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At least 793 records · Page 44Linked to original sources
PubMed2006

The variable number of tandem repeats upstream of the insulin gene is a susceptibility locus for latent autoimmune diabetes in adults.

The etiopathological relationship between latent autoimmune diabetes in adults (LADA) and classical type 1 (insulin dependent) diabetes remains unclear. Variation at the insulin gene variable number of tandem repeats (VNTR) minisatellite influences susceptibility to type 1 diabetes, but studies in LADA have been small and inconsistent. We examined the role of insulin gene variation (using flanking variants as surrogates for VNTR subtypes) in the largest case-control study of LADA to date (400 case and 332 control subjects). Highly significant associations were identified with disease, with dominant protective effects of the T allele at -23HphI (odds ratio [OR] 0.42 [95% CI 0.31-0.58], P=2.4 x 10(-8)), A allele at +1,404Fnu4HI (0.50 [0.36-0.70], P=3.2 x 10(-5)), and C allele at +3,580MspI (0.55 [0.35-0.85], P=0.0046). As with type 1 diabetes, the -23HphI variant (a surrogate for the subdivision of VNTR into class I and III alleles) most clearly defined susceptibility in LADA. However, there was no association with age at diagnosis or requirement for insulin therapy 6 years postdiagnosis. This study establishes that variation within the insulin gene region does influence susceptibility to LADA, with the direction and magnitude of effect indistinguishable from that previously reported for type 1 diabetes. In conclusion, differences in VNTR-encoded susceptibility do not explain the differences in clinical presentation that distinguish classical type 1 diabetes and LADA.

Adult↗
PubMed1998

Matrix-assisted laser desorption/ionization for short tandem repeat loci.

Matrix-assisted laser desorption/ionization was used for the detection of four base short tandem repeats (STR) for clinical samples using a time-of-flight mass spectrometer. Since STR plays an important role in genetic disease and human identification, this work indicates that laser desorption mass spectrometry has the potential to achieve rapid DNA typing for both forensic applications and genetic disease diagnosis.

DNA↗
PubMed1998

Forensic validation of the short tandem repeat HUMACTBP2 using capillary electrophoresis.

Experiments were performed to evaluate the forensic identification of the short tandem repeat (STR) HUMACTBP2 (human beta-actin-related pseudogene) using automated fluorescence-based capillary electrophoresis. The HUMACTBP2 is a complex tetranucleotide STR locus with more than 32 alleles in the range of 202-323 bp. The reproducibility of genetic typing using a fluorescent labeled allelic ladder was determined by comparison of the calculated fragment size after consecutive (within-day) and nonconsecutive (day to day) injection. The maximum variation in size (window) observed for any allele was 0.23 bp for the within-day and 0.8 bp for the day-to-day precision. Furthermore, it is possible to achieve a 1 bp resolution, the precision of the reproducibility assays being about 99.95%. Sixty blood samples and twenty stains were typed with both automated fluorescent sequencer ABI 373A and ABI 310. Identical genotypes were obtained with both techniques and the ABI 310 seemed to be more sensitive than the ABI 373A. A population sample of 197 unrelated individuals from southwest Switzerland was analyzed and the genotype frequencies observed were similar to those reported by others. Thirty-one alleles and 126 genotypes were found. The observed heterozygosity was 0.934. Mixtures from two different blood samples varying in their ratio were typed and the minor fraction was detectable to about 1:10. The practical usefulness of the HUMACTBP2 is illustrated by analyzing casework samples. This validation study proves the usefulness of the HUMACTBP2 locus in forensics and the detection efficiency using fluorescent capillary electrophoresis.

Actins↗
PubMed1991

Human variable number of tandem repeat probes as a source of polymorphic markers in experimental animals.

Human VNTR (Variable Number of Tandem Repeat) markers are examined as a source of polymorphism for linkage studies in inbred strains of mice and rats. High frequencies of cross-hybridization are found under fingerprinting conditions that detect many distinct minisatellite loci in these species. Linkage studies suggest that minisatellite markers are widely distributed in the mouse genome, in contrast to humans where they are clustered, particularly in telomeric regions. Human VNTR probes can be used to screen in mouse genomic libraries to isolate mouse specific VNTR sequences. Some of these sequences reveal fingerprint patterns under stringent hybridization conditions.

Animals↗
PubMed1995

A study of the short tandem repeat systems HUMVWA and HUMTH01 in an Austrian population sample.

