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PubMed1996

The molecular organisation of a B chromosome tandem repeat sequence from Brachycome dichromosomatica.

A high copy, tandemly repeated, sequence (Bd49) specific to the B chromosome and located near the centromere in Brachycome dichromosomatica was used to identify lambda genomic clones from DNA of a 3B plant. Only one clone of those analysed was composed entirely of a tandem array of the B-specific repeat unit. In other clones, the Bd49 repeats were linked to, or interspersed with, sequences that are repetitious and distributed elsewhere on the A and B chromosomes. One such repetitious flanking sequence has similarity to retrotransposon sequences and a second is similar to chloroplast DNA sequences. Of the four separate junctions analysed of Bd49-like sequence with flanking sequence, three were associated with the same A/T-rich region in Bd49 and the fourth was close to a 25 bp imperfect dyadic sequence. No novel B-specific sequences were detected within the genomic clones.

Base Sequence↗
PubMed2000

Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis.

Three VNTR loci were previously cloned from Mycobacterium tuberculosis in our laboratory. The VNTR sequences were used as queries to search for similar sequences in the GenBank database by the BLAST program. Direct and tandem repeats were identified visually. The search revealed 45 more loci of direct and tandem repeats. Comparison of the sequences to the ones in the genome sequence database of the M. tuberculosis CDC1551 strain revealed 22 different loci. Combining these results with previously reported experimental work, at least 24 loci should be polymorphic enough to be detected by simple PCR. The repeats are present both inside coding sequences and in intergenic regions on the 5' or 3' ends of genes. M. tuberculosis contains several VNTR. Studies of their functions may be useful for understanding the differences of phenotypes between strains.

Electrophoresis↗
PubMed2002

Population study of six short tandem repeat loci in Antalya, Turkey.

Population studies of six short tandem repeat loci were carried out in a sample of unrelated Turkish individuals living in Antalya province, southwest Turkey. After electrophoresis in polyacrylamide gels, 8 alleles could be identified for THO1, 6 for TPOX and CSF1PO, 9 for VWA, 7 for FES, and 14 for F13A01. There was a significant deviation from the Hardy-Weinberg equilibrium between observed and expected values for FES and TPOX loci.

Alleles↗
PubMed1999

Association between monoamine oxidase A activity in human male skin fibroblasts and genotype of the MAOA promoter-associated variable number tandem repeat.

Among fifteen male skin fibroblast cultures from eleven donors ranging in age from less than 1 year to 90 years old, the specific activity of monoamine oxidase A (MAO-A) differed 515-fold. Each culture had one of the two most common alleles (three or four 30-bp repeats) at the variable number tandem repeat locus positioned 1.2 kb upstream from MAOA exon 1 (uVNTR). The mean MAO-A activity in cultures with three uVNTR repeats was significantly lower than that in cultures with four repeats (1.6 +/- 1.1 and 13 +/- 12 nmol/h per milligram, respectively; P=0.032). MAO-A expression was confined to a cell sub-population varying from 0.5% to 90% of cells in different cultures. The mean specific activity in MAO-A+ cells (whole culture specific activity divided by the proportion of immunopositive cells) was lower for cultures with three repeats than for those with four (7.2 +/- 3.1 and 23.9 +/- 9.5 nmol/h per milligram protein, respectively; P=0.0013), with no overlap in activity between genotypes. Finding lower MAO-A activity in cultures with three uVNTR repeats compared to those with four is consistent with published evidence that MAO-A promoter constructs bearing three repeats have lower transcriptional activity in transfected neuroblastoma and choriocarcinoma cells. The uVNTR genotype may be a common genetic determinant of significant individual differences in oxidizing capacity for critical MAO-A substrates, which include serotonin, norepinephrine, and tyramine.

Adolescent↗
PubMed1992

A 15 base-pair AT-rich variable number tandem repeat in the type III procollagen gene (COL3A1) as an informative marker for 2q31-2q32.3.

