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At least 163 records · Page 9Linked to original sources
PubMed2002

[Genetic polymorphism of 9 STR loci in Chaoxian National Minority of China].

In order to enrich the Chinese genetic database,nine polymorphic loci of STR,such as D3S1358,vWA,FGA,TH01,TPOX,CSF1PO,D5S818,D13S317 and D7S820 were studied. Based on STR gene scan marked by fluorescence,91 unrelated Chinese Chaoxian individuals were observed.81 alleles and 196 genotypes were found. The corresponding gene frequency and genotype frequency were 0.0055-0.4615 and 0.0110-0.9890 respectively. The genogypes frequency of nine STR loci was good with the Hardy-Weinberg equilibrium (P approximately 0.05). The statistical analysis of nine STR loci showed the following: PIC (polymorphic information content) >or=0.6863, H (heterozygosity) >or=0.6919, DP (discrimination power) >or=0.8301, EPP (probability of paternity exclusion) >or=0.8590. The data studied can be used in Chinese population genetic studies and forensic medicine applications.

English Abstract↗
PubMed2005

Chromosomal duplications along the Y-chromosome and their potential impact on Y-STR interpretation.

Y-chromosome short tandem repeat (Y-STR) markers are being used as potential tools for distinguishing low levels of male DNA in the presence of excess female DNA as is present in many sexual assault samples. Usually single copy Y-STR loci produce a single amplicon in single source samples, and thus the observation of multiple peaks at such a locus could suggest to an analyst that a mixture of more than one male contributor is present in the tested sample. However, many regions of the Y-chromosome are duplicated or even triplicated in some individuals and this fact can thus complicate potential mixture interpretation. Reasons for the presence of duplications at multiple loci within a single sample are explored in the context of Y-STR marker location along the chromosome. True male-male mixtures commonly exhibit more than one locus-specific PCR product across multiple Y-STR loci that are not adjacent to one another on the Y-chromosome. In addition, duplicated loci typically possess alleles that differ by only a single repeat unit and possess similar peak heights.

Alleles↗
PubMed2002

[Genetic polymorphisms of 9 STR loci in Dongxiang ethnic group of China].

Genetic distribution for nine STR loci was determined in a Chinese Dongxing ethnic group based on STR genescan marked by fluorescence. Seventy-two alleles and 182 genotypes were observed in 94 unrelated Chinese Dongxiang individuals,with the corresponding gene frequency and genotype frequency being 0.0053-0.5825 and 0.0106-0.2660 respectively. The genotypes of nine STR loci were in accordance with the Hardy-Weinberg equilibrium (P>0.05). The statistical analysis of nine STR loci showed PIC (polymorphism information content, PIC) = or > 0.6378, H(heterozygosity, H) = or > 0.6500, DP (discrimination power, DP) = or > 0.8216, PPE (probabilities of paternity exculation, PPE) = or > 0.4903. The result indicated that there was a significant difference between Dongxiang ethnic group and the white and the black. There was no significant difference in Han nationality. These result filled the Dongxiang ethnic group-a specific group of Chinese into the genetic database and played an important role in Chinese population genetic study and forensic medicine application.

English Abstract↗
PubMed2005

An STR forensic typing system for genetic individualization of domestic cat (Felis catus) samples.

A forensic genotyping panel of 11 tetranucleotide STR loci from the domestic cat was characterized and evaluated for genetic individualization of cat tissues. We first examined 49 candidate STR loci and their frequency assessment in domestic cat populations. The STR loci (3-4 base pair repeat motifs), mapped in the cat genome relative to 579 coding loci and 255 STR loci, are well distributed across the 18 feline autosomes. All loci exhibit Mendelian inheritance in a multi-generation pedigree. Eleven loci that were unlinked and were highly heterozygous in cat breeds were selected for a forensic panel. Heterozygosity values obtained for the independent loci, ranged from 0.60-0.82, while the average cat breed heterozygosity obtained for the 11 locus panel was 0.71 (range of 0.57-0.83). A small sample set of outbred domestic cats displayed a heterozygosity of 0.86 for the 11 locus panel. The power of discrimination of the panel is moderate to high in the cat breeds examined, with an average P(m) of 3.7E-06. The panel shows good potential for genetic individualization within outbred domestic cats with a P(m) of 5.31E-08. A multiplex protocol, designed for the co-amplification of the 11 loci and a gender-identifying locus, is species specific and robust, generating a product profile with as little as 0.125 nanograms of genomic DNA.

