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PubMed2004

[A pedigree with myotonic dystrophy: non-CTG, non-CCTG repeat expansion].

OBJECTIVE: Two genetic loci are associated with the myotonic dystrophy (DM) phenotype: DM1 DMPK on chromosome 19, and DM2 ZNF9 on chromosome 3. The aim of this study was to investigate the molecular genetics of a pedigree with DM. METHODS: In twenty-six individuals from a family with DM, the CTG repeats in DMPK and CCTG repeats in ZNF9were evaluated genetically, using Long Expand trade mark Template polymerase chain reaction (PCR), Southern blotting and genomic scanning. RESULTS: The numbers of CTG and CCTG repeat were all in normal range. There was no significant difference between the CTG repeat size in DMPK gene and that 4 years later from the same individual. The Lod score values with short tandem repeats STR markers chosen in 19q and 3q were all smaller than 1, which suggested that no STR marker was linked with this DM family. CONCLUSION: There might be some other mutant in this DM pedigree. Further study should be done to find the genetic basis of this pedigree.

Adolescent↗
PubMed1997

[Distribution of alleles of microsatellite loci HUMCYAR04 and D19S253 in population samples of two Russian cities].

In population samples of Moscow and Tomsk, allelic polymorphism of microsatellite loci HUMCYAR04 and D19S253 was studied by polymerase chain reaction. Seven HUMCYAR04 alleles (181-205 bp) and nine alleles (208-240 bp) of the D19S253 locus were identified. In both population samples, the absence of statistically significant differences in the distribution of allele frequencies for these loci was demonstrated. The distribution of the observed genotype frequencies was shown to correspond to the Hardy-Weinberg equilibrium in both populations. Mendelian inheritance of these tandem repeats was demonstrated by an analysis of two large families. The parameters of polymorphism information content for the loci studied were determined; comparative analysis of allele frequencies with corresponding data for a number of populations was performed. These short tandem repeats were proposed for use in personal identification and paternity tests.

Alleles↗
PubMed2004

A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences.

MOTIVATION: One of the most interesting features of genomes (both coding and non-coding regions) is the presence of relatively short tandemly repeated DNA sequences known as tandem repeats (TRs). We developed a new PC-based stand-alone software analysis program, combining sequence motif searches with keywords such as organs, tissues, cell lines or development stages for finding exact, inexact and compound, TRs. Tandem Repeats Analyzer 1.5 (TRA) has several advanced repeat search parameters/options over other repeat finder programs as it does not only accept GenBank, FASTA and expressed sequence tag (EST) sequence files but also does analysis of multifiles with multisequences. Advanced user-defined parameters/options let the researchers use different motif lengths search criteria for varying motif lengths simultaneously. The outputs show statistical results to be evaluated by the user. The discovery of TRs in ESTs could be useful for both gene mapping and association studies and discovering TRs located in coding regions of important genes that are expressed under various conditions of environment, stress, organ, tissue and development stage. RESULTS: In this paper, we demonstrated applications of TRA using 175 899 ESTs sequences for three Arabidopsis spp. downloaded from GenBank. The EST-SSRs/ESTs ratios were found 43.1%, 15.3% and 2.34% in A.lyrata, A.thaliana and A.halleri, respectively. Analysis revealed that organs, tissues and development stages possessed different amounts of repeats and repeat compositions. This indicated that the distribution of TRs among the tissues or organs may not be random differing from the untranscribed repeats found in genomes. AVAILABILITY: The program can be obtained free by anonymous FTP from ftp.akdeniz.edu.tr/Araclar/TRA.

Arabidopsis↗
PubMed2001

Evaluation of a quadruplex short atandem repeat system (HUMVWA31/A, HUMD11S554, HUMAPOAI1, and HUMACTBP2 loci) for forensic identity testing, confident typing of complex alleles, and population databases.

