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 1,045 records · Page 58Linked to original sources
PubMed1990

Paternity testing: blood group systems and DNA analysis by variable number of tandem repeat markers.

Two recent paternity cases are reported. In the first case of paternity exclusion, deoxyribonucleic acid (DNA) restriction fragment length polymorphisms (RFLPs) on variable number of tandem repeat (VNTR) loci with multiple alleles were informative, as well as established systems of red blood antigens, red cell enzymes, serum proteins, and human leukocyte antigens. In the second case, in which both the alleged father and the first wife were deceased, the paternal genotype was determined by using genetic markers from the second wife and four children, which then were compared with the paternal alleles of the child in question, the plaintiff in this case. The high probability of paternity (0.999,998,7) made us conclude that the man probably was the actual father. The DNA analysis by VNTR probes appears to be quite valuable in the study of paternity cases.

Alleles↗
PubMed1992

In Euglena, spliced-leader RNA (SL-RNA) and 5S rRNA genes are tandemly repeated.

In Euglena gracilis, a 26 nucleotide leader sequence (spliced leader sequence = SL) is transferred by trans-splicing to the 5' end of a vast majority of cytoplasmic mRNAs (8). The SL originates from the 5' extremity of a family of closely related snRNAs (SL-RNAs) which are about 100 nucleotide long. In this paper we present the nucleotide sequences of two SL-RNA genes, confirming the sequences previously established by sequencing purified SL-RNAs. Although some SL-RNA genes are dispersed throughout the genome, we show that the majority of SL-RNA genes are located on 0.6 kb repeated units which also encode the cytoplasmic 5S rRNA. We estimate that the copy number of these repeated units is about 300 per haploid genome. The association of SL-RNA and 5S rRNA genes in tandemly repeated units is also found in nematodes but paradoxically does not exist in trypanosomes which are phylogenically much closer to Euglena. We also show that a high number of sequences analogous to the 26 nucleotide SL are dispersed throughout the genome and are not associated with SL-RNAs.

Animals↗
PubMed2000

Diversity in a variable-number tandem repeat from Yersinia pestis.

We have identified a tetranucleotide repeat sequence, (CAAA)(N), in the genome of Yersinia pestis, the causative agent of plague. This variable-number tandem repeat (VNTR) region has nine alleles and great diversity (calculated as 1 minus the sum of the squared allele frequencies) (diversity value, 0.82) within a set of 35 diverse Y. pestis strains. In contrast, the nucleotide sequence of the lcrV (low-calcium-response) gene differed only slightly among these strains, having a haplotype diversity value of 0.17. Replicated cultures, phenotypic variants of particular strains, and extensively cultured replicates within strains did not differ in VNTR allele type. Thus, while a high mutation rate must contribute to the great diversity of this locus, alleles appear stable under routine laboratory culture conditions. The classic three plague biovars did not have single identifying alleles, although there were allelic biases within biovar categories. The antiqua biovar was the most diverse, with four alleles observed in 5 strains, while the orientalis and mediaevalis biovars exhibited five alleles in 21 strains and three alleles in 8 strains, respectively. The CAAA VNTR is located immediately adjacent to the transcriptional promoters for flanking open reading frames and may affect their activity. This VNTR marker may provide a high-resolution tool for epidemiological analyses of plague.

Alleles↗
PubMed2001

A tandemly repeated DNA sequence is associated with both knob-like heterochromatin and a highly decondensed structure in the meiotic pachytene chromosomes of rice.

Highly repetitive tandem DNA sequence repeats are often associated with centromeric and telomeric regions of eukaryotic chromosomes. The rice tandem repeat Os48 is organized as long arrays of a 355 bp monomer and is mainly located in the telomeric regions. The chromosomal locations of the Os48 sequence were determined by fluorescence in situ hybridization (FISH) on rice pachytene chromosomes. The majority of the Os48 loci are associated with brightly 4',6-diamidino-2-phenylindole (DAPI)-stained and knob-like heterochromatin in rice pachytene chromosomes. As with other DNA sequences located in the heterochromatic regions, the cytosines of the CG and C(A/T)G sites within the Os48 repeat are heavily methylated. Surprisingly, a proportion of the FISH signals are highly decondensed and deviate significantly from the DAPI-stained periphery of the pachytene chromosomes. This highly decondensed chromatin structure has not been reported in pachytene chromosomes prepared from alcohol/acid-fixed meiotic samples in any other eukaryotic species. The condensation of the Os48 sequences is dynamic during prophase I of meiosis. The FISH signals derived from the Os48 repeat progress from a condensed configuration between leptonema and early pachynema into a decondensed structure from middle pachynema to diakinesis, and then return to a condensed form at metaphase I.

