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PubMed2003

The biallelic variable number of tandem repeats of the tumor necrosis factor receptor 2 promoter in systemic lupus erythematosus.

The objective of this study was to investigate whether the variable number of tandem repeats (VNTR) of the tumor necrosis factor receptor 2 (TNFR2) promoter is associated with susceptibility to systemic lupus erythematosus (SLE) and its clinical phenotypes. A biallelic VNTR within a 42-bp region in the TNFR2 gene promoter was determined by polymerase chain reaction in 88 SLE patients and 95 healthy control subjects. Clinical manifestations were analyzed in each patient and correlated with the genotypes. When the TNFR2 promoter VNTR was compared between Korean and Caucasian healthy controls with respect to allele frequencies, there was a significant difference (alleles 1 and 2: 39, 151 in Koreans vs 60, 138 in Caucasians, respectively; chi-squared test 4.38; 2 df; P=0.036). The genotype distribution of the TNFR2 promoter VNTR did not differ between SLE patients and control subjects (1.1, 1.2, and 2.2 genotypes 7, 14, 67 vs 5, 29, and 61 controls, respectively; chi-squared test 5.19; 2 df; P=0.061). According to the TNFR2 promoter genotypes in the lupus patients, clinically there was no significant difference in age at onset, anti-dsDNA titer, C4 level, systemic lupus erythematosus disease activity index (SLEDAI), Systemic Lupus International Collaborating Clinics/American College of Rheumatology (SLICC/ACR) damage index, or autoantibodies. However, the 1.1 genotype group showed the lowest C3 level and more frequent renal involvement than the 1.2 and 2.2 genotype groups. In conclusion, an ethnic difference in the TNFR2 promoter VNTR has been found and the biallelic VNTR of the TNFR2 promoter may be associated with clinical phenotypes in SLE.

Adolescent↗
PubMed1994

Report of the European DNA profiling group (EDNAP)--towards standardisation of short tandem repeat (STR) loci.

This paper describes a collaborative exercise intended to demonstrate whether uniformity of DNA profiling results could be achieved between European laboratories using short tandem repeat (STR) loci. Two different STRs were chosen--HUMTH01 and the AT-rich HUMACTBP2 (SE33). The former locus has only five common alleles, whereas the latter is complex and has at least 30 alleles. Laboratories were asked to test seven blood stains and to report the results to the coordinating laboratory. The exercise demonstrated that the simple STR systems such as HUMTH01 are more amenable to adoption as standard loci than complex AT-rich systems.

Alleles↗
PubMed1999

Tetrameric short tandem repeat (STR) system D15S233 (wg1d1): sequencing and frequency data in the japanese and Chinese populations.

We evaluated the forensic usefulness of D15S233 (wg1d1), a tetrameric short tandem repeat (STR) locus, in the Japanese and Chinese populations. Typing was performed by denaturing polyacrylamide gel electrophoresis followed by silver staining. Nine different alleles were found in 472 Japanese chromosomes and seven in 186 Chinese chromosomes. 102 alleles sequenced were composed of two kinds of repeats (AGGA and GGGA). All alleles differed in size by one tetranucleotide repeat unit, and no insertion or deletion was found. The expected unbiased heterozygosities in Japanese and Chinese were 0.766 and 0.785, respectively. No significant deviations from the Hardy-Weinberg equilibrium were found in either population. We retyped all samples using an alternative pair of flanking primers in order to detect any spurious appearances of homozygotes due to sequence variation at the primer annealing site. One heterozygous sample had unbalanced density bands when the original primer set was used, but equal density bands when our newly designed primer set was used. Sequencing analysis revealed that the sparser allele had one nucleotide substitution near the 5' end of the annealing site of the original primer region. Thus, all apparently homo/heterozygous samples were thought to be truly homo/heterozygous. We also applied the D15S233 locus to paternity testing and forensic identification. Our results suggest that this locus should be a very useful STR locus for forensic practice in Japanese and Chinese.

Journal Article↗
PubMed1997

Two novel alleles of the ATCT variable number tandem repeat locus VWF.VNTR I in intron 40 of the von Willebrand factor gene.