AIM: To evaluate a quadruplex short tandem repeat (STR) system based on the amplification of allelic products from HUMVWA31/A, HUMD11S554, HUMACTBP2, and HUMAPOAI1 loci for routine identity testing in forensic casework, and to provide details for the construction of a "multiplex allelic ladder" for confident typing of complex alleles from the quadruplex STR system and compiling a database for three representative populations living in Northern Norway (Norwegian, Saami, and Russian/Ukrainian). METHODS: The constructed "multiplex allelic ladder" consisted of 44 regularly spaced and uniform alleles, spanning from 135 to 333 bp, and included 9 HUMVWA31/A alleles (TCTA repeat unit), 9 HUMD11S554 alleles (AAAG repeat unit), and 26 HUMACTBP2 alleles (AAAG repeat unit). Confident typing of selected complex alleles from the quadruplex STR system was secured only when they were compared with their matching ladder composed of the same repetitive unit as in our constructed "multiplex allelic ladder". Using different fluorescent dyes, PCR products from the quadruplex STR system were sized with constructed allelic ladder (red labeled) in one lane. RESULTS: Population database was established for unrelated Norwegians (n=141), Saami (n=78), and Russians/Ukrainians (n=138). Combined paternity exclusions were 99.86%, 99.94%, 99.95% and the values of probability of match were 8.0x10-8, 1.4x10-8, and 1.1x10-8, in Saami, Norwegians, and Russians/Ukrainians, respectively. CONCLUSION: We conclude that by applying our constructed allelic ladder a confident typing of alleles from our quadruplex STR system may be ensured. Further, the high efficiency of the selected loci makes this system a reliable tool for use in forensic casework.

Alleles↗
PubMed2004

Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFlSTR Identifiler PCR Amplification Kit.

Analysis of length polymorphism at short tandem repeat (STR) loci utilizing the polymerase chain reaction (PCR) process has proven to be an ideal assay for human identification purposes. The short length of STR loci coupled with the amplification of target sequence through PCR allows for a robust, sensitive, and specific assay for highly polymorphic markers. A multiplex containing fifteen STR loci plus the gender-determining locus Amelogenin was developed to provide a single amplification/detection of all CODIS (Combined DNA Index System) STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA) as well as two internationally-accepted STRs (D2S1338 and D19S433). By incorporating five-dye fragment analysis technology and non-nucleotide linkers, previously optimized AmpFlSTR kit primer sequences have been maintained. This kit has been developed in accordance with the standards of the forensic community as defined by the DNA Advisory Board. Validation studies were performed to include developmental validation, and the results support the use of the AmpFlSTR Identifiler PCR Amplification Kit for human identity and parentage testing.

Animals↗
PubMed2025

tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets.

SUMMARY: "tidk" (short for telomere identification toolkit) uses a simple, fast algorithm to scan long DNA reads for the presence of short tandemly repeated DNA in runs, and to aggregate them based on canonical DNA string representation. These are telomeric repeat candidates. Our algorithm is shown to be accurate in genomes for which the telomeric repeat unit is known and is tested across a wide variety of newly assembled genomes to uncover new telomeric repeat units. Tools are provided to identify telomeric repeats de novo, scan genomes for known telomeric repeats, and to visualize telomeric repeats on the assembly. "tidk" is implemented in Rust and is available as a command line tool which can be compiled using the Rust toolchain or downloaded as a binary from bioconda. AVAILABILITY AND IMPLEMENTATION: The "tidk" Rust crate is freely available under the MIT license (https://crates.io/crates/tidk), and the source code is available at https://github.com/tolkit/telomeric-identifier.

Telomere↗
PubMed1996

A replicational model for DNA recombination between direct repeats.

