Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “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 991 records · Page 55Linked to original sources
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↗
PubMed2004

Large-scale studies of the HphI insulin gene variable-number-of-tandem-repeats polymorphism in relation to Type 2 diabetes mellitus and insulin release.

AIMS/HYPOTHESIS: The class III allele of the variable-number-of-tandem-repeats polymorphism located 5' of the insulin gene (INS-VNTR) has been associated with Type 2 diabetes and altered birthweight. It has also been suggested, although inconsistently, that the class III allele plays a role in glucose-induced insulin response among NGT individuals. METHODS: We investigated the impact of the class III allele on Type 2 diabetes susceptibility in a case-control study involving 1462 Type 2 diabetic patients and 4931 NGT subjects. We also examined the potential impact of the class III allele in genotype-quantitative trait studies in three Danish study populations containing (i) 358 young healthy subjects; (ii) 4444 middle-aged NGT subjects, 490 subjects with IFG and 678 subjects with IGT; and (iii) 221 NGT subjects, of whom one parent had Type 2 diabetes. RESULTS: There was no difference in frequency of the class III allele or in genotype distribution between the 1462 Type 2 diabetic patients and the 4931 NGT subjects. Among the 358 young subjects the class III/III carriers had significantly reduced post-IVGTT acute serum insulin and C-peptide responses (p=0.04 and 0.03 respectively). However, among the 4444 middle-aged subjects we failed to demonstrate any association between the class III allele and post-OGTT serum insulin and C-peptide levels. CONCLUSIONS/INTERPRETATION: The class III allele of the INS-VNTR does not confer susceptibility to Type 2 diabetes or consistent alterations in glucose-induced insulin release in the examined populations, which consisted of Danish Caucasians.

Adult↗
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↗
PubMed2004

Multiple-Locus Variable-Number Tandem-Repeats Analysis of Escherichia coli O157 using PCR multiplexing and multi-colored capillary electrophoresis.

The Multiple-Locus Variable-Number Tandem-Repeats Analysis (MLVA) method is currently being used as the primary typing tool for Shiga-toxin-producing Escherichia coli (STEC) O157 isolates in our laboratory. The initial assay was performed using a single fluorescent dye and the different patterns were assigned using a gel image. Here, we present a significantly improved assay using multiple dye colors and enhanced PCR multiplexing to increase speed, and ease the interpretation of the results. The different MLVA patterns are now based on allele sizes entered as character values, thus removing the uncertainties introduced when analyzing band patterns from the gel image. We additionally propose an easy numbering scheme for the identification of separate isolates that will facilitate exchange of typing data. Seventy-two human and animal strains of Shiga-toxin-producing E. coli O157 were used for the development of the improved MLVA assay. The method is based on capillary separation of multiplexed PCR products of VNTR loci in the E. coli O157 genome labeled with multiple fluorescent dyes. The different alleles at each locus were then assigned to allele numbers, which were used for strain comparison.

Animals↗
PubMed1987

Homogenization of tandemly repeated nucleotide sequences by distance-dependent nucleotide sequence conversion.

Previous work revealed that recurrent mutations (= mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, decreases with the distance between repeats. To test this possibility, evolution of an array of 11 initially homogeneous repeats was computer simulated using three models, two assuming that the likelihood of heteroduplex formation decreases with increasing distance between the repeats and one assuming that it is constant. Patterns of mutation distribution obtained in computer simulations were compared with the distribution of mutations found in the repeated arrays in the NTS of seven rDNA clones. The patterns of mutations generated by the models assuming that the likelihood of heteroduplex formation decreases as distance between the repeats increases agreed with the patterns observed in rDNA; the patterns generated by the model assuming that the likelihood is independent of distance between repeats disagreed with the patterns observed in the rDNA clones. The topology of the heteroduplex formed between DNA in adjacent repeats predicts that the most frequently occurring conversions in the NTS repeated arrays will be shorter than the length of the repeat. The topology of the heteroduplex also predicts that if the heteroduplex leads to crossing over a circular repeat is excised. It is speculated that the circle can transpose or can be amplified via rolling circle replication and subsequently transpose. It is also shown that homogenization of the NTS repeated arrays proceeds at different rates in different species.

Animals↗
PubMed2003

New method for typing Staphylococcus aureus strains: multiple-locus variable-number tandem repeat analysis of polymorphism and genetic relationships of clinical isolates.

The PCR-based methodology applied to multiple-locus variable numbers of tandem repeat (VNTR) analysis was recently shown to be a useful technique for the molecular typing of clinical isolates of several bacterial species. We have adopted this method for the molecular typing of methicillin-resistant Staphylococcus aureus. Five staphylococcal VNTR loci (sdr, clfA, clfB, ssp, and spa) were subjected to analysis, and it was shown that the method allows typing of S. aureus strains with the discriminatory power and reproducibility of pulsed-field gel electrophoresis while at the same time being rapid and applicable to analysis of large numbers of isolates.