Two new alleles, allele 9 and allele 15, of the ATCT variable number tandem repeat locus, VWF.VNTR I, of intron 40 of the von Willebrand factor (VWF) gene are described. Both alleles occurred in low frequencies, being detected in only two and one of 285 random Australian Caucasians respectively. In all, 10 alleles were observed representing between six and 15 repeats of the ATCT motif. The allele frequency distribution in this Australian population was similar to other VWF.VNTR I population studies. The additional alleles described here for the VWF.VNTR I further enhance the usefulness of this VNTR locus in human identification work.

Alleles↗
PubMed1998

Use of short tandem repeats for the analysis of genetic variability in sympatric populations of Anopheles gambiae and Anopheles arabiensis.

Anopheles gambiae and An. arabiensis were analysed at 30 short tandem repeat (STR) loci originally developed for use in An. gambiae. All specimens were collected from the same village in Kilifi district, coastal Kenya. All 30 loci were amplified in the An. gambiae specimens, whereas 25 out of 30 loci (83.3%) were successfully amplified in the An. arabiensis specimens. Both species had similar levels of polymorphism for the loci that were amplified (93.3% for An. gambiae and 92% for An. arabiensis). Median FST and RST values between the two species were 0.249 and 0.197, respectively, corresponding to Nm values of 0.75 and 0.51, respectively, and suggesting limited interchange of genes between these species. These, together with the relatively high Nei unbiased genetic distance (0.202) between the two sibling species, are consistent with the occurrence of sympatric species with limited gene flow. FST/RST values for individual loci varied greatly (FST range 0.00-0.87; RST range 0.00-0.73), indicating that the loci differ in their ability to measure levels of differentiation between these two species. Location of loci within paracentric inversions seems to be an important factor affecting levels of differentiation measured by the different loci.

Alleles↗
PubMed1981

Simian virus 40 tandem repeated sequences as an element of the early promoter.

On the late side of the simian virus 40 (SV40) DNA replication origin are several sets of tandem repeated sequences, the largest of which is 72 base pairs long. The role of these sequences was examined through construction of deletion mutants of SV40. A mutant from which one of the 72-base-pair repeated units was removed is viable upon transfection of monkey kidney cells with viral DNA. Extension of this deletion into the second repeated unit, however, leads to nonviability, as recognized by the absence of early transcription and of tumor antigen production. These observations indicate that the 72-base-pair repeated sequences form an essential element in the early viral transcriptional promoter and explain the inability of such a deleted genome to complement an early temperature-sensitive mutant of SV40, tsA, as well as the failure to replicate its DNA. In a parallel experiment it was found that the extended deletion mutant was also unable to complement a late temperature-sensitive mutant of SV40, tsB. This suggests that the extended mutant is also defective in DNA replication or late transcription (or both).

Base Sequence↗
PubMed1981

Identification of a novel class of tandemly repeated genes transcribed on lampbrush chromosomes of Pleurodeles waltlii.

Electron microscope preparations of lampbrush chromosomes from oocytes of Pleurodeles waltlii have revealed a new class of tandemly repeated genes. These genes are highly active, as judged by the close spacing of nascent transcripts. They occur in clusters of greater than 100 copies and are transcribed in units containing roughly 940 base pairs of DNA that are separated by nontranscribed spacers of an estimated DNA content of 2,410 base pairs. The size and the pattern of arrangement of these transcription units can not be correlated with any of the repetitious genes so far described.

Animals↗
PubMed2005

Sensitivities and specificities of spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat typing methods for studying molecular epidemiology of tuberculosis.

The development of PCR-based genotyping modalities (spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat [MIRU-VNTR] typing) offers promise for real-time molecular epidemiological studies of tuberculosis (TB). However, the utility of these methods depends on their capacity to appropriately classify isolates. To determine the operating parameters of spoligotyping and MIRU-VNTR typing, we have compared results generated by these newer tests to the standard typing method, IS6110 restriction fragment length polymorphism, in analyses restricted to high-copy-number IS6110 isolates. Sensitivities of the newer tests were estimated as the percentages of isolates with identical IS6110 fingerprints that had identical spoligotypes and MIRU-VNTR types. The specificities of these tests were estimated as the percentages of isolates with unique IS6110 fingerprints that had unique spoligotypes and MIRU-VNTR types. The sensitivity of MIRU-VNTR typing was 52% (95% confidence interval [CI], 31 to 72%), and the sensitivity of spoligotyping was 83% (95% CI, 63 to 95%). The specificity of MIRU-VNTR typing was 56% (95% CI, 51 to 62%), and the specificity of spoligotyping was 40% (95% CI, 35 to 46%). The proportion of isolates estimated to be due to recent transmission was 4% by identical IS6110 patterns, 19% by near-identical IS6110 patterns, 33% by MIRU-VNTR typing, and 53% by spoligotyping. The low calculated specificities of spoligotyping and MIRU-VNTR typing led to misclassification of cases, inflated estimates of TB transmission, and low positive predictive values, suggesting that these techniques have unsuitable operating parameters for population-based molecular epidemiology studies.

