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 649 records · Page 36Linked to original sources
PubMed1993

Genetic and physical map of 11 short tandem repeat polymorphisms on human chromosome 6.

A linkage map of 11 short tandem repeat polymorphisms was constructed for human chromosome 6. The order from p to qter was F13A1-D6S105-D6S254-D6S251-D6S252-D6S24 9-(ARG1-D6S87)-D6S250-D6S255-D6S253. For the region spanned by the 6q markers, the male map distance was less than half the female map distance (58 and 126.3 cM, respectively). Two-point linkage analysis was also used to position the markers relative to markers in the CEPH public database. Physical mapping of these markers was completed using a somatic cell hybrid panel that contained varying segments of chromosome 6. Two of the markers mapped to the short arm of chromosome 6; the remainder were spaced over 86.5 cM of the long arm from 6q13 to 6qter. The linkage and physical maps were completely consistent.

Base Sequence↗
PubMed1996

Molecular characterization of two species-specific tandemly repeated DNAs from entomopathogenic nematodes Steinernema and Heterorhabditis (Nematoda:Rhabditida).

Two AluI tandemly repeated DNAs were cloned from two entomopathogenic nematodes: the first one from Steinernema glaseri and the second one from Heterorhabditis bacteriophora. The monomeric units of these two satellite DNAs have a repeat length of 174 and 168 bp, respectively. These AluI repeated element families appear to constitute 5.5% of the S. glaseri genome and 5% of the H. bacteriophora genome. Their A + T contents were estimated at 55% and 57%. Moreover, the monomers of these two families are quite homogeneous in sequence, showing, on average, 3.9% and 2.7% divergence from their respective consensus sequence. These results suggest that some mechanism is acting to maintain the homogeneity of these repeated DNAs despite their abundance. We have also shown that these two DNA families are species-specific and therefore could be used for the identification of Steinernema and Heterorhabditis entomopathogenic nematode species.

Animals↗
PubMed2004

Utility of fast mycobacterial interspersed repetitive unit-variable number tandem repeat genotyping in clinical mycobacteriological analysis.

BACKGROUND: Analysis of variable numbers of tandem repeats (VNTR) of genetic elements called mycobacterial interspersed repetitive units (MIRUs) is a recently described, polymerase chain reaction (PCR)-based method used to genotype Mycobacterium tuberculosis. It is much faster, requires a smaller amount of DNA, and has approximately the same discriminatory power as the standard IS6110 restriction fragment-length polymorphism (RFLP) method. We report the adaptation and optimization of MIRU-VNTR genotyping on a capillary electrophoresis system. We describe its application to 3 typical clinical situations encountered in our laboratory (Institut Pasteur de Bruxelles, Laboratoire Tuberculose et Mycobacteries; Brussels, Belgium). METHODS: MIRU-VNTR genotyping was performed on heat-inactivated M. tuberculosis cultures obtained from clinical specimens on Lowenstein solid medium or in mycobacteria growth indicator liquid tubes (Becton Dickinson). After amplification of 12 genomic loci using 4 different multiplex PCRs, DNA fragments were separated by capillary electrophoresis using the ABI Prism 3100-Avant Genetic Analyzer (Applied Biosystems). Sizing of the PCR fragments and assignment of the various MIRU-VNTR alleles were done using the GeneScan and customized Genotyper software packages (PE Applied Biosystem). RESULTS: Clustering on the basis of IS6110 fingerprinting of isolates from 3 different patients attending the same hospital was confirmed by MIRU-VNTR typing. This concordance between 2 independent, highly discriminatory techniques was decisive in triggering an epidemiological inquiry that led to identification of a bronchoscopy-related tuberculosis nosocomial infection. A mixed tuberculosis infection in a patient whose infection was initially suspected as a result of the IS6110 RFLP method was clearly identified by MIRU-VNTR typing. Finally, automated MIRU-VNTR analysis permitted the identification of laboratory contamination in 6 liquid cultures of M. tuberculosis within several hours. CONCLUSION: These examples illustrate the utility of this genotyping technique for quick and accurate resolution of problems commonly encountered in clinical mycobacteriology.

DNA Fingerprinting↗
PubMed1994

Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystrophy.