Bacterial Proteins↗
PubMed2003

Characterization of a tandem repeat polymorphism in Legionella pneumophila and its use for genotyping.

We have analyzed the variability of minisatellite sequences (also called variable-number tandem repeats [VNTRs]) in the genome of Legionella pneumophila. Based upon the genome sequence of the Philadelphia-1 strain (serogroup 1), 25 minisatellites were selected and their polymorphisms were analyzed by PCR with the DNA of serogroup 1 to 14 reference strains. For 22 markers, a PCR product of the expected size was found with the DNA of the Philadelphia-1 strain. Most of these markers did not amplify the DNA of other Legionella species or other bacteria used as controls. A polymorphism was observed for seven markers among the L. pneumophila strains tested. To check whether these markers could be used to compare strains of L. pneumophila, we analyzed two groups of isolates from clinical and environmental samples which had been independently genotyped by other methods. The results showed that, for the isolates in these two sets of samples, VNTR typing is as informative as pulsed-field gel electrophoresis for comparison of strains. Sequencing of one minisatellite from 14 reference strains was performed. Comparison of the sequences allowed a classification and confirmed the existence of subspecies of L. pneumophila. We also tested the usefulness of one very polymorphic marker as a tool for the rapid screening of colonies grown from water samples. This allowed the rapid identification of the L. pneumophila colonies and gave a first hint as to the presence of several strains in a single sample.

Amino Acid Sequence↗
PubMed2004

Genotype and allele frequency of the variable number tandem repeat polymorphism in the VNTR6-1st of the of human telomerase reverse transcriptase (hTERT) gene in Chinese population.

The variable number of tandem repeat (VNTR) polymorphism in the intron 6 of the human telomerase reverse transcriptase(hTERT) was investigated. Seven alleles of 18, 20, 21, 22, 23, 26 and 35 repeats of the 36 bp VNTR6-1st and 14 genotypes were identified among 210 unrelated healthy Chinese individuals (Han people) living in Beijing. The 20, 22 and 35 repeats were the most frequent alleles which accounted for 94.76% of the total alleles observed. The allele frequency of the Chinese population showed no difference with that of the Korea population living in Pusan except for allele of 35 repeats. But the 5' flanking region of VNTR6-1st polymorphic sequence of the Chinese population included a 53-bp insert compared with that of korea population except for some alleles of 22 repeats.

Alleles↗
PubMed2005

[Genetic polymorphism of D6S477, D9S1118, D18S865, D19S400, and D20S161 short tandem repeat loci in Qingdao Han population].

OBJECTIVE: To illuminate the preliminary genotype and allele frequency distribution of D6S477 and the other four short tandem repeat(STR) loci in Chinese Han population in Qingdao area and to probe the possibility of their genetic application. METHODS: Two hundred ACD-blood specimens were collected from the unrelated individuals in Qingdao. The DNA samples were extracted with Chelex method and were amplified by polymerase chain reaction technique. The PCR products were analyzed by polyacrylamide gel electrophoresis and displayed using silver staining. RESULTS: The authors obtained the allele frequency distribution and preliminary genotype of D6S477, D9S1118, D18S865, D19S400 and D20S161 STR loci. No deviation from Hardy-Weinberg equilibrium was observed in the five loci. CONCLUSION: All the five loci have higher chance of exclusion and discriminating power, and they will be useful markers for researches in genetics.

Asian People↗
PubMedDate not supplied

[Human genes, containing varying numbers of absolute tandem repeats in the coding area: the possible role in pathogenesis].

Some peculiarities of the transcription of human genes with variable number of absolute tandem repeats in the coding region are discussed. The data on the association between short alleles of the apo(a) gene and atherosclerosis are analyzed. Data are described concerning the possible role of the MUC1 gene product, episialin, in carcinogenesis. The possible causes of the polydispersity of apo(a) and mucin gene transcripts are analyzed. It is supposed that RNA polydispersity is the result of the transcription of the repeat. The possible association between repeat transcription and recombination is discussed. The same inverse relationship is noted between the allele length (number of repeats) and the transcription level of the full gene for apo(a) and MUC1 genes. The possible role of the length of VNTR genes as risk factors of human pathogenesis is discussed.

Apolipoproteins A↗
PubMed1994

High resolution fluorescence in situ hybridization to linearly extended DNA visually maps a tandem repeat associated with facioscapulohumeral muscular dystrophy immediately adjacent to the telomere of 4q.