The genotype distributions for the short tandem repeat systems (STRs) HUMVWA and HUMTH01 have been studied in 128 unrelated Caucasians fromêAustria. The allelic distributions were in accordance with Hardy-Weinberg expectations. The heterozygosities were 0.82 and 0.81, whereas the mean exclusion chance was 0.62 and 0.55, respectively. In one person, a VWA-allele consisting of 11 repeats was found.

Austria↗
PubMed1995

Short tandem repeat (STR) system HumD21S11: population genetic study on an Italian population.

Allele frequencies of the Short Tandem Repeat locus HumD21S11 were determined analysing 119 unrelated individuals from the area of Milano (Northern Italy). A total of 13 alleles was detected. One allele (< 26) was found which has never been observed in a wider German population sample. The system showed neither significant deviation from Hardy-Weinberg equilibrium nor significant differences with a German population sample.

Gene Frequency↗
PubMed1997

Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera.

Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprinid fish Cyprinella spiloptera. Variation at different nucleotide positions in individual repeats supported different models of repeat evolution. One set of characters included several nucleotide variants found in all copies from a limited number of individuals, while the other set included an 8-bp deletion found in a limited number of copies in all individuals. The deletion and an associated nucleotide change appear to be the result of a deterministic, rather than stochastic, mutation process. Parallel origins of repeat arrays in different mitochondrial lineages, possibly coupled with a homogenization mechanism, best explain the distribution of nucleotide variation.

Animals↗
PubMed2005

Use of variable-number tandem repeats to examine genetic diversity of Neisseria meningitidis.

Repetitive DNA motifs with potential variable-number tandem repeats (VNTR) were identified in the genome of Neisseria meningitidis and used to develop a typing method. A total of 146 meningococcal isolates recovered from carriers and patients were studied. These included 82 of the 107 N. meningitidis isolates previously used in the development of multilocus sequence typing (MLST), 45 isolates recovered from different counties in Norway in connection with local outbreaks, and 19 serogroup W135 isolates of sequence type 11 (ST-11), which were recovered in several parts of the world. The latter group comprised isolates related to the Hajj outbreak of 2000 and isolates recovered from outbreaks in Burkina Faso in 2001 and 2002. All isolates had been characterized previously by MLST or multilocus enzyme electrophoresis (MLEE). VNTR analysis showed that meningococcal isolates with similar MLST or MLEE types recovered from epidemiologically linked cases in a defined geographical area often presented similar VNTR patterns while isolates of the same MLST or MLEE types without an obvious epidemiological link showed variable VNTR patterns. Thus, VNTR analysis may be used for fine typing of meningococcal isolates after MLST or MLEE typing. The method might be especially valuable for differentiating among ST-11 strains, as shown by the VNTR analyses of serogroup W135 ST-11 meningococcal isolates recovered since the mid-1990s.

Bacterial Typing Techniques↗
PubMed2005

[Genetic polymorphisms of fifteen short tandem repeat loci in Chengdu Han population].

OBJECTIVE: To acquire the population genetic data of fifteen short tandem repeat (STR) loci in Chengdu Han population. METHODS: A total of 210 EDTA-blood specimens were collected from the unrelated individuals in Chengdu Han population. The DNA samples were extracted with Chelex method and amplified by multiplex PCR technique. The PCR products were analyzed by an automatic genetic analyzer; the relative fragment's lengths of PCR products were calculated by gene scan analysis software and afterward genotyped by genotype software. RESULTS: Fifteen STR loci of the 210 samples showed a successful result of genotyping. The heterozygosities of the fifteen STR loci in Chengdu Han population were found to be 0.529-0.881; the combined exclusion probability and discrimination power for the fifteen STR loci in Chengdu Han population were determined to be 0.999998 and 7.3 x 10 (-17); respectively. CONCLUSION: The distinct genotype of fifteen STR loci and the sex of sample could be unveiled just through PCR and electrophoresis once, and a higher measured value could be obtained for both the combined discrimination power and the exclusion probability; the fifteen STR loci can meet the needs of the parentage testing and personal identification in forensic medicine.

Asian People↗
PubMed2006

Predicting outcomes of HLA-identical allogeneic stem cell transplants from variable number of tandem repeat disparity between donors and recipients.