The sequence of the tandem repeat sequence (D4Z4) associated with facioscapulohumeral muscular dystrophy (FSHD) has been determined: each copy of the 3.3 kb repeat contains two homeoboxes and two previously described repetitive sequences, LSau and a GC-rich low copy repeat designated hhspm3. By Southern blotting, FISH and isolation of cDNA and genomic clones we show that there are repeat sequences similar to D4Z4 at other locations in the human genome. Southern blot analysis of primate genomic DNA indicates that the copy number of D4Z4-like repeats has increased markedly within the last 25 million years. Two cDNA clones were isolated and found to contain stop codons and frameshifts within the homeodomains. An STS was produced to the cDNAs and analysis of a somatic cell hybrid panel suggests they map to chromosome 14. No cDNA clones mapping to the chromosome 4q35 D4Z4 repeats have been identified, although the possibility that they encode a protein cannot be ruled out. Although D4Z4 may not encode a protein, there is an association between deletions within this locus and FSHD. The D4Z4 repeats contain LSau repeats and are adjacent to 68 bp Sau3A repeats. Both of these sequences are associated with heterochromatic regions of DNA, regions known to be involved in the phenomenon of position effect variegation. We postulate that deletion of D4Z4 sequences could produce a position effect.

Amino Acid Sequence↗
PubMed2003

Molecular typing of Salmonella enterica serovar typhi isolates from various countries in Asia by a multiplex PCR assay on variable-number tandem repeats.

A multiplex PCR method incorporating primers flanking three variable-number tandem repeat (VNTR) loci (arbitrarily labeled TR1, TR2, and TR3) in the CT18 strain of Salmonella enterica serovar Typhi has been developed for molecular typing of S. enterica serovar Typhi clinical isolates from several Asian countries, including Singapore, Indonesia, India, Bangladesh, Malaysia, and Nepal. We have demonstrated that the multiplex PCR could be performed on crude cell lysates and that the VNTR banding profiles produced could be easily analyzed by visual inspection after conventional agarose gel electrophoresis. The assay was highly discriminative in identifying 49 distinct VNTR profiles among 59 individual isolates. A high level of VNTR profile heterogeneity was observed in isolates from within the same country and among countries. These VNTR profiles remained stable after the strains were passaged extensively under routine laboratory culture conditions. In contrast to the S. enterica serovar Typhi isolates, an absence of TR3 amplicons and a lack of length polymorphisms in TR1 and TR2 amplicons were observed for other S. enterica serovars, such as Salmonella enterica serovar Typhimurium, Salmonella enterica serovar Enteritidis, and Salmonella enterica serovar Paratyphi A, B, and C. DNA sequencing of the amplified VNTR regions substantiated these results, suggesting the high stability of the multiplex PCR assay. The multiplex-PCR-based VNTR profiling developed in this study provides a simple, rapid, reproducible, and high-resolution molecular tool for the epidemiological analysis of S. enterica serovar Typhi strains.

Alleles↗
PubMed1996

General approach to analysis of polymorphic short tandem repeat loci.

Polymerase chain reaction amplification products of 22 known polymorphic short tandem repeat (STR) loci were subjected to denaturing polyacrylamide gel electrophoresis and detected using a silver staining method. Loci that amplified efficiently and revealed the fewest amplification-related artifacts with this detection method were selected for development of allelic ladders. The combination of allelic ladders and silver stain detection provides an inexpensive and general non-isotopic analytical method for DNA identification. This approach has immediate application in forensic analysis, paternity determination, human cell line identification and monitoring of bone marrow transplants. It can also be adapted to more general applications of genetic analysis in human and other species including detection of genetic disorders and cancers.

Black or African American↗
PubMed1998

[Application of capillary non-gel sieving electrophoresis to the analysis of short tandem repeat in phenylalanine hydroxylase gene and gene diagnosis of phenylketonuria].