Base Sequence↗
PubMed1995

Rapid typing of variable number of tandem repeat locus in the human apolipoprotein B gene for DNA diagnosis of heart disease by polymerase chain reaction and capillary electrophoresis.

The apolipoprotein B (apoB) variable number of tandem repeat (VNTR) alleles containing larger repeat units is a risk factor for coronary heart disease. Capillary electrophoresis (CE) in entangled polymer solution was applied to the analysis of polymerase chain reaction (PCR) amplified apoB VNTR locus for DNA diagnosis of heart disease. The CE separation gives an excellent resolution of two alleles differing by one or two 16 bp repeat units in the DNA size range up to 600 bp with high speed. The apoB alleles differing in length by 2 or 4 repeat units are readily distinguishable by CE in the DNA size range from 600 to 1000 bp. The plate number achieved was 1 million plates per meter. CE combining with PCR provides an excellent technique for accurate determination of the number of repeat units of apoB VNTR alleles and differentiation of heterozygous from homozygous individuals. Using the CE technique, the apoB VNTR loci from some individuals in genotyping were examined towards precise DNA diagnosis for coronary heart disease.

Apolipoproteins B↗
PubMed1998

Site-specific insertion of a SINE-like element, Cp1, into centromeric tandem repeats from Chironomus pallidivittatus.

A SINE-like dispersed element, Cp1, from the dipteran Chironomus pallidivittatus was found to show site-specific insertion into two different centromeric tandem repeats. The insertions result in identical target site duplications of nine base-pairs. In contrast, extracentromeric Cp1 elements, which are polymorphic and degenerate, are previously known to be surrounded by different target site duplications. The intracentromeric Cp1 is uniform in structure and contains a single pol III unit, upstream of which 87 bp arms of a palindrome surround a 103 bp unique sequence. The numbers of Cp1 elements per centromere were determined in microdissected material and were found to be in the range of five to ten units per centromere. The well-defined insertion properties, correlated to chromosomal localization, suggest that Cp1 is likely to be a component of importance for the centromere. Similarities of Cp1 and its parts to functionally identified centromeres in Saccharomyces cerevisiae and Schizosaccharomyces pombe are discussed.

Animals↗
PubMed1986

The telomeres of the linear mitochondrial DNA of Tetrahymena thermophila consist of 53 bp tandem repeats.

We have cloned and sequenced the telomeric DNA of the linear mitochondrial DNA (mtDNA) of T. thermophila BVII. The mtDNA telomeres consist of a 53 bp sequence tandemly repeated from 4 to 30 times, with most molecules having 15 +/- 4 repetitions. The previously recognized terminal heterogeneity of the mtDNA is completely accounted for by the variability in the number of repeats. The 53 bp repeat does not resemble known telomeric DNA in sequence, repeat size, or number of repetitions. The termini occur at heterogeneous positions within the 53 bp repeat. The junction of the telomeric repeat with the internal DNA is at a different position within the telomeric repeat on each end of the mtDNA. We propose a model for the maintenance of the mtDNA ends involving unequal homologous recombination.

Animals↗
PubMed2001

The variable number of tandem repeats polymorphism of the dopamine transporter gene is not associated with significant change in dopamine transporter phenotype in humans.