BACKGROUND AND OBJECTIVES: Detecting differences in the variable number of tandem repeats (VNTR) between a recipient and a donor has already been used to monitor the degree of chimerism after allogeneic stem cell transplantation (SCT). Alongside major histocompatibility complex disparity, the disparity of various polymorphous proteins encoded by several genes may play a critical role in the pathogenesis of graft-versus-host disease (GVHD) in allogenic SCT. However, the biological effect of VNTR disparity has scarcely been studied. BACKGROUND AND OBJECTIVES: Eighty-four patients receiving an SCT from an HLA-identical sibling (n=68) or an unrelated donor (n=16) were analyzed. The patients were transplanted because of acute myeloid leukemia (ns=48), acute lymphoblastic leukemia (n=8), chronic myeloid leukemia (n=15), non-Hodgkin's lymphoma (n=18) and myelodysplastic syndrome (n=3). Polymerase chain reaction analysis was performed to amplify three VNTR regions (D1S80, D1S111, and D17S5). These regions were classified as fully matched, partially matched, or mismatched between donors recipients. RESULTS: A strong correlation was observed between D1S80 matching status and transplant outcomes in terms of overall survival (p=0.0179) and non-relapse mortality (p=0.0305), but not for the D1S111 or D17S5 disparity. The fully matched D1S80 pairs showed a better overall survival (72% vs 38%) and lower non-relapse mortality (17% vs 50%) compared to the partially matched or mismatched pairs. In multivariate analyses, a fully matched D1S80 pair was found to be an independent favorable prognostic factor for overall survival (p=0.03) and non-relapse mortality (p=0.05). In addition, D1S80 disparity was significantly associated with the occurrence of gut chronic GVHD (p=0.05). INTERPRETATION AND CONCLUSIONS: The present data suggest that disparities in D1S80--located in chromosome 1--are associated with an increased incidence of gut chronic GVHD and non-relapse mortality.

Adolescent↗
PubMed1994

Rapid analysis of the short tandem repeat HUMTH01 by capillary electrophoresis.

Using capillary electrophoresis, we demonstrate separation and analysis of the short tandem repeat HUMTH01 in under 10 min with 3 bp resolution. Separation of the PCR products, which range in size from 179 to 203 bp, is achieved using hydroxyethyl cellulose as the separation medium and a novel single-step voltage gradient. Internal standards on either side of the alleles are used to size the PCR products with an average standard deviation of 0.5 bp. DNA typing patterns obtained with this system are compared to samples separated by polyacrylamide slab gel electrophoresis.

Cellulose↗
PubMed1996

Establishing the robustness of short-tandem-repeat statistics for forensic applications.

Before the introduction of a four-locus multiplex short-tandem-repeat (STR) system into casework, an extensive series of tests were carried out to determine robust procedures for assessing the evidential value of a match between crime and suspect samples. Twelve databases were analyzed from the three main ethnic groups encountered in casework in the United Kingdom: Caucasians, Afro-Caribbeans, and Asians from the Indian subcontinent. Independence tests resulted in a number of significant results, and the impact that these might have on forensic casework was investigated. It is demonstrated that previously published methods provide a simple procedure for correcting allele frequencies--and that this leads to conservative casework estimates of evidential value.

Alleles↗
PubMed1995

[The variable number of tandem repeats in the renin gene of rats and possible significance in hypertension].

The variable number of tandem repeats (VNTR) in the first intron of renin gene for the spontaneously hypertensive rat (SHR), its controls Wistar-Kyoto (WKY), renal hypertensive rat, and Sprague-Dawley rat (SD) were compared by polymerase chain reaction (PCR) method. An analysis of VNTR from WKY, Wistar and SD showed that there are two different renin gene alleles and three genetypes 2.0kb/2.0kb, 2.0kb/1.8kb, 1.8kb/1.8kb. The genetype from renal hypertensive rats is same as those seen in the normal controls. However, compared with the WKY, Wistar and SD genes, a "deletion" of approximately 1.0kb was found in the first intron of the SHR renin gene. Our results strongly suggest that the cause and mechanism of elevated blood pressure is complex, and the molecular basis of the genetic-prone hypertension is existed.

Animals↗
PubMed2024

Sequencing the orthologs of human autosomal forensic short tandem repeats provides individual- and species-level identification in African great apes.

BACKGROUND: Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. RESULTS: The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. CONCLUSIONS: Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

Animals↗
PubMed1999

DNA methylation pattern of a tandemly repeated LacZ transgene indicates that most copies are silent.

