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PubMed1996

French Caucasian population data obtained from fluorescently detected HUMvWFA31/A and HUMF13A01 short tandem repeat loci.

Allele and phenotype frequencies for two tetranucleotide STR (short tandem repeat or microsatellite) systems, HUMvWFA31/A and HUMF13A01, were obtained from a sample of approximately 240 unrelated individuals randomly selected from the French Caucasian population. PCR (polymerase chain reaction) products were analysed on 6% polyacrylamide denaturing gels and visualized using fluorescently labelled primers on the automated 373A ABI DNA sequencer (Applied Biosystems Inc.). French Caucasian allele frequencies were compared to other published Caucasian data. Conditions were optimised for the quadruplex PCR amplification of these two STR loci together with the HUMFESFPS and HUMTH01 loci and the quadruplex PCR was also performed on various forensic DNA samples.

Alleles↗
PubMed1998

Comparison of slab gel electrophoresis and capillary electrophoresis for the detection of the fluorescently labeled polymerase chain reaction products of short tandem repeat fragments.

The sizing capability of slab gel electrophoresis for short tandem repeat (STR) fragments was compared to the sizing capability of capillary electrophoresis (CE). Both systems used automated laser fluorescence detection to detect four fluorescent dyes, enabling the use of an internal lane standard within each sample. The STR fragments were amplified using a multiplex polymerase chain reaction (PCR) in which the STR fragments Hum CD-4, Hum TH01, Hum D21S11 and Hum SE33 were amplified simultaneously. The reproducibility of the size calling was determined for both systems. The average standard deviation obtained for the slab gel system was 0.2, which was comparable to the standard deviation of 0.12 obtained for the CE system. The CE system produced results comparable to those obtained on the slab gel system, with a level of precision of +/- 1.0 bp (between instruments).

DNA↗
PubMed1997

The screening of 13 short tandem repeat loci in the Chinese population.

Population studies of 13 short tandem repeat (STR) loci were carried out on Chinese in Taiwan. The STR loci included HUMF13B, HUMF13A01, HUMFES/FPS, HUMFABP, HUMPLA2A1, HUMTPOX, HUMTH01, HUMVWFA31/A, HUMCSFIPO, HUMLPL, HUMGPP3A09, HUMCYAR04 and HUMCD4. DNA samples from 100 unrelated individuals were screened. The STR allele patterns were detected by the fluorescence detector of an automated DNA sequencer. Two PCR amplifications were performed for each STR locus in this study. The first PCR amplification strategy used 26 base pairs of the T7 sequence extension in the 5' end of the forward primer of each STR locus. The second PCR amplification used a dye-labeled T7 primer instead of the forward primer in the first PCR amplification, and the first PCR products as template to produce fluorescent dye-labeled PCR products. PCR products of different STR loci with overlapping allele sizes could be detected in the same lane of the polyacrylamide gel on an automated DNA sequencer using different colored dye-labeled T7 primers. There was no need to directly conjugate the fluorescent dye to individual STR primers. The PCR products were obtained using 2 ng of template DNA in 25 microliters of PCR reaction mixture. No deviations from the Hardy-Weinberg equilibrium were observed for the 13 STR loci. The distributions of these STR alleles were different from those of Caucasians or Blacks. The probability of matching from the combination of the 13 STR loci was 5.9 x 10(-10) for our Chinese population. However, HUMF13B, HUMLPL and HUMCD4 loci were not as highly polymorphic as observed in other populations.

Alleles↗
PubMed1997

The HumD21S11 system of short tandem repeat DNA polymorphisms in Japanese and Chinese.

HumD21S11 is a short tandem repeat DNA polymorphic system with a complex basic structure of (TCTA)4-6 (TCTG)5-6 (TCTA)3 TA (TCTA)3 TCA (TCTA)2 TCCA TA (TCTA)n. Using the allelic ladder prepared by us, the distribution of alleles among Japanese and Chinese was investigated, and four new alleles 28.2, 34, 35.2, and 36.2, were discovered. DNA sequencing was performed on the newly found alleles as well as on family samples and led to the discovery of different gene structures within alleles 28 and 32. Forensic materials, including hairs and seminal stains, were tested in parallel with blood samples from the same individual and were successfully typed for D21S11.

