Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Short tandem repeat”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources
PubMed1997

Characterization of four short tandem repeat loci (THO1, VWA31/A, CD4, and TP53) in northern Portugal.

Allele and genotype frequencies for two tetrameric and two pentameric short tandem repeat (STR) loci (THO1, VWA31/A, CD4, and TP53) were determined in a population sample from northern Portugal. Genotyping of PCR amplification products was done using polyacrylamide gel electrophoresis followed by silver staining; heteroduplex analysis was performed to distinguish THO1 genotypes involving allele 10 and the nonconsensus allele 9.3. For all loci allele frequencies fitted the distribution patterns generally observed in European populations. The observed genotype distributions do not deviate significantly from Hardy-Weinberg expectations, although for VWA31/A a significant excess of heterozygotes involving allele 17 was found. Mother-child pair analyses confirmed the regular Mendelian pattern of inheritance. Because the information content of these systems is high and because their genotyping is technically reliable and simple, CD4, THO1, VWA31/A, and TP53 are appropriate genetic systems for anthropological genetics.

Antigens, CD↗
PubMed2001

Short tandem repeat polymorphism linkage to the androgen receptor gene in prostate carcinoma.

BACKGROUND: Due to high polymorphism, common sequences, and ubiquitous presence, short tandem repeats (STRs) may enhance genomic typing to determine prostate carcinoma (CaP) predisposition. The human phosphoglycerate kinase (PGK1) gene is located within Xq11-Xq13, a region implicated in familial prostate carcinoma, androgen insensitivity, perineal hypospadias, and other genitourinary abnormalities. The PGK1 STR is the most polymorphic site described in the Xq11-Xq13 interval and was investigated for its ability to detect differences comparing a heterogeneous CaP population versus controls. METHODS: We compared PGK1 STR allele sizes in 103 localized CaP patients with 299 control subjects to evaluate the STR's ability to detect potential CaP predisposing genetic factors. Allele sizes were measured with an automated DNA sequencer after polymerase chain reaction (PCR) based copying of the PGK1 STR region. Allele sizes were compared using chi square and Mann-Whitney U tests. RESULTS: Among 402 subjects, there were 10 distinct allele sizes consisting of five common and five relatively rare alleles. The PGK1 STR, 12 allele (12 tetrameric repeats) was more common among patients with CaP (p=0.03). Allele 13 was more common in CaP patients > 60 years old than among younger patients (p< 0.005). CONCLUSIONS: Our findings suggest that STRs in the Xq11-Xq13 region and other regions may provide a means to rapidly scan genetic loci in large populations of CaP patients and controls. Within limitations, STRs offer the advantage of relatively uniform protocols that could potentially provide a means to comprehensively scan genomes at known predisposing loci.

Aged↗
PubMed1998

Genotyping of forensic short tandem repeat (STR) systems based on sizing precision in a capillary electrophoresis instrument.

Automated fluorescence analysis of polymerase chain reaction (PCR)-amplified short tandem repeat (STR) systems by capillary electrophoresis (CE) is becoming an established tool both in forensic casework and in the implementation of both state and national convicted offender DNA databases. A new capillary electrophoresis instrument, the ABI Prism 310 Genetic Analyzer, along with the Performance Optimized Polymer 4 (POP-4) provides an automated and precise method for simultaneously analyzing ten fluorescently labeled STR loci from a single PCR amplification kit, which provides a power of discrimination of approximately one in five billion from a single PCR amplification. Data are presented on sizing precision, sizing accuracy, and resolution for the STR loci in the AmpFlSTR Profiler kit. Sizing accuracy is highly dependent on the electrophoresis system, and therefore the reporting of alleles based on the nucleotide size obtained from an electrophoresis system is not recommended for forensic work. The precision of the 310 capillary electrophoresis system, coupled with software developed for automated genotyping of alleles based on the use of an allelic ladder, allows for accurate genotyping of STR loci. Sizing precision of < or = 0.16 nucleotide standard deviation was obtained with this system, thus allowing for accurate genotyping of length variants that differ in length by a single nucleotide.