The Pgk-1,2-lacZ transgene consists of the ubiquitously-expressed Pgk-1 promoter driving expression of the E. coli lacZ reporter gene. We studied the expression of this transgene in a mouse strain carrying 8-9 tandem copies of this construct. When inherited through the male germ line, the transgene was expressed in all tissues examined but when inherited through the female germ line, the transgene became irreversibly inactivated. The lacZ region is a CpG-rich island that was essentially entirely methylated in all copies of the silent, maternally-inherited transgene. At the active transgenic locus, all but one of the copies were entirely methylated. This one unmethylated copy was adjacent to the cellular DNA and was presumed to be the expressed transgene copy. These results suggest that the tandem repeats of transgenes become silenced by a mechanism associated with DNAmethylation and that proximity to the cellular genome may be important in maintaining expression against the spread of inactivation from the adjacent silent transgenes.

Animals↗
PubMed2025

Polygenic variants in DNA repair genes are associated with neurodevelopmental disorders, regression and increased burdens of somatic variants and short tandem repeat expansions.

PURPOSE: Developmental regression, characterized by the loss of acquired milestones, occurs in some individuals with neurodevelopmental disorders (NDDs); yet, its molecular basis remains unclear. Studies suggest that DNA damage repair (DDR) genes, such as FAN1, may protect against neurological dysfunction by modulating the somatic stability of short tandem repeats (STRs). This study explores the contribution of DDR gene variants in NDD cases presenting with regression. METHODS: We analyzed 1087 NDD patients, focusing on those carrying variants in DDR genes and presenting regression. We assessed the sensitivity to DNA damage using mitomycin C on lymphoblastoid cells. Somatic variants and STR expansions were evaluated through high-depth short-read genome sequencing. To further investigate the pathogenetic role of STR expansions, we performed long-read genome sequencing on the most severely affected proband. RESULTS: Probands with regression carried multiple DDR gene variants, several within the Fanconi anemia pathway. Their lymphoblastoid cells showed increased sensitivity to mitomycin C-induced cytotoxicity compared with parental and control samples. Probands with severe phenotypes and regression exhibited an accumulation of somatic variants and STR instability, enriched in neurodevelopmental genes. CONCLUSION: Our findings suggest that polygenic DDR gene variants may contribute to developmental regression in NDDs by promoting the accumulation of somatic variants and STR expansions.

Humans↗
PubMed2001

Extensive allelic variation among Francisella tularensis strains in a short-sequence tandem repeat region.

Members of the genus Francisella and the species F. tularensis appear to be genetically very similar despite pronounced differences in virulence and geographic localization, and currently used typing methods do not allow discrimination of individual strains. Here we show that a number of short-sequence tandem repeat (SSTR) loci are present in F. tularensis genomes and that two of these loci, SSTR9 and SSTR16, are together highly discriminatory. Labeled PCR amplification products from the loci were identified by an automated DNA sequencer for size determination, and each allelic variant was sequenced. Simpson's index of diversity was 0.97 based on an analysis of 39 nonrelated F. tularensis isolates. The locus showing the highest discrimination, SSTR9, gave an index of diversity of 0.95. Thirty-two strains isolated from humans during five outbreaks of tularemia showed much less variation. For example, 11 of 12 strains isolated in the Ljusdal area, Sweden in 1995 and 1998 had identical allelic variants. Phenotypic variants of strains and extensively cultured replicates within strains did not differ, and, for example, the same allelic combination was present in 55 isolates of the live-vaccine strain of F. tularensis and another one was present in all 13 isolates of a strain passaged in animals. The analysis of short-sequence repeats of F. tularensis strains appears to be a powerful tool for discrimination of individual strains and may be useful for a detailed analysis of the epidemiology of this potent pathogen.

Alleles↗
PubMed2005

Responses of human T cells to peptides flanking the tandem repeat and overlapping the signal sequence of MUC1.

The epithelial mucin MUC1 is one of the few tumour-associated antigens identified for breast cancer. Several MUC1-derived peptides binding HLA-A*0201 molecules have been identified that correspond to sequences outside the tandem repeat. Immunisation with some of these peptides induces protective antitumour immunity in mice. Another HLA-A*0201-binding peptide has been identified in a human system. We have evaluated the CD8(+) T-cell responses to all these peptides using peripheral blood lymphocytes from breast cancer patients and normal donors. Specific CD8(+) T-cell responses could be generated in vitro against some of these peptides but only after several rounds of in vitro restimulation, and they did not recognise human cells endogenously expressing the antigen. Nevertheless, T cells recognised by HLA-A*0201 tetramers carrying a peptide from the signal sequence (LLLLTVLTV) could be detected in the peripheral blood of some HLA-A*0201(+) breast cancer patients but not in healthy adults. This peptide is the only one of those tested which was identified in the human system, and the results emphasize the potential problems involved in translation of data from laboratory animal models to the human system.

Animals↗