Alleles↗
PubMed2002

Analysis of the polymorphic structure of the D7S808-short tandem repeat (STR) locus.

We analyzed the polymorphic structure of the short tandem repeat (STR) (AARG) locus D7S808 by DNA sequencing and examined the D7S808 allele distribution in a Japanese population. The sequence analysis confirmed that this locus consists of repeats of the tetranucleotides cttt and cctt, but that the number of repeats of the cctt motif does not vary with the allele, and that this STR polymorphism is due to variation in the number of cttt repeats alone. Although the results in this study suggest that the numbers of repeats range from 7 (allele 7) to 22 (allele 22), alleles 9, 10, 19, and 21 were not observed in the Japanese samples examined. Analysis of DNA samples from 355 unrelated individuals revealed the occurrence of 286 heterozygotes (observed heterozygosity 80.6%). Alleles 15, 14, 16, and 17 had high frequencies of 0.261, 0.192, 0.166, and 0.120, respectively and, together with allele 7 with a slightly high frequency of 0.059, showed a bimodal distribution. In addition, we prepared primers yielding shorter amplification products (232-292 bp) than those (435-480 bp) obtained with the originally reported primers. The newly designed primers can be used for polymerase chain reaction, making this locus extremely useful in forensic science practice.

Journal Article↗
PubMed2000

Structural analysis of multifunctional peptide motifs in human bifunctional tRNA synthetase: identification of RNA-binding residues and functional implications for tandem repeats.

Human bifunctional glutamyl-prolyl-tRNA synthetase (EPRS) contains three tandem repeats linking the two catalytic domains. These repeated motifs have been shown to be involved in protein-protein and protein-nucleic acid interactions. The single copy of the homologous motifs has also been found in several different aminoacyl-tRNA synthetases. The solution structure of repeat 1 (EPRS-R1) and the secondary structure of the whole appended domain containing three repeated motifs in EPRS (EPRS-R123) was determined by nuclear magnetic resonance (NMR) spectroscopy. EPRS-R1 consists of two helices (residues 679-699 and 702-721) arranged in a helix-turn-helix, which is similar to other RNA binding proteins and the j-domain of DnaJ, and EPRS-R123 is composed of three helix-turn-helix motifs linked by an unstructured loop. When tRNA is bound to the appended domain, chemical shifts of several residues in each repeat are perturbed. However, the perturbed residues in each repeat are not the same although they are in the same binding surface, suggesting that each repeat in the appended domain is dynamically arranged to maximize contacts with tRNA. The affinity of tRNA to the three-repeated motif was much higher than to the single motif. These results indicate that each of the repeated motifs has a weak intrinsic affinity for tRNA, but the repetition of the motifs may be required to enhance binding affinity. Thus, the results of this work gave information on the RNA-binding mode of the multifunctional peptide motif attached to different ARSs and the functional reason for the repetition of this motif.

Amino Acid Motifs↗
PubMed1998

Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat.

In 10,844 parent/child allelic transfers at nine short-tandem-repeat (STR) loci, 23 isolated STR mismatches were observed. The parenthood in each of these cases was highly validated (probability >99.97%). The event was always repeat related, owing to either a single-step mutation (n=22) or a double-step mutation (n=1). The mutation rate was between 0 and 7 x 10(-3) per locus per gamete per generation. No mutations were observed in three of the nine loci. Mutation events in the male germ line were five to six times more frequent than in the female germ line. A positive exponential correlation between the geometric mean of the number of uninterrupted repeats and the mutation rate was observed. Our data demonstrate that mutation rates of different loci can differ by several orders of magnitude and that different alleles at one locus exhibit different mutation rates.

Adult↗
PubMed1990

Family studies in von Willebrand's disease by analysis of restriction fragment length polymorphisms and an intragenic variable number tandem repeat (VNTR) sequence.