OBJECTIVE: To establish a sensitive, accurate and reliable method for analysis of short tandem repeat (STR) markers for gene diagnosis, capillary electrophoresis (CE) was used for analysis of a polymorphic tetranucleotide (TCTA)n in intron 3 of the phenylalanine hydroxylase (PAH) gene. METHODS: Capillary non-gel sieving electrophoresis (CNGSE) system was used to analyze PCR products of PAH STR among 61 normal Chinese individuals and 6 phenylketonuria (PKU) families. RESULTS: The PCR fragments that differ 4 bp from each other were well separated by CNGSE. Ten alleles were identified, with a continuous distribution from 224 bp to 260 bp. The largest allele (260 bp) was first detected in Chinese population. The alleles frequencies were calculated and PIC is 0.738. The genotypes of PAH STR of total 80 Chinese people were also analyzed and the heterozygosity is 75%. We used this procedure to PAH gene linkage analysis in 6 PKU families, in which pathogenic gene could be affirmed in 3 families, including one case of prenatal diagnosis. CONCLUSIONS: In comparison with denaturing polyacrylamide gel electrophoresis, CE is an accurate, rapid, automatic and with high resolution analytical tool. CE in combination with PCR is a hopeful technique and might be widely used for gene diagnosis of genetic diseases in the future.

Alleles↗
PubMed2005

Genetic variation at nine short tandem repeat loci among islanders of the eastern Adriatic coast of Croatia.

We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820) among six populations from Croatia: five distributed in the islands of the eastern Adriatic coast and one from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies; however, the absolute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, namely, heterozygosity, number of alleles, and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast to the two measures of genetic variation, allele size variance and within-locus heterozygosity, the imbalance index (beta) indicates evidence of recent expansion of population sizes in all islands and in the mainland. High mutation rates of the studied loci together with local drift effects are likely explanations for interisland genetic variation and the observed lack of reduced genetic diversity among the island populations.

Alleles↗
PubMed1992

Size polymorphisms due to changes in the number of O-glycosylated tandem repeats in the Dictyostelium discoideum glycoprotein PsA.

The molecular weight polymorphism in the Dictyostelium discoideum cell surface glycoprotein PsA is due to incremental copies of an O-glycosylated tandem tetrapeptide repeat. Allelic variation at the pspA locus results in a PsA glycoprotein with three, four or five tandem copies of Pro-Thr-Val-Thr. The simplest explanation for the origin of this polymorphism is an unequal crossing over event in the ancestral gene containing four copies. Each Thr in the tandem repeat is substituted with carbohydrate, which is completely absent from PsA in strains carrying a glycosylation defective modB mutation. Glycosylated tandem repeats appear to be a common feature of cell surface glycoproteins which are characterized by short domains rich in Pro and Thr or Ser. It is probable that the glycosylated repeat domain acts as a "spacer" peptide that projects the globular domain above the glycocalyx.

Amino Acid Sequence↗
PubMed2006

[Genetic polymorphism of six short tandem repeat loci on the X chromosome in a Han race population in China].

OBJECTIVE: To investigate the alleles and genotype frequencies of 6 short tandem repeat (STR) loci DXS7130, DXS1214, DXS6799, DXS6804, DXS7424 and DXS7133 on the X chromosome in Chinese Han individuals living in Shaanxi province of Northwest China. METHODS: The 6 X-chromosomal STR loci were typed by PCR, denatured polyacylamide gel electrophoresis and silver stain. RESULTS: Among females from Xi'an Han population, the numbers of alleles in the 5 loci (DXS7130, DXS6799, DXS6804, DXS7424 and DXS7133) were detected to be 9, 6, 6, 7, and 7 respectively; the numbers of genotypes were 21, 14, 15, 17 and 12 respectively; and the number of alleles in the DXS1214 was 8. Exact tests demonstrated that genotype frequencies of females had no departure from Hardy-Weinberg equilibrium. CONCLUSION: The six loci of X-chromosomal STRs are appropriate for individual identification, paternity test involving in female child and for study in related disease.

Asian People↗
PubMed2006

Genetics and genomics of core short tandem repeat loci used in human identity testing.

Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

Alleles↗
PubMedDate not supplied

[Tetranucleotide tandem repeat polymorphism of the CFTR gene intron 6B in populations of the Volga-Ural region].

The allele and genotype frequencies of the tetranucleotide tandem repeat (TTR) of CFTR intron 6B were analyzed in eight ethnic populations of the Volga-Ural region, including Bashkir, Tatar, Chuvash, Mari, Mordvinian, Udmurt, Komi-Permyak, and Russian. The most common TTR allele 7 varied in frequency from 0.636 in Chuvash to 0.805 in Mordvinians. The frequency of the second common allele 7 ranged from 0.188 in Mordvinians to 0.333 in Chuvash. Allele 8 was found in about 8% of Udmurts and Mari; occurred in a few Bashkirs, Tatars, Mordvinians, and Komi-Permyaks; and was not observed in Russians. The genetic diversity coefficient was minimal in Mordvinians (0.496) and in Tatars (0.505), indicating their low heterogeneity in TTR. The observed heterozygosity was maximal in Udmurts (0.532) and Komi-Permyaks (0.560) and minimal in Mordvinians (0.297). In total, the populations proved to be heterogeneous in TTR allele frequency distribution, the interpopulation difference being significant in most cases.