Alleles↗
PubMed1995

Swiss population data and forensic efficiency values on 3 tetrameric short tandem repeat loci-HUMTH01, TPOX, and CSF1PO-derived using a STR multiplex system.

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci were determined in a Swiss population sample (n = 100) using the GenePrint STR Multiplex System, electrophoresis of the PCR products in DNA sequencing gels and subsequent detection of allelic fragments by silver staining. The loci are HUMTH01, TPOX, and CSF1PO. The observed heterozygosities are 83.0%, 60.0%, and 72.0%, respectively. The discrimination power determined for the individual loci is 0.914, 0.780, and 0.860, respectively, and the combined discrimination power for the triplex is 0.997. All loci meet Hardy-Weinberg expectations and after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence. Moreover, independence of alleles at these STR loci with other PCR-based loci derived from the same Swiss population sample, previously reported, were considered. These loci were DQA1, LDLR, GYPA, HBGG, D7S8, GC and D1S80. Again, after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence among alleles at the 10 different PCR-based loci. Thus, the allelic frequency data can be used in human identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Swiss population.

Alleles↗
PubMed1994

Swiss population data on three tetrameric short tandem repeat loci--VWA, HUMTHO1, and F13A1--derived using multiplex PCR and laser fluorescence detection.

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci VWA, HUMTHO1, and F13A1 were determined in a Swiss population sample using multiplex PCR and subsequent electrophoresis in DNA sequencing gels processed by automated laser fluorescence detection. The technique allows single base pair resolution and rapid typing, with a concomitant reduction in the potential for human transcriptional typing errors. All loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the 3 loci. The allelic frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a multiple STR locus DNA profile in the Swiss population.

Alleles↗
PubMed1996

PCR typing of DNA fragments of the two short tandem repeat (STR) systems upstream of the human myelin basic protein (MBP) gene in Danes and Greenland Eskimos.

DNA from the double short tandem repeat (STR) system MBP (locus 18q23-pter) was amplified by the polymerase chain reaction (PCR) and the two polymorphic repeat systems were separated by cutting with the restriction enzyme NlaIII. The lengths of the DNA fragments of the two MBP STR systems MBP-A and MBP-B were analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 112 unrelated Danes, 140 unrelated Greenland Eskimos, and 88 Danish mother/child pairs were analyzed. The distributions of MBP phenotypes were in Hardy-Weinberg equilibrium in both the Eskimo and Danish populations. Significant differences were observed between the distribution of fragments ('alleles') in Greenland Eskimos and in Danes. The allele MBP-A7 was considerably more frequent in Eskimos (0.2214) than in Danes (0.0775) and also the allele MBP-B9 was considerably more frequent in Eskimos (0.225) than in Danes (0.06). Strong gametic associations were found between fragments from MBP-A and MBP-B series in both Danes and Eskimos. Some of the associations were different in Danes and Eskimos. In the 88 Danish mother/child pairs, the segregation of the MBP genotypes were in accordance with a genetic model of co-dominant inheritance and no mutation was found. Two MBP STR regions with irregular structures were sequenced. One fragment had a single base G to A transition at position 124 in the primer binding region between the MBP-A and MBP-B regions. In the other fragment, a deletion starting at position 117 and including the primer binding region between MBP-A and MBP-B regions was found.

Alleles↗
PubMed2003

Nine short tandem repeat loci analysis in aged semen stains using the AmpFLSTR Profiler Kit and description of a new vWA variant allele.

Nine short tandem repeat (STR) loci, D3S1358, D5S818, vWA, TH01, D13S317, TPOX, FGA, D7S820 and CSF1PO, were investigated in semen stains of various ages using the AmpFLSTR Profiler Kit. The nine STR loci were typed from semen stains stored for up to 25 years with the application of 1-10 ng DNA. This system provides a useful tool in medicolegal individualization of aged semen stains. During this investigation we found a new variant allele 18.1 at the vWA locus.

