377, GATA31E08, DXS7423, DXS8378, DXS9895, DXS10074, DXS6809, DXS7133, DXS101, DXS6807) were successfully amplified by multiplex PCR and divided into four groups. According to measures of allele frequency, the higher alleles frequency were 16, 11, 46, 11, 14, 10, 15, 15.2, 35, 11, 25, and 11 while the lowest alleles frequency were 11, 9, 52,53, 7, 17, 14, 13, 12.2,17, 36, 15, 16, 22, 29, and 17 that observed at the 12 loci respectively. Forensic efficiency parameter for DXS8377 locus in the first group showed highest polymorphic allele in the Iraqi Arab population with the frequencies ranging from 0.005 to 0.16%. The power of discrimination (PD) value ranged from 0.663 for DXS7423 locus and 0.9066 for DXS8377 locus. In addition, the polymorphism information content (PIC) value ranged from 0.602974 for DXS7423 locus to 0.899206 for DXS8377 locus. ConclusionsOverall the X-STR markers become used as an important source of information beside the autosomal and Y-STR markers, especially for kinship testing and haplotype analysis.

Linkage, recombination and mutation rate analyses of 16 X-chromosomal STR loci in Sri Lankan Sinhalese pedigrees.

This study investigated genetic linkage, recombination fractions and mutation rates of 16 X chromosomal short tandem repeat (X-STR) markers using a recently developed multiplex PCR assay for Sinhalese population of Sri Lanka, by analyzing 81 three-generation families including 81 grandfathers with daughters and 162 grandsons. In addition, 31 two generation families involving mother father daughter trios were included for mutation analysis. The analysis of recombination fractions between marker pairs identified two linkage blocks (maximum LOD scores > 3.0) each spanning a physical distance of 44.35Mb and 6.04Mb respectively. Though recombination events are usually rare among closely linked markers, crossovers were observed for markers located < 1.0Mb apart. The recombination fractions observed are not fully concordant with those reported earlier, including the second-generation Rutgers combined linkage-physical map. This suggests that linkage is not uniform among different populations. However, the overall and marker-specific mutation rates of the present study did not differ from previous reports, though it needs confirmation with a much larger sample set. The findings presented here will provide the baseline information required for biostatistical calculations conducted using X-STR markers, in complex kinship analysis of Sinhalese population.

Genetic structure and polymorphisms of Gelao ethnicity residing in southwest china revealed by X-chromosomal genetic markers

X-chromosome short tandem repeat markers (X-STRs), due to their special inheritance models, physical location on a single chromosome and the absence of recombination in male meiosis, play an important role in forensic and population genetics. While a series of genetic analyses focusing on the genetic diversity and forensic characteristics of X-STRs are well studied for ethnically/linguistically diverse and demographically large Chinese populations, genetic evidence from Gelao ethnicity is still sparse. Here, we genotyped the first batch of 19 X-STRs in 513 Chinese Gelao individuals (265 females and 248 males), and reported genetic polymorphisms, forensic characteristics based on the single locus and seven linkage groups. DXS10135 with the highest PIC (0.9106) and LG1 (DXS10148-DXS10135-DXS8378) with the largest HD (0.9970) are polymorphic and informative. The CPDs in Gelao males and females are respectively larger than 0.999999999997095 and 0.99999999999999999999918, and the combined MECs are larger than 0.999999975715109. Subsequently, we investigated the population relationships among 14 Chinese populations based on 19 X-STRs and among 23 populations based on 11 overlapped X-STRs. Our results revealed genetic differentiations among Tibeto-Burman, Altaic and other Chinese homogenous populations, and demonstrated that Guizhou Gelao has the genetically closer relationships with Han Chinese and geographically close Guizhou Miao.

Filipino DNA variation at 12 X-chromosome short tandem repeat markers

Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq™ DNA Signature Prep kit of the MiSeq® FGx™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications.

Curiosities of X chromosomal markers and haplotypes.