Bashkiria↗
PubMedDate not supplied

Tandem repeats in complete bacterial genome sequences: sequence and structural analyses for comparative studies.

A series of complete bacterial genome sequences have recently become available and powerful methods have been developed for the identification of tandem repeats on a very large scale. It is thus possible to derive extensive comparative descriptions of such repeats at the level of complete genomes, as illustrated here for three different bacterial genomes: Escherichia coli, Haemophilus influenzae, and Mycobacterium tuberculosis. Such sequence analyses can be usefully complemented by structural characterisations of the repeats.

Bacteria↗
PubMed2002

The tandem repeated irritation test: a new method to assess prevention of irritant combination damage to the skin.

The effect of a protective cream was tested in a new tandem repeated irritation test with tandem application of 0.5% sodium lauryl sulphate (SLS) and undiluted toluene. The irritants were applied twice daily for 30 min to the ventral forearms of 20 volunteers. Irritant cutaneous reactions were quantified by a visual score, transepidermal water loss, chromametry and skin capacitance. Concurrent application of SLS/toluene induced stronger reactions than those caused by twice daily application of each irritant on its own. A protective effect of the protective cream was obtained against all treatment combinations and was significant for SLS/SLS (p < or = 0.01) and SLS/ toluene (p < or = 0.05). Our results indicate that the tandem repetitive irritation test has great potential in the evaluation of skin care products to prevent irritant contact dermatitis.

Adolescent↗
PubMed2001

5S ribosomal and U1 small nuclear RNA genes: a new linkage type in the genome of a crustacean that has three different tandemly repeated units containing 5S ribosomal DNA sequences.

We investigated the 5S ribosomal RNA (rRNA) genes of the isopod crustacean Asellus aquaticus. Using PCR amplification, three different tandemly repeated units containing 5S rDNA were identified. Two of the three sequences were cloned and sequenced. One of them was 1842 bp and presented a 5S rRNA gene and a U1 small nuclear RNA (snRNA) gene. This type of linkage had never been observed before. The other repeat consisted of 477 bp and contained only an incomplete 5S rRNA gene lacking the first eight nucleotides and a spacer sequence. The third sequence was 6553 bp long and contained a 5S rRNA gene and the four core histone genes. The PCR products were used as probes in fluorescent in situ hybridization (FISH) experiments to locate them on chromosomes of A. aquaticus. The possible evolutionary origin of the three repeated units is discussed.

Animals↗
PubMed2004

Single-nucleotide polymorphisms in the rRNA operon and variable numbers of tandem repeats in the lipoprotein gene among Mycoplasma genitalium strains from clinical specimens.

We characterized the single-nucleotide polymorphisms in the rRNA operon and variable numbers of tandem repeats in the lipoprotein gene MG309 among Mycoplasma genitalium strains from clinical specimens by PCR and sequencing. Analysis of 31 M. genitalium-infected patient specimens and 7 American Type Culture Collection strains identified six types of rRNA sequences and 11 different numbers of MG309 repeats. Examination of sequential specimens from 10 patients showed that these genotypes were stable for at least 5 weeks. These data suggest the potential usefulness of the rRNA genotypes and the MG309 repeats for genotyping of M. genitalium.

Base Sequence↗
PubMed2004

Design of a multiplex PCR for genotyping 16 short tandem repeats in degraded DNA samples.

The molecular genotyping of individuals and reconstruction of kinship through short and high polymorphic DNA markers, so-called short tandem repeats (STR), has become an important and efficient method in anthropology and forensic science. The here introduced experimental design describes a multiplex PCR capable of simultaneously amplifying 16 STRs and the sex determinant locus amelogenin in a short fragment lengths range from 84 bp to 275 bp. Thus, the design depends predominantly on the routines for DNA typing of historical samples with highly degraded ancient DNA. It is shown, that the newly designed multiplex PCR is suitable for successful typing of both forensic and historical material.

Alleles↗