Animals↗
PubMed2005

Analysis of non-suspect samples lacking visually identifiable sperm using a Y-STR 10-plex.

Y-STRs are valuable in the investigation of sexual assaults in which autosomal STR genotype interpretation is challenging. To detect male DNA from compromised sexual assault evidence, 45 non-suspect samples were differentially extracted and analyzed with 10 Y-STRs. These samples were positive for the presence of human seminal fluid, but were negative for spermatozoa by microscopic examination. Y-STR data were obtained in approximately 86.2% of the epithelial or sperm fractions. On samples yielding incomplete profiles, results were obtained on an average of 5 loci per sample. The inability to obtain results may be due to insufficient amplifiable male DNA, PCR inhibition, or unfounded accusations of sexual assault. This study indicates that it is possible to obtain a male STR profile even in the absence of visually identifiable spermatozoa. Furthermore, Y-STR loci should become components of CODIS if they are to be used in solving non-suspect sexual assaults.

Acid Phosphatase↗
PubMed2006

[Analysis of free foetal DNA in maternal plasma using STR loci].

BACKGROUND: Problems of maternal and foetal genotype differentiation of maternal plasma in pregnant women are solved generally by real-time systems. In this case the specific probes are used to distinguish particular genotype. Mostly gonosomal sequences are utilised to recognise the male foetus. This work describes possibilities in free foetal DNA detection and quantification by STR. METHODS AND RESULTS: Artificial genotype mixtures ranging from 0,2 % to 100 % to simulate maternal and paternal genotypes and 27 DNA samples from pregnant women in different stage of pregnancy were used for DNA quantification and detection. Foetal genotype was confirmed by biological father genotyping. The detection was performed in STR from 21st chromosome Down syndrome (DS) responsible region by innovated (I) QF PCR which allows to reveal and quantify even very rare DNA mosaics. The STR quantification was assessed in artificial mixtures of genotypes and discriminability of particular genotypes was on the level of few percent. Foetal DNA was detected in 74 % of tested samples. CONCLUSIONS: The IQF PCR application in quantification and differentiation between maternal and foetal genotypes by STR loci could have importance in non-invasive prenatal diagnostics as another possible marker for DS risk assessment.

DNA↗
PubMed2006

[Developing of a new multicolor-fluorescent labeled STR amplification kit].

OBJECTIVE: To develop a PCR-based STR system for genotyping of 18 loci (Amelogenin, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D16S539, TH01, TPOX, CSF1PO, D7S820, D2S1338, D19S433, D12S391 and D19S253). METHODS: By using primers labeled with four color fluorescent (FAM, HEX, TAMRA and ROX), two multiplex amplification reaction systems were developed to genotype Amelogenin and 17 STR loci. RESULTS: Amelogenin and these 17 STR loci were genotyped successfully in different kinds of biological samples by the kit. CONCLUSION: The STR amplification kit developed in our study gives a new approach to genotype these 18 loci in a efficient, steady and reliable way.

Alleles↗
PubMed1995

French Caucasian population data for HUMTH01 and HUMFES/FPS short tandem repeat (STR) systems.