DNA rearrangement (recombination) mediated by direct repeats is a major cause of genome instability. In Escherichia coli, direct repeats in close proximity can mediate efficient recA-independent intramolecular recombination, which produces multiple products. Using plasmid substrates, three basic forms of products have been revealed: the monomeric deletion product and two dimeric products. The frequency of recombination has been shown to be affected by structural factors such as the length of the repeat and the distance between the repeats. We show here that these factors also affect the relative abundance of each form of the product. Recombination between very short tandem repeats yields exclusively the monomeric product. Lengthening the repeats increases the abundance of the dimeric products. Increasing the distance separating the repeats sharply reduces the formation of the monomeric product. These results can be explained by a model for DNA rearrangement (recombination) involving DNA replication. We propose that misalignment of the repeats at the replication fork creates a recombinogenic intermediate that can be differentially processed to form the three basic products. The proposed sister-strand recombination mediated by direct repeats might be a general mechanism for deletion and/or amplification of repeated sequence in both prokaryotic and eukaryotic genomes.

DNA Replication↗
PubMed2001

New alleles and mutational events in D12S391 and D8S1132: sequence data from an eastern German population.

To investigate the DNA mutation rate and pattern in the hypervariable short tandem repeat (STR) locus D12S391 and in the locus D8S1132, samples from an eastern German population (Dresden area) were analysed. A duplex PCR was applied, using short amplification products for D12S391 (129-177bp) and a modified reverse primer for D8S1132 (127-182bp). The sequences of some rare and new variant alleles are described. At the locus D12S391, 13 regular and six incomplete alleles with different lengths were found, exhibiting several sequence structures. Two isolated father/child mismatches were observed in a total of 648 meioses. Novel alleles 13.1, 14.1 and 27 were discovered at the locus D8S1132. Three parent/child mismatches were found in a total of 672 meioses.

Adult↗
PubMed1995

Recurrent simple tandem repeat mutations during human Y-chromosome radiation in Caucasian subpopulations.

The haplotypes at four polymorphic loci of the Y chromosome were determined in 245 Caucasian males from 12 subpopulations. The data show that haplotype radiation occurred among Caucasians. Haplotype radiation was accompanied by recurrent mutations at STR loci that caused partial randomization of haplotype structure. The present distribution of alleles at short tandem repeats (STRs) can be explained by a mutation pattern similar to those described for autosomal STRs. The degree of variation among groups of subpopulations was assayed by using the Analysis of Molecular Variance. The results confirm a faster divergence of the Y chromosome as compared to the rest of the genome.

Haplotypes↗
PubMed2000

Extended structural variation of a pentanucleotide repeat in the GSTP1 gene: characterisation in a normal population and in thyroid and gastric tumours.

The promoter region of the human GSTP1 gene contains a polymorphic short tandem repeat (STR) locus consisting of pentanucleotide repeat units (ATAAA). In this work we report the existence of a total of 26 alleles in a Caucasian population. While differences in size (ranging from one to five base pairs) were responsible for the major variation, in five size-defined classes, two alternative sequences were found. Automatic fragment sizing and sequencing analysis revealed that this polymorphism is of a highly complex nature in contrast with previous reports. A genetic population study was carried out on a random sample from Portugal showing no deviation from Hardy-Weinberg equilibrium. Somatic instability studies were also performed on gastric and thyroid tumours using this STR: no instability was detected in thyroid tumour tissues when compared with their normal counterpart but in gastric tumour tissues microsatellite instability (MSI) was detected in 9.6% of the cases and loss of heterozygosity (LOH) also in 9.6% of the cases studied. The results obtained with GSTP1 in gastric cancer were compared with previously reported data on MSI using BAT-26 and several dinucleotide repeat markers.

Alleles↗
PubMed1989

Tandem repeated sequences within the terminal region of the fowlpox virus genome.

A 6.2 kb BamHI terminal fragment from fowlpox virus has been cloned and the nucleotide sequence was determined. The fragment was cloned by S1 digestion of viral DNA and therefore does not contain the covalently closed terminal loop. The cloned sequences comprise a short (230 bp) unique region at the terminal end, which is adjacent to a 3.87 bp long, AT-rich region consisting of sets of short tandemly repeated units, 32 and 56 bp long. The remainder of the fragment is composed of a 2.18 kb unique region containing three major open reading frames. The amino acid sequence encoded by one of these has some similarity to that of platelet-derived growth factor.