Segments of repeating DNA, termed variable number tandem repeats, within the genome are often used as polymorphic markers. Here we report such a repeat in the intervening sequence 25 of the type III procollagen gene (COL3A1) located at 2q31-q32.3. The region containing intervening sequence 25 of the COL3A1 gene was amplified using the polymerase chain reaction and the products were analyzed by agarose gel electrophoresis and dideoxynucleotide sequencing. The repeat consisted of an AT-rich unit of 15 base-pairs (ATATATATATGAGAC). Seven different alleles were identified containing between three and nine repeats of the 15 base-pair unit. The allele heterozygosity was 73% in 117 unrelated individuals. The alleles were shown to be inherited in a Mendelian fashion in three large families. This marker should prove useful in linkage studies for COL3A1, and for linkage studies of other genes on the long arm of chromosome 2. The information extends and complements a report on the same repeat recently published by Lee et al. (J. Biol. Chem. 266: 5256, 1991 a).

Alleles↗
PubMed1987

Variable number of tandem repeat (VNTR) markers for human gene mapping.

A large collection of good genetic markers is needed to map the genes that cause human genetic diseases. Although nearly 400 polymorphic DNA markers for human chromosomes have been described, the majority have only two alleles and are thus uninformative for analysis of genetic linkage in many families. A few known marker systems, however, detect loci that respond to restriction enzyme cleavage by producing a fragment that can have many different lengths. This polymorphism is due to variation in the number of tandem repeats of a short DNA sequence. Because most individuals will be heterozygous at such loci, these markers will provide linkage information in almost all families. Ten oligomeric sequences derived from the tandem repeat regions of the myoglobin gene, the zeta-globin pseudogene, the insulin gene, and the X-gene region of hepatitis B virus, were used to develop a series of single-copy probes. These probes revealed new, highly polymorphic genetic loci whose allele sizes reflected variation in the number of tandem repeats.

Chromosome Mapping↗
PubMed2001

A model for the involvement of Okazaki fragments maturation in the expansion of short tandem repeats.

We propose a model for the expansion of short tandem repeats (ESTR), a phenomenon which has been found to occur in human DNA and is associated with a dozen of neuromuscular diseases. The model is based mainly on theoretical considerations and recovers experimental data from the literature; it also finds support in preliminary results obtained by us in multiprimed polymerase chain reactions designed to assess the effects of a downstream primer on the fidelity of the elongation of an upstream one. The model links the occurrence of the ESTR to a defective maturation of the Okazaki fragments (OF), and in particular to an improper processing of their 3' termini. This may occur when the last OF approaches the 5' terminus of the previous one in a susceptible region of the template. It is postulated here that when a growing OF has progressed past the priming region and its main portion has been synthesized, upon approaching its conclusion, the final elongation may take place in a region of the template where certain triplets are repeated: in that case a series of aberrations on the elongation mechanism may occur. These aberrations could involve (a) the displacement of the 5' terminus of the penultimate, properly matured OF, enacted by the incoming 3' terminus of the last OF, (b) the switch of the latter to the displaced strand of the former as template, (c) the fold-back on itself of the growing 3' terminus of the last OF, (d) its assumption of an unusual structure because of the repetition, and (e) some impairment of its removal by structure-specific exo-endonuclease(s). Derangements of this last part of the process may trigger the ESTR.

Base Sequence↗
PubMed2002

[Genetic polymorphism of fifteen short tandem repeat loci in Chinese Drungs].

OBJECTIVE: To study the short tandem repeat (STR) polymorphism in Chinese Drungs (Tulungs). METHODS: The genetic distributions of fifteen STR loci were investigated with the use of coamplification, genescan and genotype from 67 Drungs. RESULTS: There were 144 STR alleles in Drung nationality, with their frequencies ranging from 0.0077 to 0.7846, heterozygosity(H) 0.3723-0.8639, discrimination power(DP) 0.5567-0.9548, probability of paternity exclusion(EPP) 0.2738-0.8358, polymorphism information content (PIC) 0.3461-0.8456 the accumulative DP 0.99999998 and EPP 0.99999894. CONCLUSION: The results of this study on the STR polymorphism in Chinese Drungs could be used as a basis for the genetic structure of Chinese ethnic groups and also be of significant application in anthropology and forensic science.