Bacterial Typing Techniques↗
PubMed2001

Effects of substitution of conserved amino acid residues on the sugar-binding property of the tandem-repeat 32-kDa galectin of the nematode Caenorhabditis elegans.

The 32-kDa galectin (LEC-1) of the nematode Caenorhabditis elegans (C elegans) is composed of two tandemly repeated homologous sequences, each containing a carbohydrate-recognition domain (CRD). Using the polymerase chain reaction (PCR) with LEC-1 cDNA as a template and "megaprimers", we performed site-directed mutagenesis to substitute conserved amino acid residues in these domains. The resultant mutated LEC-1s were produced in E. coli, and their binding abilities were estimated by affinity chromatography. When one of the conserved amino acid residues in the first lectin domain was substituted, the binding ability of the mutant protein to asialofetuin-agarose was reduced but still remained. The binding ability of such mutants was similar to that of the recombinant half molecule containing the second lectin domain (Ch). However, when mutations were introduced into the second lectin domain, the binding ability of these mutant lectins to asialofetuin-agarose was significantly reduced just like the half recombinant molecule containing the first lectin domain (Nh). The different effects of the substitution of amino acid residues on the two lectin domains suggest that the binding properties of the two sites are different and that LEC-1 acts as a "heterobifunctional crosslinker."

Animals↗
PubMed1996

Detection of chimerism and early engraftment after allogeneic peripheral blood stem cell or bone marrow transplantation by short tandem repeats.

Chimerism can be monitored after HLA-matched allogeneic bone marrow transplantation (BMT) or allogeneic peripheral blood stem cell transplantation (PBSCT) by detecting polymorphisms in short tandem repeats (STR). The purpose of our study was to document early complete chimerism in BMT and PBSCT recipients using STR, and to determine whether the initial WBC recovery correlated with the days required to attain complete chimerism. A total of 5 patients (2 PBSCT and 3 BMT) were followed by STR after transplantation. Peripheral blood obtained prior to transplantation was used to determine the 2 most informative STR probes for each donor/recipient pair. STR were amplified by polymerase chain reaction (PCR) with 8 commercial probes, and PCR products were visualized with silver staining. Peripheral blood was evaluated daily post-transplantation for WBC counts and to identify the presence of mixed or full chimerism by STR. The sensitivity of the STR technique varied from 0.05 to 1%, depending on the probe. Full chimerism was documented between day 9 and 14 in PBSCT recipients and on day 14 and 16 in BMT recipients. The initial rise in WBC occurred within 3 days of the onset of full chimerism, indicating that full chimerism is a more sensitive indicator of early engraftment. Periodic recipient monitoring using STR after complete chimerism identifies those patients who revert to mixed chimeras. The STR method may be useful in future studies to determine the significance of early engraftment and the clinical implications of sustained complete chimerism or mixed chimerism.

Adult↗
PubMed1993

A highly polymorphic (ACT)n VNTR (variable nucleotide of tandem repeats) locus inside intron 12 of COL1A2, one of the two genes involved in dominant osteogenesis imperfecta.

A new, highly polymorphic, region consisting of variable number of tandem repeats (VNTR) is described that occurs within intron 12 of the COL1A2 gene. This VNTR consists of the trinucleotide ACT repeated from 6 to 12 times. Of the six alleles so far detected four are common in the three major races. The two rare alleles, (ACT)11 and (ACT)12, have been found only in Africans. In addition, a rapid technique has been developed that can be used successfully with very small amounts of even partially degraded DNA, thus allowing the use of this VNTR for forensic applications. Since dominant OI can be due to mutations at either of two loci (COL1A1 and COL1A2) prenatal diagnosis becomes feasible in the majority of the affected families only if a very informative marker is available for both of these genes. This VNTR provides a very powerful marker for COL1A2. In fact the heterozygosity for it ranges from 0.634 to 0.741 with PIC values from 0.562 to 0.696, respectively. Since trinucleotide repeats can be "unstable," and sometimes pathogenic, the unexplained collagenopathies (or suspected collagenopathies) should be analyzed from this point of view.