We have previously identified a microsatellite variable number tandem repeat region of the nucleotide sequence ATCT within intron 40 of the von Willebrand factor (vWF) gene. By polymerase chain reaction (PCR) amplification of this region, eight major alleles have been demonstrated in the South Wales population, with an overall heterozygosity rate of 75%. Direct sequencing has shown that the alleles correspond to lengths of between six and 14 ATCT repeats. In the present study we describe the use of this variable repeat sequence and previously reported restriction fragment length polymorphisms (RFLP) to study inheritance patterns in families with type I, IIA and severe type III von Willebrand's disease (vWD). The results confirm that analysis of this precisely localized intragenic locus provides a highly informative marker for gene tracking studies in the major forms of vWD.

Base Sequence↗
PubMed2006

Locus-specific mutational events in a multilocus variable-number tandem repeat analysis of Escherichia coli O157:H7.

Multilocus variable-number tandem repeat analysis (MLVA) is a validated molecular subtyping method for detecting and evaluating Escherichia coli O157:H7 outbreaks. In a previous study, five outbreaks with a total of 21 isolates were examined by MLVA. Nearly 20% of the epidemiologically linked strains were single-locus variants (SLV) of their respective predominant outbreak clone. This result prompted an investigation into the mutation rates of the seven MLVA loci (TR1 to TR7). With an outbreak strain that was an SLV at the TR1 locus of the predominant clone, parallel and serial batch culture experiments were performed. In a parallel experiment, none (0/384) of the strains analyzed had mutations at the seven MLVA loci. In contrast, in the two 5-day serial experiments, 4.3% (41/960) of the strains analyzed had a significant variation in at least one of these loci (P < 0.001). The TR2 locus accounted for 85.3% (35/41) of the mutations, with an average mutation rate of 3.5 x 10(-3); the mutations rates for TR1 and TR5 were 10-fold lower. Single additions accounted for 77.1% (27/35) of the mutation events in TR2 and all (6/6) of the additions in TR1 and TR5. The remaining four loci had no slippage events detected. The mutation rates were locus specific and may impact the interpretation of MLVA data for epidemiologic investigations.

DNA, Bacterial↗
PubMed2000

Identification and chromosomal location of a new tandemly repeated DNA in maize.

Two clones of a new family of tandemly repeated DNA sequences have been isolated from a maize random genomic DNA library. MR68 is 410 bp, representing a monomeric unit and MR77 is 1222 bp, containing three units. The copy number was estimated to be about 3000 per 1C maize genome. Its methylation pattern was also determined. Fluorescent in situ hybridization (FISH) indicates that the sequence is located on the subtelomeric region of the long arm of chromosomes 3 and 6, as well as on the satellite of chromosome 6.

Base Sequence↗
PubMed1997

Combined polymorphism associated with a 3-bp deletion in the 5'-flanking region of a tetrameric short tandem repeat at the CYP19 locus.

Allele frequencies for a tetrameric short tandem repeat locus, CYP19, were determined in 220 unrelated Japanese individuals. The frequency distribution was similar to that of a previous report. However, PCR amplification using two sets of primers suggested that one allele consisting of 7 TTTA repeats (the allele 7) was divided into two separate ones, 7P (standard) and 7(-3), which differed in length for 3 bp. Sequence analysis of the two alleles revealed that the smaller 7(-3) had a 3-bp deletion in the 5'-flanking region of the tetrameric repeat. The deletion was also observed as the allele 7(-3) in non-Japanese such as Caucasians and Africans; it was only found in a part of the allele 7 [7(-3)], but not in the other alleles, in all examined populations. In the Japanese population, the deletion was observed in 39.6% of the allele 7, or 24.8% of all of the alleles. When the STR polymorphism at the CYP19 locus was combined with the polymorphic deletion adjacent to the repeat region, the numerical indices of genetic polymorphisms (heterozygosity, polymorphism information content and the power of discrimination) in Japanese rose from 0.541, 0.46 and 0.723 to 0.723, 0.66 and 0.864, respectively. Accordingly, the combined polymorphism at the CYP19 locus can be considered appropriate for hereditary analysis in the field of forensic science.