Alleles↗
PubMed2000

Thiopurine methyltransferase polymorphic tandem repeat: genotype-phenotype correlation analysis.

BACKGROUND: Thiopurine methyltransferase (TPMT) is a genetically polymorphic enzyme that catalyzes the S-methylation of thiopurine drugs such as 6-mercaptopurine. Recently, a variable number tandem repeat (VNTR) within the TPMT promoter has been reported to "modulate" levels of this enzyme activity. METHODS: We set out to perform genotype-phenotype correlation analysis for the polymorphic TPMT tandem repeat in 1211 clinical laboratory samples in which red blood cell (RBC) TPMT activity had been measured and to compare those results with data for 279 control DNA samples. RESULTS: TPMT VNTR length varied from three to nine repeats ( *V3 to *V9), but the most common alleles were *V4 and *V5, with frequencies in the control samples of 0.54 and 0.36, respectively. The clinical laboratory samples were then stratified into those with "low," "intermediate," or "high" levels of RBC TPMT activity; that is, samples presumed to be homozygous for open reading frame (ORF)-based variant alleles, heterozygous for those alleles, or homozygous for the "wild-type" ORF sequence, respectively. TPMT VNTR genotype *V4/*V5 was associated with significantly higher RBC TPMT activity than were *V4/*V4 or *V5/*V5. Lowest activity levels were associated with genotypes that included an allele with more than 5 repeat elements. However, all of these effects were quantitatively small. Finally, there was linkage disequilibrium between VNTR allele *V5 and TPMT*3A, the most common ORF-based polymorphism associated with very low TPMT activity in white persons. CONCLUSIONS: These observations suggest that, in addition to the striking effects of ORF-based single nucleotide polymorphisms on TPMT activity, the VNTR within the 5'-flanking region of the TPMT gene also may modulate levels of RBC TPMT activity.

Adolescent↗
PubMed2005

Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci.

We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2-6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K> or =3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.

Asia, Southeastern↗
PubMed2005

A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci.

The use of expert systems to interpret short tandem repeat DNA profiles in forensic, medical and ancient DNA applications is becoming increasingly prevalent as high-throughput analytical systems generate large amounts of data that are time-consuming to process. With special reference to low copy number (LCN) applications, we use a graphical model to simulate stochastic variation associated with the entire DNA process starting with extraction of sample, followed by the processing associated with the preparation of a PCR reaction mixture and PCR itself. Each part of the process is modelled with input efficiency parameters. Then, the key output parameters that define the characteristics of a DNA profile are derived, namely heterozygote balance (Hb) and the probability of allelic drop-out p(D). The model can be used to estimate the unknown efficiency parameters, such as pi(extraction). 'What-if' scenarios can be used to improve and optimize the entire process, e.g. by increasing the aliquot forwarded to PCR, the improvement expected to a given DNA profile can be reliably predicted. We demonstrate that Hb and drop-out are mainly a function of stochastic effect of pre-PCR molecular selection. Whole genome amplification is unlikely to give any benefit over conventional PCR for LCN.

Computer Graphics↗
PubMed2000

Loss of heterozygosity detected in a short tandem repeat (STR) locus commonly used for human DNA identification.

Short tandem repeat (STR) markers are commonly used in basic genetic research and in human identification testing. Clinically, STRs can be used to study genetic alterations in tumors. A genetic deletion common to many types of cancer is referred to as the loss of heterozygosity (LOH). Numerous examples of LOH in cancer have been described and some have been mapped to areas located in close proximity to markers employed in human identity testing. Despite this fact, LOH has rarely been observed for STR loci commonly employed in forensic testing. Recently, for medico-legal purposes, we were asked to determine whether a tissue biopsy originated from a particular individual. For a reference source we assessed two specimens, one from normal tissue and one from cancerous tissue. When both reference specimens were used to generate DNA profiles, we observed LOH at one STR locus, D13S317. As demonstrated in other cancers only the cancerous biopsy demonstrated LOH. The forensic community should be cognizant of these unusual circumstances because, as identification of human DNA continues to be used more extensively, certain instances will arise in which reference material will not be readily available. In these situations, archived specimens may be employed as a reference source. Clinical specimens such as tissue biopsies should be used with caution if they have not been confirmed to contain normal tissue.