Amino Acid Sequence↗
PubMed1992

Organization of repeated sequences in the region downstream to rRNA genes in the rDNA episome of Entamoeba histolytica.

The E. histolytica rDNA episome consists of a 3.7 kb HindIII fragment located downstream of the rDNA inverted repeats. We have determined the complete nucleotide sequence of this fragment and have shown that it is comprised of two families of short tandem repeats, the 170 bp DraI repeat and the 144 bp ScaI repeat. Each DraI repeat unit consists of 12-mer sequences with near complete homology to yeast consensus autonomously replicating sequence. In addition, a 21-mer subrepeat structure is also present in each unit. The sequence of the ScaI repeat is about 90% homologous with the sequence of another family of 145 bp tandem repeats, the PvuI repeats reported to be present upstream of the rRNA genes (3). Compared with most other parts of the rDNA episome, the downstream region showed frequent restriction fragment length polymorphism. This was due to changes in the number of tandem DraI repeat units. The loss of these repeats might explain how rDNA length heterogeneity observed in the clones of HM1:IMSS could have arisen. On the other hand, the number of ScaI repeat units in these clones remained unchanged. The repeat units found in the 3.7 kb HindIII fragment show superficial resemblance to equivalent regions of the intergenic spacers of higher eukaryotes. Moreover, these repeated sequences seem to be specific for the pathogenic strain of E. histolytica.

Animals↗
PubMed2005

Sex differences in clinical and genetic determinants of levodopa peak-dose dyskinesias in Parkinson disease: an exploratory study.

BACKGROUND: Several factors, both clinical and genetic, may account for the risk of developing levodopa-induced peak-dose dyskinesias (PDD) in patients with Parkinson disease, but it is unclear how these factors interact for modulating the individual susceptibility for PDD. OBJECTIVE: To examine clinical and genetic risk factors for determining individual susceptibility of PDD in patients with Parkinson disease. DESIGN: Cohort study. SETTING: Referral center for Parkinson disease in Calabria, southern Italy. Patients Two hundred fifty patients with Parkinson disease were screened for the presence or absence of PDD following a short-term levodopa administration, and 215 subjects were available for further evaluations, including genotypic analysis of the CA dinucleotide short tandem repeat (CAn-STR) polymorphism located in the dopamine receptor D2 gene (DRD2). RESULTS: One hundred five patients (48.8%) exhibited PDD following short-term levodopa administration, and 110 patients (51.2%) did not. Multivariate logistic regression analysis showed that independent predictors for the occurrence of PDD were female sex, earlier age at onset of Parkinson disease, longer duration of treatment, and higher dose of levodopa. Genetic factors related to the DRD2 CAn-STR polymorphism were not independent predictors for PDD in the total population, but they had a strong protective effect on the appearance of PDD when the multivariate analysis was performed in men (odds ratio, 0.34 [95% confidence interval, 0.14-0.84]). In women, a genetic protective effect on PDD was not evident. CONCLUSIONS: Risk factors for PDD, both clinical and genetic, act in different ways for men and women. Genetic factors related to the DRD2 polymorphic status have a protective effect on PDD development in men but not in women. A female sex-related effect for the risk of PDD may be so strong that it overcomes any protective effect due to genetic factors.

Age of Onset↗
PubMed1997

Sequence polymorphism at the tetranucleotide repeat of the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus.

The tetranucleotide repeat polymorphism in the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus has become a widely used short tandem repeat (STR) system in paternity testing and human identification. The discrimination index of this locus has been reported to be as high as 99.65%. To study the overall variability of this locus, 222 alleles were sequenced in our laboratory. Here, we report the sequences of the 102 different alleles observed. In addition to the length polymorphism, up to ten different sequence variants for single fragment lengths have been detected.

Actins↗
PubMed2001

Automated fluorescence analysis of CAG repeats at the human androgen receptor gene (HUMARA): evaluation of polymorphism in an Italian sample and report of a new allele.