The recent technology of amplification of DNA sequences by the polymerase chain reaction (PCR) has already proved to be a very useful tool for the analysis of variable number of tandem repeat (VNTR) loci. Short tandem repeat (STR) loci appear as other promising PCR-based identification systems. In fact, DNA typing based on PCR amplification of STRs is very sensitive and allows to overcome major problems encountered when using the RFLP method, such as typing of very small amounts of DNA, highly degraded DNA or mixtures of DNA from more than one individual. Two STR systems, HUMTH01 (a tetranucleotide repeat (AATG) sequence located on chromosome 11) and HUMFES/FPS (a tetranucleotide repeat (ATTT) sequence located on chromosome 15) were investigated in order to determine allele and genotype frequencies for a French caucasian population sample. HUMTH01 and HUMFES/FPS alleles were amplified by the use of PCR and amplified STR sequences were analyzed on 6% Hydrolink Long Ranger gels and visualized by silver staining. The study was conducted on a sample of unrelated individuals (N approximately 190) randomly selected from the French caucasian population. The genotype distributions met Hardy-Weinberg expectations for both HUMTH01 and HUMFES/FPS STR systems. Furthermore, an additional allele, never reported before was observed at the HUMFES/FPS locus: it migrates as an allele containing 7 repeat units and corresponds to the smallest allele identified for this locus.

Alleles↗
PubMed1996

Validation of multiplex polymorphic STR amplification sets developed for personal identification applications.

Polymorphic short tandem repeat (STR) loci, which typically consist of variations in the number of 3-7 base pair repeats present at a site, provide an effective means of personal identification. Typing can be accomplished by amplification of genomic DNA using the polymerase chain reaction (PCR) and locus-specific primers, separation of amplified alleles using gel electrophoresis and their display using silver staining or fluorescent detection. Primers for several STR loci can be combined in a single multiplex reaction so typing of multiple loci can be accomplished rapidly and with less DNA than required if each locus were analyzed separately. Before such muliplex systems are used in forensic or paternity applications, it is desirable that they undergo testing for their reliability. This study evaluates the performance of two STR triplex systems, one containing the loci HUMCSF1PO, HUMTPOX, and HUMTH01, and the other containing HUMHPRTB, HUMFESFPS, and HUMVWFA31. Protocols for amplification of these two triplexes, and their corresponding monoplexes, were evaluated for sensitivity of detection, resistance to changes in the annealing temperature of the amplification protocol, and the ability to identify the minority contributor in amplification of mixed samples. In addition, five laboratories determined the alleles of twenty DNA samples, each extracted by one of four different extraction methods. The results illustrate that the two STR triplex systems and the monoplex systems contained within them can be used with as little as 0.25 ng of DNA template. Both triplexes amplified with 100% success using the Perkin Elmer Model 480 thermal cycler. With the GeneAmp 9600 System, the CTT triplex amplified with 100% success and the HFv triplex in 95.6% of attempts. These experiments meet many requirements for use in validation of DNA typing systems for forensic cases and paternity identification.

Anthropology, Physical↗
PubMedDate not supplied

Gene flow in the Iberian Peninsula determined from Y-chromosome STR loci.

In this work, seven multiallelic short-tandem repeat (STR) loci from the nonrecombining region of the human Y-chromosome (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, and DYS393) were typed in a sample of residents in the Basque Country (RBAS). In all, 40 different Y-STR haplotypic combinations were identified, resulting in a value of haplotypic diversity of 0.979. Y-STR data compiled from previous works were used for studying Y-chromosome diversity in the Iberian Peninsula and for assessing the effects of migratory movements on the genetic background of the population living currently in territories traditionally occupied by native (autochthonous) Basques. An analysis of the spatial distribution of allelic frequencies of the Y-STRs revealed a geographic pattern characterized by variation gradients (frequency clines) oriented for the most part in the direction southwest-northeast. Accordingly, a neighbor-joining analysis showed a relative polarization between populations located in the northeast and center of the Iberian Peninsula, and the rest of the samples considered. The study sample (RBAS) occupied an intermediate position in the population tree between the autochthonous Basques (BASQ) and the remaining samples. Interestingly, the RBAS collection only showed genetic heterogeneity with that of native Basques (PhiST = 0.013, P < 0.05). Estimates of admixture proportions in the gene pool of RBAS indicated a high level of hybridization with Basque (56%) and non-Basque (44%) genes, which could explain the genetic differentiation observed between BASQ and RBAS.