DNA Fingerprinting↗
PubMed2000

Color-coding reveals tandem repeats in the Escherichia coli genome.

Genomic DNA contains a wide variety of repetitive sequences. In Escherichia coli, there have been several classes of repetitive sequences reported, some of which cluster as tandem repeats. We propose a novel method for analyzing symbolic sequences by two-dimensional pattern formation with color-coding. We applied this method for searching tandem repeats in the E. coli genome and found approximately 50 repeats with periods longer than 30 bases. The longest repeat has a period of 1267 bases.

Base Sequence↗
PubMed1996

Sequence variation found in the flanking region of a trimeric short tandem repeat at the PLA2 locus: its considerable effect on estimating alleles.

Amplified alleles at the PLA2 short tandem repeat locus were sequenced and analyzed using different combinations of the PCR primer. When changing one side of the primers from the previous design to our original one, additional alleles, which had been previously hidden, could be newly detected in two out of 60 DNA samples of unrelated Japanese individuals. The sequence data revealed both 'hidden alleles' to be accompanied by a 3-bp deletion in the 5'-flanking region of the trimeric short tandem repeat. The position of the deletion corresponded to the exact 3' end of the primer, which had been formerly used. In the present case, both of the base numbers, which constituted the core repeat unit and which were deleted in the 'hidden alleles', were equal. Therefore, it was impossible to distinguish an allele from that with not only an additional trimeric repeat but a 3-bp deletion without the sequence analysis. This result indicates that the estimated allele size does not always reflect the difference in the repeat number even if the alleles regularly differ in size by one repeat unit. Moreover, this study suggests the presence of apparent homozygotes, of which the fellow of the heterozygous alleles is hidden by an unsuccessful amplification due to the sequence variation.

Alleles↗
PubMedDate not supplied

[Detection of tandem repeats in the genome of Citellus genus using restrictases].

DNA from ground squirrels of the Citellus genus (Rodentia, Sciuridae) were analysed by centrifugation in the presence of CsCl followed by digestion by restriction endonucleases. Digestion of DNA of two species C. undulatus and C. fulvus by 10 of the 16 restriction endonucleases used led to formation of electrophoretically discrete fragments that are multiple to 330 b.p. in length which points out the tandem organization of repetitive sequences similar to the satellite DNA of many mammal species. However, upon centrifugation we failed to reveal a satellite band in these species; hence the tandem repeats refer to the class of cryptic satellites in the ground squirrels and do not differ in base composition from the remaining part of DNA. The main fraction of the genome was revealed in the form of discrete fragments by cleavage with HindIII and AluI. Both of these restriction endonucleases were used for comparative analysis of DNA of 12 Citellus species. It has been shown that DNA of all species can be digested by HindIII and yields a series of fragments that are multiple to 330-30 b.p. in length and the total content of which varies from species to species within 4-22%. The fraction of the tandem repeats does not correlate with the systematic position of species nor with the amount of heterochromatin in the chromosomes. AluI cuts the DNA of 11 species yielding 110 and 220 b.p. fragments compared to only 60 and 280 b.p. in the DNA of C. dauricus. Under HindIII digestion we can also reveal the tandem repeats in marmot, which is phylogenetically close to the Citellus of the Marmota genus, but they have another periodicity--180 b.p. We propose that the age of ground squirrels repeats is 2-3 million years and they are significantly younger than the marmot repeats.

Animals↗
PubMed2002

A variable number of tandem repeats result in polymorphic alpha -isopropylmalate synthase in Mycobacterium tuberculosis.