A 40 base polymorphism of a variable number of tandem repeats (VNTR) has been described in the 3' untranslated region of the gene (SLC6A3) coding for the dopamine transporter (DAT). Despite being located in the untranslated region of the gene, this polymorphism has been associated with clinical phenotypes associated with dysregulation of dopamine transmission, such as attention deficit hyperactivity disorder and cocaine-induced paranoia. To examine the neurochemical phenotype associated with this polymorphism, we compared amphetamine-induced dopamine release (measured as displacement of the radiotracer [123I]IBZM) and DAT expression (measured with [123I]beta-CIT) in the striatum with Single Photon Computerized Emission Tomography (SPECT). Our sample included 59 subjects, 31 healthy controls and 29 patients with schizophrenia. No significant association was found between VNTR polymorphism and amphetamine-induced dopamine release or DAT density in the total sample, nor when each diagnostic group was considered separately. Thus, we did not replicate the findings of two previous studies, which had suggested that the 9 repeat allele was associated with either an increased or decreased DAT expression, albeit in different patient populations.

Adult↗
PubMedDate not supplied

Identification and chemical synthesis of a tandemly repeated immunogenic region of Plasmodium knowlesi circumsporozoite protein.

Complementary DNA clones that code for the immunogenic region of the Plasmodium knowlesi circumsporozoite protein were shown to contain a tandemly repeating 36-base pair unit. A synthetic dodecapeptide corresponding to the predicted reading frame of the repeating nucleotide unit behaved, in an immunoradiometric assay, identically with the native P. knowlesi circumsporozoite protein. The repeating 36-base pair unit occurred 12 times within the gene and accounts for at least one-third of the amino acid sequence of the surface antigen protein.

Amino Acid Sequence↗
PubMed1997

Characterization of short tandem repeats from thirty-one human telomeres.

Completion of genetic and physical maps requires markers from the ends (telomeres) of every human chromosome. We have searched for short tandem repeats (microsatellites) in cosmid and P1 clones and generated 661 sequence-tagged sites (STS) from the terminal 300 kb of 31 human chromosome ends. PCR assays were successfully designed for 58 microsatellites and mapped both genetically and on radiation hybrids (RHs) to confirm their telomeric location. Sequence analysis revealed marked variation in sequence composition, consistent with the hypothesis that even very highly GC-rich chromosome bands (the T bands) are not homogenous. The STSs that we have generated will be a necessary resource for the construction of physical maps of these complex regions of the genome.

Base Sequence↗
PubMed2005

Highly diverse variable number tandem repeat loci in the E. coli O157:H7 and O55:H7 genomes for high-resolution molecular typing.

AIM: Evaluation of the Escherichia coli genome for variable number tandem repeat (VNTR) loci in order to provide a subtyping tool with greater discrimination and more efficient capacity. METHODS AND RESULTS: Twenty-nine putative VNTR loci were identified from the E. coli genomic sequence. Their variability was validated by characterizing the number of repeats at each locus in a set of 56 E. coli O157:H7/HN and O55:H7 isolates. An optimized multiplex assay system was developed to facility high capacity analysis. Locus diversity values ranged from 0.23 to 0.95 while the number of alleles ranged from two to 29. This multiple-locus VNTR analysis (MLVA) data was used to describe genetic relationships among these isolates and was compared with PFGE (pulse field gel electrophoresis) data from a subset of the same strains. Genetic similarity values were highly correlated between the two approaches, through MLVA was capable of discrimination amongst closely related isolates when PFGE similar values were equal to 1.0. CONCLUSIONS: Highly variable VNTR loci exist in the E. coli O157:H7 genome and are excellent estimators of genetic relationships, in particular for closely related isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: Escherichia coli O157:H7 MLVA offers a complimentary analysis to the more traditional PFGE approach. Application of MLVA to an outbreak cluster could generate superior molecular epidemiology and result in a more effective public health response.

Alleles↗
PubMed2006

Assessment of an optimized mycobacterial interspersed repetitive- unit-variable-number tandem-repeat typing system combined with spoligotyping for population-based molecular epidemiology studies of tuberculosis.