Chromosomes, Human, Y↗
PubMed2004

New satellite DNA in Lacerta s. str. lizards (Sauria: Lacertidae): evolutionary pathways and phylogenetic impact.

A new tandemly repeated (satellite) DNA family namely Agi160, from Lacerta agilis and Lacerta strigata (Lacerta sensu stricto (s. str.), Linnaeus 1758) have been cloned and sequenced. Agi160 is found in the above two species, as well as two other representatives of the same genus, L. viridis and L. media. DNA hybridization did not reveal it in Darevskia, Podarcis, Zootoca, Eremias, Ophisops, and Gallotia - the other genera of the family Lacertidae. The results suggest that Agi160 is a Lacerta s. str. specific family of tandem DNA repeats. However, a comparison between sequences of Agi160 and CLsat repeat units revealed 60 bp regions 62-74% identical. The latter is a satellite DNA family typical for Darevskia (syn. "L. saxicola complex") (Grechko et al., Molecular-genetic classification and phylogenetic relatedness of some species of Lacertidae lizards by taxonoprint data. Mol Biol 32:172-183, 1988.). Both Agi160 and CLsat tandem repeats share several common features (e.g., the same AT content and distribution of multiple short A-T runs, internal structure of repeated units, the presence of conservative regions). These data are indicative of their common origin and a possibly strong selective pressure upon conserving both satellites. A comparative analysis of structure, organization, and abundance of these two families of satDNA reveals evolutionary pathways that led to their formation and divergence. The data are consistent with the hypotheses of the concerted evolution of satellite DNA families. The possibility of use of Agi160 as a phylogenetic tool, defining relationships within Lacerta s. str., as well as within the whole family of Lacertidae is discussed.

Animals↗
PubMed1982

A secondary promoter for elongation factor Tu synthesis in the str ribosomal protein operon of Escherichia coli.

The str operon of Escherichia coli contains genes for ribosomal proteins S12 and S7 and for elongation factors EF-G and EF-Tu (Jaskunas et al. 1975). We have subcloned various segments of DNA from this operon onto multicopy plasmids. We found that cells carrying a recombinant plasmid which lacks the major promoter for the str operon but contains the 5' portion of the EF-Tu gene synthesize a novel protein which we have identified as a truncated EF-Tu molecule. Moreover, cells carrying plasmids with an intact EF-Tu gene synthesize the elongation factor at a 3- to 5-fold higher rate than haploid cells. Thus the EF-Tu gene can be expressed in the absence of the major promoter for the str operon. This expression is not due to read-through from plasmid promoters, but it is dependent on the presence of the distal portion of the EF-G gene on the plasmids. These results indicate that there is a secondary promoter for EF-Tu expression, apparently located within the structural gene for elongation factor EF-G.

Cloning, Molecular↗
PubMed1996

Population genetics of STR loci in Caucasians.

STR loci are becoming increasingly important in forensic casework. In order to be used fairly and efficiently, the population genetics of these loci must be investigated and the implications for forensic inference assessed. A key population genetics parameter is the "coancestry coefficient", or FST, which is the correlation between two genes sampled from distinct individuals within a subpopulation. We present analyses of STR data, at geographic scales which range from national to regional, from the UK and other European sources. We implement a likelihood-based method of estimating FST, which has important advantages over alternative methods: it allows a range of plausible values to be assessed, rather than presenting a single point estimate, and it allows a subpopulation to be compared with a larger population from which a database has been drawn, which is the relevant comparison in forensic work. Our results suggest that values of FST appropriate to forensic applications in Europe are too large to be ignored. With appropriate allowance, however, it is possible to make use of STR evidence in a way which is efficient yet avoids overstatement of evidential strength.