Recent progress in forensic genetics has introduced a number of closely located short tandem repeat (STR) markers on the X chromosome. Inevitably, dependencies arise that have to be accounted for. This paper will in detail explore the complex statistical interpretation of X-chromosomal STR markers, focusing on likelihood calculations. Specifically, we will investigate how the phase uncertainty of haplotypes comes into play in the statistical evaluations and what curious effects this phenomenon can have. The starting point is the different real cases where the weight of evidence has provided unexpected results that require further investigation in order to be fully understood. We will touch upon subjects such as association between alleles, recombinations, and mutations. The aim of this study is to facilitate a better understanding of the interaction between the concepts in addition to provide an understanding why good estimates of haplotype frequencies are crucial. The individual subjects have been discussed in other fields, whereas this study will focus on forensic applications where few studies have been conducted relating to the understanding of how these concepts interact.

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.

Development and characterization of a new 12-plex ChrX miniSTR system.

Short tandem repeat (STR) markers are extensively used for human identification as well as paternity and forensic casework. X-chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. This study presents the development and characterization of a new X-chromosomal short tandem repeat (STR) multiplex using short amplicon (<200 bp). A total of 366 samples from Punjabi population and 346 samples from Sindhi population were typed for 11 X-chromosomal STR markers: DXS101, DXS6789, DXS6793, DXS7132, DXS7423, DXS7424, DXS8378, DXS9902, GATA31E08, GATA172D05, and HPRTB along with sex-typing locus, amelogenin. Each marker showed a high degree of polymorphism, and the multiplex was sensitive down to 250 pg of human DNA. A total of 78 alleles were found with 5-11 alleles for each marker. The population data can be used as reference database for Sindhi and Punjabi populations.

English

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. This study presents development of a new X-chromosomal STR multiplex kit providing short-amplicon (&lt;200 bp) fragments. About 200 samples from Punjabi population were typed for seven X-STR markers: DXS101, DXS6789, DXS7132, DXS7423, DXS8378, GATA172D05 and GATA31E08. A total of 51 alleles were detected in the range of five to 10 alleles for each marker. The data can be used as reference database for Punjabi population along with the current battery of autosomal STR for forensic case work to increase the discrimination capacity and strengthen the existing system. &nbsp; Key words:&nbsp;X-chromosome short tandem repeats (X-STRs),&nbsp;mini-STRs, Punjabi population.

Allele frequency distribution of twelve X-chromosomal short tandem repeat markers in four U.S. population groups

A total of 853 samples from the four major U.S. population groups (African American, Asian, Caucasian, and Hispanic) were typed using the Qiagen ® Investigator Argus X-12 kit. Allele frequency distributions are reported here for each of the 12 X-STR markers ( DXS10103, DXS8378, DXS7132, DXS10134, DXS10074, DXS10101, DXS10135, DXS7423, DXS10146, DXS10079, DXS10148, and HPRTB).

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.

Population genetic study of four closely-linked X-STR trios in Koreans

We investigated four X chromosomal short tandem repeat (X-STR) markers (DXS10079, DXS10103, DXS10146, and DXS10148) in 450 unrelated Koreans (300 males and 150 females), and evaluated their forensic usage in relation to the four X-STR linkage groups. Forensic statistical parameters for these X-STR markers indicated that they are highly informative for forensic application in Koreans. No significant deviations from Hardy-Weinberg equilibrium were observed in any of the four X-STR markers. In addition, we present haplotypes and their frequency data for four linkage groups each comprised of three X-STRs (DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074, DXS10103-HPRTB-DXS10101, and DXS10146-DXS10134-DXS7423) in 300 males. Haplotype diversity values in the four linkage trios were all higher than 0.98, and 77.1% of all haplotypes showed a frequency less than 0.01. Therefore, the four closely-linked X-STR trios will contribute to complex kinship testing in Koreans.

Development of a five ChX STRs loci typing system

We investigated the polymorphism of five X-chromosomal short tandem repeat markers (ChrX STRs) loci (DXS7132, DXS981, DXS6803, DXS6809, and DXS6789) and their value for forensic applications. A fluorescent multiplex polymerase chain reaction (PCR) for amplifying five ChrX STRs loci in the same PCR reaction was set up. A total of 827 unrelated individuals of the Han nationality in China were tested. The results show that the five loci in the multiplex system provide high polymorphism information for forensic identification and paternity testing, particularly for difficult paternity-deficient cases.