Base Sequence↗
PubMed2006

Development and application of Multiple-Locus Variable number of tandem repeat Analysis (MLVA) to subtype a collection of Listeria monocytogenes.

In this study we report the development and application of a Multiple-Locus Variable number of tandem repeat Analysis (MLVA) strategy for subtyping Listeria monocytogenes. Genome profiles of a collection of forty-five food-borne L. monocytogenes isolates were compared using MLVA. These isolates were obtained as part of an active surveillance programme of foods in the south-east region of Ireland. MLVA successfully discriminated amongst the isolates. The method was easy to perform, relatively fast and could be deployed in any molecular laboratory with basic laboratory equipment. This approach is a valuable tool, which has the capability to provide comparable results when compared with other more established typing methods, including pulsed-field gel electrophoresis (PFGE).

Bacterial Typing Techniques↗
PubMed2005

A single-molecule PCR approach to the measurement of induced expanded simple tandem repeat instability in vitro.

Sensitive and precise models are needed to identify potential genotoxicity at environmentally relevant doses of mutagens. The size length alterations in expanded simple tandem repeat (ESTR) loci have been used as a biomarker of genetic instability caused by a variety of agents in the mouse germline. The mechanisms operating in both spontaneous and induced instability are poorly understood. We have developed a single-molecule polymerase chain reaction (SM-PCR) method to investigate mutation at the mouse ESTR locus Ms6-hm in the murine C3H/10T1/2 embryonic cell line. Growth of cells to levels of high cell density induced increased ESTR instability, with mutation frequencies 5.1-fold (+/-2.8) over sub-confluent cultures. Accordingly, cell cultures were maintained at sub-confluent levels for further investigations of the induction of ESTR mutation by genotoxic agents. Treatment with the DNA alkylating agent N-nitroso-N-ethylurea (ENU) resulted in a 1.94-fold (+/-1.1) increase in mutation frequency, similar to responses measured previously in the germline in vivo. Therefore, mutagen exposure can also affect somatic (non-meiotic) rapidly dividing mouse cells. This SM-PCR approach eliminates the requirement of sub-cloning individual treated cells, thereby, reducing the time needed to screen for ESTR mutation, and will be a very useful tool for future investigations into the mechanisms involved in ESTR mutation.

Alleles↗
PubMed2000

Monitoring of residual disease and guided donor leucocyte infusion after allogeneic bone marrow transplantation by chimaerism analysis with short tandem repeats.

In this study, we analysed the chimaeric status of peripheral blood leucocytes (PBLs) in recipients of allogeneic bone marrow transplantation (BMT) with the use of short tandem repeat (STR) microsatellite markers for monitoring the efficacy of BMT and donor leucocyte infusions (DLIs). A set of four STR markers was used with a highly discrimative capacity between individuals. STRs were detected by polymerase chain reaction (PCR) and were analysed by gene scanning (STR-GS). Between June 1990 and December 1998, 52 patients treated with BMT for chronic myeloid leukaemia (CML) were analysed. Seventeen patients relapsed after BMT and two patients never achieved remission after BMT. Fourteen of the 17 patients achieved a complete donor chimaerism after BMT, as detected by the presence of only donor STR-GS fragments, and in three cases a weak recipient STR-GS signal remained persistently detectable after BMT. A reappearance or increase of recipient STR-GS signals was indicative of relapse, which was mostly detected by STR-GS several months before relapse was diagnosed clinically. Nineteen patients were treated with DLI for reappearance of CML after BMT which resulted in complete remission in 17 patients, concordant with the disappearance of recipient STR-GS signals. More importantly, DLI treatment could be guided based upon the STR-GS data, which prevented unnecessary extra DLI courses that could cause toxicity. This study indicates that STR-GS is an effective and reliable method for monitoring BMT recipients.

Adult↗
PubMed2001

Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis.