A locus of variable number of the tandem repeat, VNTR4155, resides in the putative leuA gene, encoding for alpha -isopropylmalate synthase (alpha -IPMS) of Mycobacterium tuberculosis, a repeat that is unique to the bacterium. The objective was to determine whether the polymorphic VNTR4155 was translated and resulted in a polymorphic protein. The putative leuA gene of the M. tuberculosis H37Rv strain was cloned by PCR and expressed in a His-tagged form in Escherichia coli. The enzymatic properties of the purified protein were studied. The protein was used as an antigen to immunize rabbits. Soluble proteins of several strains of M. tuberculosis were examined by Western blot analysis. The polymorphism of VNTR4155 was due to the presence of different copy number of the 57-bp tandem repeat. The putative alpha -IPMS of various strains of M. tuberculosis had different sizes, varying directly with the length of their VNTR4155.

2-Isopropylmalate Synthase↗
PubMed2000

Assembly and release of human immunodeficiency virus type 1 Gag proteins containing tandem repeats of the matrix protein coding sequences in the matrix domain.

We have constructed human immunodeficiency virus (HIV) gag mutants by increasing the matrix protein (MA) sequences via tandemly repeated duplication of the central 107-MA codons. Instead of a total of 132 amino acid residues for the wild-type MA, the resultant mutants designated as MA2, MA3, and MA4 contained a total of 242, 352, and 462 codons in the MA domains, respectively. Analysis indicated that the addition of 110 or 220 amino acid residues to the MA did not significantly affect the assembly, release, and processing of particles; however, particle production was markedly reduced when another copy of 110 residues was added to the MA. Subcellular fractionation analysis suggested that the MA tandem repeat mutations enhanced the Gag membrane affinity, in a manner which correlated with the copy number of MA sequences. The effects of enhanced membrane affinity were substantially reduced when sequences downstream of the capsid (CA) domain were deleted. Sucrose density gradient fractionation analysis showed that particles produced by the large insertion mutants possessed wild-type (wt) HIV particle density. Truncation of sequences downstream of the nucleocapsid (NC) domains of the mutants did not influence the budding of particles. In contrast, particle budding was severely impaired when sequences downstream of the CA domain were truncated. Particle densities for the large Gag proteins, which were truncated at the C-terminus of CA, were about 1.12-1.14 g/ml lower than that for wt. Our results suggest that the HIV MA domain could adopt insertions of large protein sequences, and strongly support the proposal that the NC and p2 domains play a crucial role in the process of correct Gag protein packing.

Cell Line↗
PubMed2006

Use of short tandem repeats for DNA fingerprinting to rapidly diagnose graft-versus-host disease in solid organ transplant patients.

BACKGROUND: Graft-versus-host disease (GVHD) is a rare complication following liver transplantation and carries a poor prognosis with mortality approaching 90-95%. Diagnosis of GVHD is often delayed due to early symptoms mimicking more common, entities such as drug reactions and viral syndromes. To date, definitive diagnosis has been difficult and has relied on a constellation of clinical and histopathologic variables. We present the use of short tandem repeat DNA "fingerprinting" technology as a method of early, definitive diagnosis of GVHD in patients after liver transplantation. METHODS: A patient status-postorthotopic cadaveric-liver transplant, with an uncomplicated immediate posttransplant course, presented 4 weeks after transplant with fever, diarrhea, and maculopapular rash on her palms, soles, and back. The patient's condition worsened despite empiric treatment for an infectious etiology. Skin and rectal biopsies were suspicious for GVHD. RESULTS: DNA was isolated from the skin and rectal biopsies as well as from a donor lymph node. PCR amplification was done for nine highly polymorphic short tandem repeats for each specimen and a unique DNA "fingerprint" was obtained from each. DNA from skin and rectum demonstrated mixed chimerism with both donor and recipient alleles detected. Thorough analysis confirmed GVHD. CONCLUSION: Short tandem repeats for DNA fingerprinting represents an efficient and reproducible method for the definitive diagnosis of GVHD after liver transplantation. Rapid detection of GVHD using this technology, coupled with early initiation of therapy, may lead to improved survival for patients with GVHD after solid organ transplant.

DNA Fingerprinting↗