Gene Frequency↗
PubMedDate not supplied

Short tandem repeat (STR) variation in eight village populations of the island of Korcula (Croatia).

The aim of this study was to analyse short tandem repeat (STR) variation using the data on nine loci (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, D7S820) in the populations from eight villages on the island of Korcula, Croatia, in order to analyse its genetic and population structure. The analysis of STR data in this study indicated an appreciable degree of genetic homogeneity among the studied village populations on the island, even though a so-called 'east-west dichotomy' and differentiation between the inhabitants of the most recent settlement and the remaining ones was indicated with respect to the loci CSF1PO and TPOX, respectively. The validity of STR markers in assessing genetic structure of small populations and especially in determining the relationships among geographically closely related but reproductively isolated groups remains to be further evaluated, especially in terms of a larger number of studied loci in order to possibly find specific markers useful for resolving genetic patterns of variability at regional levels.

Croatia↗
PubMed2003

Analysis of short tandem repeat (STR) polymorphisms by the powerplex 16 system and capillary electrophoresis: application to forensic practice.

Allele and genotype frequencies for 15 short tandem repeat (STR) polymorphisms--D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA--in a Japanese population were estimated. No deviations of the observed allele frequency from Hardy-Weinberg equilibrium expectations were found for any of the systems studied. Between 2 new pentanucleotide STR loci, Penta E and Penta D, for which there is only limited data regarding the allelic distribution in Japanese, the Penta E locus was found to be highly polymorphic and exhibited a tri- or tetra-modal distribution pattern having allelic peaks with 5, 11, 15 and 20 repeats. The distribution was significantly different from that of the other ethnic groups. Statistical parameters of forensic importance, the power of discrimination (PD), observed and expected heterozygosity values (H), polymorphism information content (PIC), power of discrimination (PD), matching probability (pM), power of exclusion (PE), and typical paternity index (PI), were calculated for the loci. These parameters indicated the usefulness of the loci in forensic personal identification and paternity testing among Japanese. The systems Penta E, FGA, D18S51 and D8S1179 were the most informative. This method was successfully applied to forensic personal identification and paternity testing among Japanese, thereby confirming its efficacy for forensic practice.

Adult↗
PubMed2003

[Genetic polymorphism of six short tandem repeat loci in the Han population in Hebei province of China].

OBJECTIVE: This article reports a population genetic study on six short tandem repeat(STR) loci, D7S820, D19S253, D12S391, D5S818, D16S539 and D8S1179, in a sample of unrelated Chinese Han individuals(n=122-173) living in Hebei province. METHODS: DNA extraction from blood samples (200 in number) and multiplex amplification of the above six loci were carried out. Using denaturing polyacrylamide gel electrophoresis and silver stain, the authors investigated the distribution of allele frequencies of the six loci in Han population in Hebei province. RESULTS: The STR polymorphisms at all of the six loci were observed in Chinese Han population in Hebei province. The observed heterozygosities of D7S820, D19S253, D12S391, D5S818, D16S539 and D8S1179 were 0.828, 0.757, 0.769, 0.837, 0.785 and 0.852, respectively. The measured values of the power of discrimination (PD) were 0.914, 0.919, 0.940, 0.909, 0.917, 0.944; of the mean exclusion chance(MEC) 0.618, 0.740, 0.801, 0.557, 0.655, 0.696 and of the polymorphism information content (PIC) in Chinese 0.771, 0.760, 0.762, 0.708, 0.776 and 0.794, respectively. CONCLUSION: The genotype distributions of the six STR were in accordance with Hardy-Weinberg equilibrium. The numerical values of the PD and MEC are relatively high in Hebei province, and thus can be of significant application in population genetics and forensic medicine.

Asian People↗
PubMed2004

[Genetic polymorphisms of short tandem repeat loci D3S1358, D13S317, D5S818 from Nongqu Mongolia].