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder. The FSHD locus has been linked to the most distal genetic markers on the long arm of chromosome 4. An EcoRI fragment length polymorphism segregates with the disease in most FSHD families. Within the EcoRI fragment lies a tandem array of 3.2 kb repeats. Deletions of integral copies of this repeat have been associated with the disease. The 3.2 kbp repeat has recently been shown to cross-hybridize to several regions of heterochromatin in the human genome and DNA sequence analysis reveals strong homology to a class of heterochromatin repeats, LSau. In this report, we demonstrate that the 3.2 kbp tandem repeat lies adjacent to a subtelomeric sequence, which is within 5-14 kb of the telomeric repeat (TTAGGG)n. Direct visual fluorescence hybridization to linearly extended strands of DNA enabled the visualization of this subtelomeric sequence as a short string of signals at the end of a longer string of signals from the differentially labeled 3.2 kbp tandem repeat. Furthermore, in support of our data showing that the 3.2 kbp repeat lies in close proximity to the telomere of 4q, we demonstrated the lack of hybridization of total human DNA to this same region. Our results indicate that the tandem array of 3.2 kbp repeats, disrupted in FSHD, lies immediately adjacent to the telomere of 4q and that the gene responsible for FSHD is likely located proximal to the tandem repeat.

Animals↗
PubMed1996

Validation of the Applied Biosystems Prism 377 automated sequencer for the forensic short tandem repeat analysis.

The Applied Biosystems (ABI) Prism 377 DNA sequencer has been evaluated in an attempt to increase the throughput of samples for short tandem repeat (STR) analysis, in both forensic casework and the UK National Criminal Intelligence DNA Database. The gel system assessed consisted of 0.2 mm, 4% acrylamide 6 M urea gels, with a well-to-read distance of 36 cm. Gels were run at a constant voltage of 3 kV and constant temperature of 51 degrees C. The run time of our second generation multiplex (SGM) STR system was achieved in less than 2 h. Rigorous validation has been performed on the instrument hardware and software. Complete resolution of 1 base differences was obtained, up to and beyond 350 bases; sizing precision across gels was more than 2-fold higher than the 373A and the sensitivity was increased by one third.

Autoanalysis↗
PubMed1997

Detection and quantitative characterization of artificial extra peaks following polymerase chain reaction amplification of 14 short tandem repeat systems used in forensic investigations.

Detection on automated DNA sequencers of polymerase chain reaction (PCR) products of tetra- and penta-nucleotide short tandem repeat (STR) loci frequently reveals one or more extra peaks along with the true, major allele peak. The most frequent extra peak pattern is a single smaller peak which is one repeat unit shorter than the true allele peak. The existence of such artificial peaks is of special importance when the methods are used for forensic investigations because the artificial extra peaks may simulate true alleles when samples containing mixtures of DNA from different individuals are analyzed. We have investigated the relative levels of formation of extra peaks in 14 STR marker systems. We found that not only the parameters of the PCR but also factors determining the stringency during the post-PCR and pre-electrophoresis handling of samples were of importance for the formation of extra peaks. In our hands, the amounts of extra peaks were reduced (i) if the samples were effectively denatured immediately before loading, (ii) if they contained substantial amounts of formamide (i.e. > or = 50%), and (iii) if the temperature of the electrophoresis gel was above a certain level (i.e. > or = 43 degrees C). The results suggest that extra peaks may in part be due to re-annealing of the PCR product under suboptimal conditions. When efforts had been made to reduce the post-PCR formation of extra peaks, the relative peak areas of the extra peaks ranged from 1% to 17% of those of the true alleles. Similar results were obtained when the PCR products were analyzed under native conditions. Low-copy genome analysis excluded that somatic heterogeneity of the STR regions caused the extra peaks. The systems HumVWA31A, HumFibra/FGA, and D21S11 were especially affected by low-stringency conditions, while Hum-TH01, HumCD4, and D12S391 were virtually unaffected by low-stringency conditions. Replacement of the Taq DNA polymerase with DNA polymerases with lower processivity resulted in higher levels of extra peaks. Our results support the hypothesis that extra peaks are produced due to slipped-strand mispairing.

DNA↗
PubMed1994

Involvement of transposition in dispersion of tandem repeat sequences (TrsA) in rice genomes.

We describe a method to identify and characterize DNA fragments containing the junction of AA genome-specific tandem repeat sequences (here called TrsA) with adjacent chromosomal sequences of rice by the polymerase chain reaction (PCR) using a pair of primers that hybridize with TrsAs and a flanking non-TrsA sequence. With this method, we obtained results suggesting that TrsA sequences present at two loci (here called trsA1 and trsA2) are flanked by direct repeats of chromosomal sequences of 172 bp and about 440 bp in length, respectively. These results support the idea that the TrsA sequences have been inserted into each locus by transposition, resulting in duplication of the chromosomal sequence used as target. We also describe a method to identify and characterize TrsA sequences repeated in only a few copies in the rice genome by PCR, using a pair of primers that hybridize with two different portions in the TrsA sequence, and demonstrate that TrsA sequences are present not only in rice strains with the AA genome, but also in those with non-AA genomes. The TrsA sequences were present at the trsA1 locus in all the rice strains examined, indicating that TrsA was inserted and amplified at the locus before the divergence of the various species of rice in the Oryza genus. TrsA sequences were present at the trsA2 locus, however, only in an O. sativa IR36 strain, indicating that TrsA was inserted and amplified at this locus during divergence of rice strains with the AA genome.