Alleles↗
PubMed1997

Interlaboratory evaluation of short tandem repeat triplex CTT.

An interlaboratory comparison of typing results for Short Tandem Repeats (STRs) at the GenBank loci HUMCSF1PO, HUMTPOX, HUMTH01, and HUMVWFA31 using the "CTT triplex" and "CTTv quadruplex" has been evaluated. These STRs all have a nominal four basepair (bp) repeat. Seven different samples were distributed to 41 laboratories. The 34 laboratories that returned results used a wide variety of analytical systems. Comparable results were obtained for all samples at all loci when results were reported as an allelic name. Raw sizing results obtained from internal-lane sizing standards differed by nearly five bp at some loci. Many different factors contribute to this observed sizing variability, including choice of sizing standards and matrix composition. Although sizing results can be made more comparable by locus-specific offsets or calibration to a comprehensive set of alleles at each locus, samples typed to the allelic name can now be validly compared regardless of analytical method. Interlaboratory comparison of raw allelic size remains problematic.

Algorithms↗
PubMed2002

Evidence for repeat-induced gene silencing in cultured Mammalian cells: inactivation of tandem repeats of transfected genes.

Foreign DNA can be readily integrated into the genomes of mammalian embryonic cells by retroviral infection, DNA microinjection, and transfection protocols. However, the transgenic DNA is frequently not expressed or is expressed at levels far below expectation. In a number of organisms such as yeast, plants, Drosophila, and nematodes, silencing of transfected genes is triggered by the interaction between adjacent or dispersed copies of genes of identical sequence. We set out to determine whether a mechanism similar to repeat-induced gene silencing (RIGS) is responsible for the silencing of transgenes in murine embryonal carcinoma stem cells. We compared the expression of identical reporter gene constructs in cells carrying single or multiple copies and found that the level of expression per integrated copy was more than 10-fold higher in single-copy integrants. In cells carrying tandem copies of the transgene, many copies were methylated and clones frequently failed to express both copies of near-identical integrated alleles. Addition of extra copies of the reporter gene coding sequence reduced the level of expression from the same reporter driven by a eukaryotic promoter. We also found that inhibitors of histone deacetylase such as trichostatin A forestall the silencing of multicopy transgenes, suggesting that chromatin mediates the silencing of transfected genes. This evidence is consistent with the idea that RIGS does occur in mammalian embryonic stem cells although silencing of single-copy transgenes also occurs, suggesting that RIGS is only one of the mechanisms responsible for triggering transgene silencing.

Animals↗
PubMed2006

Genetic polymorphism at 15 tetrameric short tandem repeat loci in four aboriginal tribal populations of Bengal.

POPULATIONS: This study reports the genetic polymorphism observed at 15 short tandem repeat loci D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433, and FGA in four aboriginal populations of Bengal. The analysis was performed to decipher the suitability of CODIS as well as six other highly polymorphic and unlinked markers in Forensic Testing. Studied populations include four tribes: Karmali, Kora, Maheli, and Lodha.

DNA Fingerprinting↗
PubMed2002

A new pentaplex system to study short tandem repeat markers of forensic interest on X chromosome.

A new method has been optimised to amplify five X chromosome short tandem repeat (STR) markers of interest in forensic medicine: human phosphoribosyl transferase (HPRTB), DXS101, androgen receptor (ARA), DXS7423 and DXS8377. Markers were conveniently amplified in a single PCR reaction with fluorochrome-labelled primers, which allowed the analysis of fragment sizes after injection into a capillary electrophoresis system. The most common alleles of each locus were sequenced and used in a control ladder to type unknown samples.

Adult↗
PubMed2005

Use of a novel panel of nine short tandem repeats for exact and high-resolution fingerprinting of Aspergillus fumigatus isolates.