An optimized set of 24 mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) loci, including a discriminatory subset of 15 loci, has recently been defined for the typing of Mycobacterium tuberculosis. Here, we evaluated the performances of this MIRU-VNTR typing system in combination with spoligotyping for the detection of transmission chains in a population-based study comprising 91% of culture-confirmed tuberculosis patients reported in 2003 in Hamburg, Germany. Of the 154 isolates investigated, more than 90% had high IS6110 copy numbers (>/=6). IS6110 restriction fragment length polymorphism (RFLP) typing resulted in 13 clusters, 5 of which had a confirmed epidemiological link. All five, as well as six of the eight IS6110 clusters with no identified epidemiological link, were perfectly matched by MIRU-VNTR typing with the 24 loci. Two IS6110 clusters were split by differences into 6 to 12 MIRU-VNTR loci, clearly supporting the absence of a link, as judged by contact tracing data. In contrast, only one MIRU-VNTR cluster, grouping what were probably epidemiologically unlinked isolates, was split by IS6110 RFLP. However, these isolates were also distinguished by spoligotyping. Both the optimized 24-locus and 15-locus sets thus showed a comparable to slightly better predictive value, especially when combined with spoligotyping, than the current gold standard IS6110 RFLP for the study of tuberculosis transmission in Hamburg. Because the epidemiological characteristics of this setting are similar to those of many developed countries, these results support the wide applicability of this real-time genotyping approach for population-based studies of M. tuberculosis transmission.

Bacterial Typing Techniques↗
PubMed2005

Comparison of multiple-locus variable-number tandem-repeat analysis with pulsed-field gel electrophoresis, spa typing, and multilocus sequence typing for clonal characterization of Staphylococcus aureus isolates.

Multiple-locus variable-number tandem-repeat analysis (MLVA), a new PCR-based method of typing Staphylococcus aureus, was compared to pulsed-field gel electrophoresis (PFGE), spa typing, and multilocus sequence typing (MLST) on a group of 59 S. aureus (mostly methicillin-resistant) clinical isolates. The aim of the study was to establish possible criteria of clustering MLVA patterns and to check concordance levels between the results produced by MLVA and the three other typing methods. As in our earlier study, MLVA turned out to have discriminatory power similar to that of PFGE. Comparison of data obtained by the two approaches allowed us to propose a 70% or ca. 80% cutoff value of the similarity between two MLVA patterns, depending on a cutoff level applied to interpret the PFGE results, 75% or ca. 90%, respectively. The cutoff values corresponded to the difference of up to six or four bands, respectively, among maximum 14 bands in total produced by two isolates in the analysis. The MLVA clusters matched well those obtained by PFGE, and they were also consistent in general with clusters generated by spa typing and MLST, these latter methods characterized lower resolution. Our results suggest that MLVA may be reliable in shorter-term S. aureus epidemiological studies, including analyses of outbreaks and hospital-to-hospital strain transmission events. Well-known advantages of typing methods based on PCR (low cost, short time, and easiness of performance) make MLVA a method that may be useful in a variety of laboratories, including those performing routine microbiological analyses within medical centers.

Anti-Bacterial Agents↗
PubMed1997

Multiplex DNA typing of short-tandem-repeat loci on the Y chromosome.

To facilitate evolutionary and forensic studies of DNA polymorphisms on the Y chromosome, we devised a multiplex amplification procedure for short-tandem-repeat (STR) loci. Four tetranucleotide STR loci (DYS19, DYS390, DYS391, and DYS393) were simultaneously amplified with FAM-labeled primers and genotypes were determined with an automated DNA sequencer. We typed 162 males from three U.S. populations (African-Americans, European-Americans and Hispanics) and found that the haplotype diversities range from 0.920 to 0.969. This quadruplex system provides a facile means of genotyping these Y chromosome STRs, and should be useful in population genetic and forensic applications.

Adult↗
PubMed2006

[Polymorphisms of seven short tandem repeat loci: D1S2142, D1S3733, D2S1774, D3S2459, D21S1409, D21S1437 and D21S2055 of Chinese Han population in Chengdu].