Base Sequence↗
PubMed1992

A polymorphism detected in a variable number of tandem repeats (VNTR) of the seminal vesicle secretion (SVS) IV gene in inbred rats.

The second intron of the rat SVS IV gene contains a tandem repeat region of 20-bp sequences. This region was amplified using the polymerase chain reaction to detect variations. Three alleles, characterized by amplified fragments of 750, 490, and 390 bp, respectively, were found in 24 strains examined. This variation segregated in F1 and backcross progeny in an autosomal codominant manner. We tentatively designated this locus Svs-4. Analysis of linkages between the Svs-4 locus and other loci revealed that it was closely linked to the Svp-1 (less than 2.9%) and the a (10.0 +/- 6.7%) loci, which belong to rat linkage group IV. The Svp-1 and Svs-4 loci, however, were differently distributed among the inbred rat strains.

Alleles↗
PubMed1996

Structural variation in the alleles of a short tandem repeat system at the human alpha fibrinogen locus.

This paper reports the sequences of 22 alleles identified at the HumFGA (human alpha fibrinogen) short tandem repeat locus in the British Caucasian and Afro-Caribbean populations. Alleles at the lower end of the observed size range were found to increase in size by 4-bp increments with the repeat unit following the pattern TC(TCTT)n. However, 5 alleles were identified that differed in size by 2 bp from the 4 bp increment as a result of the deletion of a TC dinucleotide, or the addition of a TT dinucleotide, immediately prior to the 1st repeat unit. Alleles at the upper end of the observed size range were found to have a more complex repeat unit structure and also exhibited duplication of both 5' and 3' flanking sequences. A nomenclature for the designation of HumFGA alleles is proposed on the basis of this sequence data.

Base Sequence↗
PubMed1989

Patterns of intra- and interarray sequence variation in alpha satellite from the human X chromosome: evidence for short-range homogenization of tandemly repeated DNA sequences.

A number of processes, such as sequence conversion, unequal crossingover, and molecular drive, have been postulated to explain the homogenization of tandemly repeated DNA families. To investigate the nature and extent of such processes in the alpha satellite family of centromeric DNA, we determined the nucleotide sequence of approximately 700 bp from each of 40 representative alpha satellite repeats from six sources of human X chromosomes, obtaining a total of approximately 28 kb of sequence data. Sequence divergence among the repeats examined was low, with an average pairwise difference of approximately 1%. Pairwise comparisons of all repeats indicate that the degree of similarity for those repeats in physical proximity (within approximately 15 kb) of each other is significantly greater than that for randomly located repeats, from either the same or different X chromosomes, suggesting that the mechanisms predicted to homogenize these arrays are effectively short-range in action. Analysis of individual patterns of sequence variation allows the assignment of haplotypes for five high-copy-number diagnostic positions and reveals distinct positions of equilibrium and disequilibrium within the repeat. These analyses address hypotheses about the origin of the observed patterns of variation throughout alpha satellite evolution.

Base Sequence↗
PubMed2004

Multiple-locus variable-number tandem-repeats analysis of Salmonella enterica subsp. enterica serovar Typhimurium using PCR multiplexing and multicolor capillary electrophoresis.

The multiple-locus variable-number tandem-repeats analysis (MLVA) method is currently being used as the primary typing tool for Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) isolates in our laboratory. Our published initial MLVA was performed using a single fluorescent dye and the different patterns were assigned from gel images. Here we present a new and significantly improved assay using multiple dye colors, enhanced PCR multiplexing and the introduction of two new loci for better adaptation to capillary electrophoresis with increased speed. The different MLVA patterns are now based on allele sizes entered as character values, thus removing the uncertainties introduced when analyzing band patterns from gel images. We additionally propose an easy numbering scheme for the identification of separate isolates that will facilitate exchange of typing data. A total of 106 human, bird, animal and food isolates of S. Typhimurium, including 16 with definite type (DT) 104, were used for the development of the improved MLVA. The method is based on capillary separation of multiplexed PCR products from five VNTR loci in the S. Typhimurium genome labeled with multiple fluorescent dyes. The different alleles at each locus were then assigned allele numbers, which were used for strain comparison.

Alleles↗