Here we describe a new panel of short tandem repeats (STRs) for a novel exact typing assay that can be used to discriminate between Aspergillus fumigatus isolates. A total of nine STR markers were selected from available genomic A. fumigatus sequences and were divided into three multicolor multiplex PCRs. Each multiplex reaction amplified three di-, tri-, or tetranucleotide repeats, respectively. All nine STR markers were used to analyze 100 presumably unrelated A. fumigatus isolates. For each marker, between 11 and 37 alleles were found in this population. One isolate proved to be a mixture of at least two different isolates. With the remaining 99 isolates, 96 different fingerprinting profiles were obtained. The Simpson's diversity index for the individual markers ranged from 0.77 to 0.97. The diversity index for the multiplex combination of di-, tri-, and tetranucleotide repeats ranged from 0.9784 to 0.9968. The combination of all nine markers yielded a Simpson's diversity index of 0.9994, indicative of the high discriminatory power of these new loci. In theory, this panel of markers is able to discriminate between no less than 27 x 10(9) different genotypes. The multicolor multiplex approach allows large numbers of markers to be tested in a short period of time. The exact nature of the assay combines high reproducibility with the easy exchange of results and makes it a very suitable tool for large-scale epidemiological studies.

Aspergillus fumigatus↗
PubMed2004

Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis.

BACKGROUND: Yersinia pestis, the agent of plague, is a young and highly monomorphic species. Three biovars, each one thought to be associated with the last three Y. pestis pandemics, have been defined based on biochemical assays. More recently, DNA based assays, including DNA sequencing, IS typing, DNA arrays, have significantly improved current knowledge on the origin and phylogenetic evolution of Y. pestis. However, these methods suffer either from a lack of resolution or from the difficulty to compare data. Variable number of tandem repeats (VNTRs) provides valuable polymorphic markers for genotyping and performing phylogenetic analyses in a growing number of pathogens and have given promising results for Y. pestis as well. RESULTS: In this study we have genotyped 180 Y. pestis isolates by multiple locus VNTR analysis (MLVA) using 25 markers. Sixty-one different genotypes were observed. The three biovars were distributed into three main branches, with some exceptions. In particular, the Medievalis phenotype is clearly heterogeneous, resulting from different mutation events in the napA gene. Antiqua strains from Asia appear to hold a central position compared to Antiqua strains from Africa. A subset of 7 markers is proposed for the quick comparison of a new strain with the collection typed here. This can be easily achieved using a Web-based facility, specifically set-up for running such identifications. CONCLUSION: Tandem-repeat typing may prove to be a powerful complement to the existing phylogenetic tools for Y. pestis. Typing can be achieved quickly at a low cost in terms of consumables, technical expertise and equipment. The resulting data can be easily compared between different laboratories. The number and selection of markers will eventually depend upon the type and aim of investigations.

Africa↗
PubMed2006

[Polymorphisms analysis of short tandem repeat loci D21S1433, D21S1442, D21S1444, D21S2051 in Guangdong Han nationality in China].

OBJECTIVE: To investigate the polymorphic distribution of short tandem repeat (STR) sequences D21S1433, D21S1442, D21S1444, D21S2051 in Guangdong Han nationality in China. METHODS: Using quantitative fluorescens PCR technology, the authors analyzed 200 unrelated samples to acknowledge the allele frequency, heterozygosity and other genetic information. RESULTS: D21S1433, D21S1442, D21S1444, D21S2051 were tested in 200 samples, which were tested to be statistical according to Hardy-Weinberg equilibrium (P> 0.05), 9, 10, 9 and 5 alleles were detected separately in each STRs. The heterozygosity of each STR was 0.818, 0.820, 0.770, and 0.261. The polymorphic information content > 0.7 in D21S1433, D21S1442, D21S1444, while D21S2051 owned only 0.247 polymorphic information. CONCLUSION: D21S1433, D21S1442, D21S1444 are found to have high heterozygosity and polymorphic information content, and they could provide useful markers for genetic purposes, while D21S2051 is not informative in Guangdong Han nationality in China.

Alleles↗