The HUMARA CAG repeats polymorphism was studied in an Italian population sample. Polymerase chain reaction amplification and automated fluorescent analysis were used. A total of 19 and 15 repeats was observed in female and male subjects, respectively, and one new allele was found. The authors conclude that this X-linked short tandem repeat, typed without ambiguity and with a heterozygosity of 0.902, is useful in parentage testing of female subjects.

DNA↗
PubMed1990

Highly repetitive DNA sequences in cyanobacterial genomes.

We characterized three distinct families of repeated sequences in the genome of the cyanobacterium Calothrix sp. strain PCC 7601. These repeated sequences were present at a level of about 100 copies per Calothrix genome and consisted of tandemly amplified heptanucleotides. These elements were named short tandemly repeated repetitive (STRR) sequences. We used the three different Calothrix STRR sequences as probes to perform Southern hybridization experiments with DNAs extracted from various cyanobacterial strains, Bacillus subtilis, and Escherichia coli. The three different STRR sequences were found as repetitive genomic DNA components specific to the heterocystous strains tested. The role of the STRR sequences, as well as their possible use in taxonomic studies, is discussed.

Bacillus subtilis↗
PubMed1996

Loss of heterozygosity analysis defines a critical region in chromosome 1p22 commonly deleted in human malignant mesothelioma.

Previous cytogenetic analysis has revealed frequent losses of chromosome 1p21-22 in human malignant mesothelioma, suggesting that the loss or inactivation of a tumor suppressor gene's) residing at this site may contribute to the tumorigenic conversion of mesothelial cells. To more precisely define the location of the target gene, primary tumor specimens and cell lines from 50 malignant mesotheliomas were examined for loss of heterozygosity using short tandem repeat polymorphism (STRP) markers. Nineteen STRP markers established by the Cooperative Human Linkage Center were selected for the initial screening of the entire short arm of chromosome 1. Thirty-seven cases (74%) showed allelic losses at least at one locus in 1p. Thirty-six of these cases showed losses of 1p21-22, including 23 with partial deletions involving this region. To obtain a higher resolution map of this region, another 13 STRP markers from the Genethon map were used to define the shortest region of overlapping deletions to a 4-cM segment flanked by the loci D1S435 and D1S236. The chromosomal location of the critically deleted region was confirmed to be within 1p22 by karyotypic and fluorescence in situ hybridization analyses.

Chromosomes, Human, Pair 1↗
PubMed2001

[Schizophrenia and dopamine D4 gene polymorphism in Chinese population: association analysis].

OBJECTIVE: To investigate the association of the 48 bp variable number tandem repeat (VNTR) polymorphism in the dopamine D4 receptor (DRD4) gene exon III with schizophrenia in Chinese Han population. METHODS: Case-control association study was adopted to analyze the association between the 48 bp VNTR polymorphism of DRD4 gene exon III in 510 DSM-IV schizophrenics and 171 psychiatrically normal controls. RESULTS: (1) The DRD4 gene 48 bp VNTR polymorphism was manifested as 2-7 repeats, with the 4 repeats the most common (78.6% in schizophrenics and 76.9% in controls respectively). The frequency of 2 repeats was 16.2% and 19.3% in the schizophrenics and controls respectively. (2) The genotypic frequency was statistically significantly different between the schizophrenics and the controls. The genotypic frequency of short tandem repeats (2/2 and 2/3 genotype) was lower in patients (3.3%) than in controls (10.5%) (chi 2 = 14.88, df = 2, P = 0.00). (3) the frequency of the genotype with 4-repeat allele in patients was higher (95.9%) than in controls (88.3%) (chi 2 = 13.00, df = 1, P = 0.000). CONCLUSION: The most common allele in Chinese schizophrenics was 4 repeats in the 48 bp VNTR polymorphism of DRD4 gene exon III. The repeat number of 48 bp is probably associated with schizophrenia. Lack of 2-3 repeats or excess of genotype with 4-repeat allele may be associated with increased vulnerability to schizophrenia.

Adult↗