OBJECTIVE: To understand the allele structure and genetic polymorphism at D3S1358, D13S317, D5S818 short tandem repeats (STRs) loci in Nongqu Mongolian of China, and to construct a preliminary database. METHODS: The allele frequencies of the three STRs loci in 291 unrelated individuals from Nongqu Mongolian were analyzed by polymerase chain reaction and polyacrylamide gel electrophoresis. RESULTS: Six, ten, and eight alleles were observed at D3S1358, D13S317, D5S818, respectively, and all 3 loci met Hardy-Weinberg equilibrium. The statistical analysis of 3 STR loci showed the heterozygosity >or=0.7332, the polymorphic information content >or=0.6884; the combined discrimination power and the probabilities of paternity exclusion were 0.9991 and 0.9806 respectively. CONCLUSION: All three of the loci in this study were found to have high heterozygosity and polymorphic information content, so they could provide useful markers for genetic purposes. These results could serve as valuable data to enrich the Mongolian genetic database and play an important role in Chinese population genetic application.

Chromosome Mapping↗
PubMed2004

[Allele frequencies and species specificity of six short tandem repeat loci in Chinese population].

OBJECTIVE: To develop a set of new markers for forensic application, the authors have chosen 6 short tandem repeat(STR) loci to study the allele frequencies and species specificity in Chinese Han population in Chengdu. METHODS: One hundred and ten EDTA-blood samples were collected from the unrelated individuals in Chengdu city, Sichuan province. DNA was extracted by Chelex-100 and amplified by the polymerase chain reaction(PCR). Polyacrylamide gel electrophoresis (PAGE) and silver staining were used to analyze the PCR products. RESULTS: The polymorphisms of all 6 STR loci have been obtained in Chinese Han population in Chengdu, the alleles of D4S2366, D4S2367, D6S474, D6S1281, D2S1396 and D20S601 being 7, 7, 6, 7, 5, 7, the observed heterozygosity of them being 0.802, 0.708, 0.770, 0.627, 0.542, 0.672, the discrimination power of them being 0.887, 0.828, 0.849, 0.848, 0.794, 0.865; and the power of exclusion of them being 0.602, 0.441, 0.544, 0.325, 0.227, 0.386. Evaluated by comparison with the data from 14 different animals as controls, the 6 STR loci contain good specificity of human beings. CONCLUSION: The 6 STR loci are highly polymorphic and can play a key role in species identification. They are new candidate markers for forensic personal identification and paternity testing.

Animals↗
PubMed2005

[Genetic polymorphism of Y-chromosome short tandem repeat in Elunchun ethnic group of China].

OBJECTIVE: To reveal the allelic frequencies and haplotype frequencies of ten Y-chromosome short tandem repeats(STR) loci (DYS392, DYS438, DYS439, DYS456, DYS459, DYS460,DYS461, DYS462, DYS389I and DYS389II systems) in an Elunchun population sample. METHODS: PCR and polyacrylamidegel electrophoresis(PAGE) followed by silver staining were performed to analyze the blood samples from 102 unrelated Elunchun male individuals. RESULTS: The allele diversity values for each locus ranged from 0.418(DYS461) to 0.727(DYS389 I). Gene diversities were higher than 0.5 except DYS462(0.479) and DYS461 (GATAA7.2)(0.418). Furthermore, 101 haplotypes from 10 Y-chromosome STRs loci were found in the sample and a high haplotype diversity 0.99 was determined. CONCLUSION: The above findings suggest that the ten Y-chromosome STR loci are valuable Y-specific markers for establishing Y-STR database, understanding human origin, paternity testing and personal identification.

China↗
PubMed1995

[Analysis of short tandem repeats polymorphism in the phenylalanine hydroxylase gene and its application to prenatal gene diagnosis of phenylketonuria].