Francisella tularensis, the etiological agent of tularemia, is found throughout the Northern hemisphere. After analyzing the F. tularensis genomic sequence for potential variable-number tandem repeats (VNTRs), we developed a multilocus VNTR analysis (MLVA) typing system for this pathogen. Variation was detected at six VNTR loci in a set of 56 isolates from California, Oklahoma, Arizona, and Oregon and the F. tularensis live vaccine strain. PCR assays revealed diversity at these loci with total allele numbers ranging from 2 to 20, and Nei's diversity index values ranging from 0.36 to 0.93. Cluster analysis identified two genetically distinct groups consistent with the current biovar classification system of F. tularensis. These findings suggest that these VNTR markers are useful for identifying F. tularensis isolates at this taxonomic level. In this study, biovar B isolates were less diverse than those in biovar A, possibly reflecting the history of tularemia in North America. Seven isolates from a recent epizootic in Maricopa County, Ariz., were identical at all VNTR marker loci. Their identity, even at a hypervariable VNTR locus, indicates a common source of infection. This demonstrates the applicability of MLVA for rapid characterization and identification of outbreak isolates. Future construction of reference databases will allow faster outbreak tracking as well as providing a foundation for deciphering global genetic relationships.

Animals↗
PubMed2004

Lack of support for a role of the insulin gene variable number of tandem repeats minisatellite (INS-VNTR) locus in fetal growth or type 2 diabetes-related intermediate traits in United Kingdom populations.

The insulin gene variable number of tandem repeats minisatellite (INS-VNTR) class III allele is associated with altered fetal growth, type 2 diabetes risk (especially when paternally inherited), and insulin and IGF2 gene expression. Further studies are needed to establish the role of the INS-VNTR in fetal growth and assess whether its effects depend on the parent of origin. We analyzed the INS-VNTR-linked -23 Hph1 polymorphism in 2283 subjects, comprising 1184 children and 1099 parents. There were no differences (P < 0.05) in birth weight between offspring of the three genotypes: III/III (n = 108) vs. I/I (n = 558), effect size, -8 g (P = 0.87); and I/III (n = 464) vs. I/I, effect size, -19 g (P = 0.54). We observed no differences in head circumference [III/III (n = 95) vs. I/I (n = 470), effect size, -0.14 cm; P = 0.31] or birth length. No differences were observed when stratifying by postnatal growth realignments [nonchangers III/III (n = 37) vs. I/I (n = 170), effect size, -43 g; P = 1.00] or by parent of origin of the class III allele (presence of paternal III allele effect size, -15 g; P = 0.74). INS-VNTR was nominally associated (P < 0.05) with body mass index and insulin resistance, but not with beta-cell function, in young adults. In the largest study to date, we found a lack of support for a role for INS-VNTR in fetal growth and nominal association with type 2 diabetes-related intermediate traits.

Adult↗
PubMed1997

Polymorphism of short tandem repeat (STR) loci PLA2, D3S2459, D8S315 (kw38), CYP19, D3S1359, FGA, and D8S1132 in the Japanese and Chinese populations.

We report a study of polymorphism for seven short tandem repeat (STR) loci in Japanese and Chinese populations. Among 104 to 134 individuals in the both population samples, eight alleles were revealed for locus PLA2, thirteen for D3S1359, eleven for FGA, eight for D8S315 (kw38), ten for D8S1132, five for CYP19, and seven for D3S2459. They correspondingly constituted 10 to 39 genotypes therein. For most of the STRs, there was only a single allele active as the most frequent one among the others, except locus D3S1359 in Chinese samples (two alleles, 206 bp and 210 bp, frequency = 0.273 each). Also, the population genotype configurations were locus specific, varying in the patterns of commonest genotypes on each locus, e.g., one pattern for loci CYP19, D3S1359, and D8S315, one and two for loci PLA2 and D3S2459, two for locus D8S1132, and one and four for locus FGA. The distributions of observed genotypes were in Hardy-Weinberg Equilibrium. Furthermore, the seven STRs were exhibited highly polymorphic and informative for the both populations, and the alleles could be easily separated in electrophoresis and correctly interpreted with side-to-side allelic ladders. Together, the results suggest that the tri- and tetra-meric STRs are useful genetic markers for forensic practice.

Alleles↗