Cross-Cultural Comparison↗
PubMed2003

Characterization of eight Y-STR loci and haplotypes in a Chinese Han population.

In this study we analyzed the eight Y-STR loci, DYS443, DYS444, DYS448, DYS453, DYS455, DYS456, DYS457 (DYS437) and DYS458, investigated haplotype distributions of these Y-STR loci in a Chinese Han population, and sequenced alleles of the eight loci for clarifying the structure. Extracted DNA was amplified by PCR and the PCR products were analyzed by non-denaturing horizontal polyacrylamide gel electrophoresis with a discontinuous buffer system. Alleles were sequenced on an ABI 3700 using a Dye Terminator Cycle sequencing kit. DYS443, DYS453, DYS455 and DYS456 were found to be simple repeat systems, while DYS444, DYS448, DYS457 (DYS437) and DYS458 were complex repeat systems. The gene diversities of DYS443, DYS444, DYS448, DYS453, DYS455, DYS456, DYS457 (DYS437) and DYS458 were 0.7742, 0.7671, 0.7453, 0.3545, 0.0549, 0.6988, 0.6148 and 0.8213, respectively. The haplotype diversity for 8 Y-STR loci was 0.9996, and the discrimination capacity was 0.9815. The results indicate that these eight loci are useful Y-linked markers for forensic applications.

Alleles↗
PubMed2006

MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis.

We sought to evaluate a more effective system for analyzing X-chromosomal short tandem repeats (X-STRs) in highly degraded DNA. To generate smaller amplicon lengths, we designed new polymerase chain reaction (PCR) primers for DXS7423, DXS6789, DXS101, GATA31E08, DXS8378, DXS7133, DXS7424, and GATA165B12 at X-linked short tandem repeat (STR) loci, devising two miniX-multiplex PCR systems. Among 333 Japanese individuals, these X-linked loci were detected in amplification products ranging in length from 76 to 169 bp, and statistical analyses of the eight loci indicated a high usefulness for the Japanese forensic practice. Results of tests on highly degraded DNA indicated the miniX-STR multiplex strategies to be an effective system for analyzing degraded DNA. We conclude that analysis by the current miniX-STR multiplex systems offers high effectiveness for personal identification from degraded DNA samples.

Asian People↗
PubMed2005

Y-STR typing of an Austrian population sample using a 17-loci multiplex PCR assay.

Y-chromosomal STR haplotypes were determined from a sample of 135 unrelated men and 70 sons from Tirol (Austria) using the AmpFlSTR Yfiler PCR amplification kit (Applied Biosystems) that coamplifies 17 Y-STRs. The panel of markers includes the 9-loci European minimal haplotype (minHt) and, in addition, the markers DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 (Y GATA C4) and Y GATA H4. A total of 130 different haplotypes (125 were unique) were identified by the 17 Y-STR markers, an increase of 19 compared with the minHt. The gene diversity of DYS635, DYS456 and DYS458 exceeded 0.75 and only that of the duplicated marker DYS385 (0.86) was higher. Consistently high haplotype diversity values were found in all tested Y-SNP haplogroups. Because the simultaneous analysis of 17 Y-STR systems offers a high power of discrimination at minimum sample consumption, the Yfiler kit is a promising tool for forensic applications.

Austria↗
PubMed2006

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.

Female↗
PubMed1997

A population study of the STR loci HUMLPL, HUMF13B, and HUMF13A01 in Hungary.

Allele frequencies of the three STR systems HUMLPL, HUMF13B, and HUMF13A01 were determined in a Hungarian population sample of 223 unrelated Caucasian individuals. All loci met Hardy-Weinberg expectations and there was no evidence for association of alleles among the three STR loci. In addition, little evidence was found for departures from expectations of independence between any of the three STR and other previously investigated microsatellite polymorphisms.

Alleles↗