There is a polymorphic tetranucleotide short tandem repeats (STR) sequence in the intron 3 of the phenylalanine hydroxylase (PAH) gene. The polymorphism of this STR sequence in Chinese was analysed on 36 normal individuals and 16 PKU families. After PCR amplification, the DNA fragments were separated on polyacrylamide sequencing gel and visualized by silver-staining. Seven alleles were identified with frequencies of 0.028, 0.042, 0.014, 0.138, 0.542, 0.208 and 0.028 in normal populations, and 0.016, 0.078, 0.047, 0.312, 0.375, 0.156 and 0.016 in PKU families, and PICs of 0.585 and 0.693, respectively. This polymorphic marker is very useful in quick prenatal gene diagnosis in PKU families, and prenatal gene diagnosis was performed by linkage analysis in two pregnancies at risk.

Alleles↗
PubMed2026

A novel relationship between time offsets in capillary electrophoresis and DNA sequence variations in short tandem repeats.

Next-generation sequencing (NGS) provides increased discriminatory power in forensic DNA analysis due to the detection of isoalleles. Differences in sequences between alleles allow for a second layer of differentiation between DNA contributors beyond the number of short tandem repeat (STR) repeat units. However, because NGS is a more time and resource-intensive analysis than conventional capillary electrophoresis (CE), laboratories may benefit from indicators that suggest NGS is likely to provide added value. This study examined whether CE migration offsets, measured as residuals in the OSIRIS analysis software, can differ significantly among STR isoalleles. Residuals represent the time offset between a sample allele peak and its corresponding allelic ladder peak. Paired CE and NGS data from 95 single source samples were analyzed for CE-based residual differences, as the NGS data provided the sequence information of the corresponding isoalleles. Residual values differed significantly among isoalleles at several STR loci. Statistically significant differences were identified at D16S539 and D3S1358, as well as at specific allele lengths within D12S391, D13S317, and D8S1179. These findings demonstrate that CE residual variation can reflect underlying STR sequence differences between contributors. In practice, residual-based metrics could help laboratories to identify casework reference samples where NGS is likely to provide additional discrimination, without the need for processing outside of a routine CE workflow. Due to the potentially large number of isoalleles, community wide efforts to aggregate CE residual differences versus isoallele sequences may be useful in the validation and implementation of this approach to add value to forensic DNA analyses.

Electrophoresis, Capillary↗
PubMed1997

United Arab Emirates population data on three DNA tetrameric short tandem repeat loci: HUMTHO1, TPOX and CSF1PO--derived using multiplex polymerase chain reaction and manual typing.

Allele and genotype frequencies for three tetrameric short tandem repeat (STR) loci: HUMTHO1, TPOX, and CSFIPO, were determined in a United Arab Emirates (UAE) national population sample (n = 119). The loci were amplified simultaneously and the PCR products were separated in polyacrylamide DNA sequencing gels. Detection of the DNA fragments was accomplished using silver staining. Allele designations were determined by comparison to an allelic ladder. One allele at each locus was sequenced to confirm the nature of the repeats and their number. Alleles at the HUMTHO1 and TPOX loci were distributed bimodally, while CSF1PO showed unimodal distribution. The observed heterozygosities were 76% for HUMTHO1, 64% for TPOX, and 71% for CSF1PO. No deviation from the Hardy-Weinberg expectations was observed in the genotype distribution for the loci TPOX and CSF1PO, but the HUMTHO1 locus did depart from HWE based on the likelihood ratio and the exact test. No correlation was detected between the alleles at any of the three pairs of loci. The allelic frequency data of these three loci in the UAE population sample can thus be used in human identity testing.

DNA↗
PubMed1998

A study on the short tandem repeat system ACTBP2 (SE33) in an Austrian population sample.

Population genetic studies were carried out on 932 caucasians from Austria using the short tandem repeat system ACTBP2 (SEE33). A sequenced allelic ladder was used for typing (Möller et al. 1995). After native polyacrylamide gel electrophoresis all 26 alleles of the ladder were found as well as 194 alleles which migrated differently from those in the ladder. Forensically relevant parameters were calculated (discrimination power: 0.989, mean exclusion chance: 0.854, observed heterozygosity 0.946). An allele consisting of 9 repeats which is not part of the allelic ladder was also found. In 692 meioses 5 mutations were found (mutation rate 0.72%).

Actins↗