OBJECTIVE: To obtain the data in polymorphism distribution of the seven short tandem repeat (STR) loci: D1S2142, D1S3733, D2S1774, D3S2459, D21S1409, D21S1437 and D21S2055 of Chinese Han population in Chengdu, and evaluate the polymorphism data usefulness to the forensic science. METHODS: PCR, polyacrylamide gel electrophoresis (PAGE) and silver staining techniques were used to analyze the DNA samples from unrelated individuals of Chinese Han ethnic group in Chengdu. RESULTS: Eleven alleles and twenty-three genotypes were observed in D1S2142. Eight alleles and nineteen genotypes were observed in D1S3733. Eight alleles and fifteen genotypes were observed in D2S1774. Seven alleles and nineteen genotypes were observed in D3S2459. Six alleles and twelve genotypes were observed in D21S1409. Nine alleles and twenty-six genotypes were observed in D21S1437. Twenty alleles and seventy-seven genotypes were observed in D21S2055. The genotype distributions of the seven STR loci showed no deviation from the Hardy-Weinberg equilibrium. The parentage testing of 50 cases revealed an autosomal codominant inheritances and no mutations happened to seven STR loci. CONCLUSION: These data indicate that D1S2142, D1S3733, D2S1774, D3S2459, D21S1409, D21S1437 and D21S2055 have good polymorphism, with high probability of exclusion and probability of discrimination power as well as being loci available as the candidate genetic markers to forensic parentage testing and personal identification.

Alleles↗
PubMedDate not supplied

[The polymorphism of the tandem repeats in the dystrophin gene in the Ukrainian population].

The genetic heterogeneity of populations of different regions of Ukraine was studied using four polymorphic LNA sequences (GTAA-tandem repeats from the 3'-untranslated region of the dystrophin gene, the polymorphic systems pERT87-15--BamHI, pERT8718--TaqI, and pERT87-15--XmnI of the pERT locus of human chromosome X). We analyzed 500 DNA samples of healthy donors from the Kiev, Lvov, Poltava, and Lugansk regions. The above-mentioned polymorphic DNA sequences were used as markers to determine genetic distances between the regional populations of Ukraine. The data obtained indicate the existence of significant genetic differences among the regional populations of Ukraine. DNA polymorphism in the pERT87-8--TaqI system contributes the most significantly to these differences.

Alleles↗
PubMed2001

Mitochondrial inheritance in Schistosoma mansoni: mitochondrial variable number tandem repeat mutation produces noise on top of the signal.

The Schistosoma mansoni mitochondrial genome contains tandemly arrayed copies of a 62-base repeat motif. The tandem array is highly polymorphic with respect to number of repeats and commonly exhibits heteroplasmy. This study shows that a very high rate of mutation rapidly produces new repeat lengths (new haplotypes) for this mitochondrial variable number tandem repeat. A maternal inheritance pattern is also demonstrated for this repeat sequence, while the high mutation rate causes some offspring to exhibit nonmaternal haplotypes. Frequent generation of new haplotypes can be observed within samples of clonal cohorts taken from monomiracidial snail infections. These same clonal cercarial groups, when crossed, produce F1 generations that exhibit the maternal set of haplotypes, across all individuals, with the frequent addition of new mutant haplotypes. In each of 2 crosses, a subset of the recently arisen haplotypes match paternal haplotypes by chance (30.4% and 18.8%), thus giving the false appearance of partial paternal inheritance of mitochondria.

Animals↗
PubMed2000

Infrared fluorescent automated detection of thirteen short tandem repeat polymorphisms and one gender-determining system of the CODIS core system.

We used an infrared (IR) automated fluorescence monolaser sequencer for the analysis of 13 autosomal short tandem repeat (STR) systems (TPOX, D3S1358, FGA, CSF1PO, D5S818, D7S820, D8S1179, TH01, vWA, D13S317, D16S359, D18S51, D21S11) and the X-Y homologous gene amelogenin system. These two systems represent the core of the combined DNA index systems (CODIS). Four independent multiplex reactions, based on the polymerase chain reaction (PCR) technique and on the direct labeling of the forward primer of every primer pair, with a new molecule (IRDye800), were set up, permitting the exact characterization of the alleles by comparison with ladders of specific sequenced alleles. This is the first report of the whole analysis of the STRs of the CODIS core using an IR automated DNA sequencer. The protocol was used to solve paternity/maternity tests and for population studies. The electrophoretic system also proved useful for the correct typing of those loci differing in size by only 2 bp. A sensibility study demonstrated that the test can detect an average of 10 pg of undegraded human DNA. We also performed a preliminary study analyzing some forensic samples and mixed stains, which suggested the usefulness of using this analytical system for human identification as well as for forensic purposes.

Automation↗