SEARCH · Search PubMed

Results for “tandem repeat”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources

PubMed1993

Primary structure of the variable regions of a monoclonal antibody MUSE11 recognizing the tandem repeat domain of a mucin core protein, MUC1.

A monoclonal antibody (MAb) MUSE11 recognizes an epitope in the tandem repeat domain of a mucin core protein, MUC1. We show that the epitope of MAb MUSE11 could be within the continuous amino acid sequence PDTRPAPG. Since there is increasing evidence indicating that this region is highly immunogenic, cDNA cloning of the variable regions of heavy-chain (VH) and of light-chain (VL) of MAb MUSE11 was performed by using RT-PCR to provide a basis for analyzing the structure of the antibody-antigen complex and for producing anti-idiotypic antibodies. The deduced amino acid sequence revealed that the VH and VK of MAb MUSE11 could be assigned to subgroups IIIA and II of mouse immunoglobulin heavy and light chains, respectively. When compared with the V regions of other MAbs in the same subgroup, the complementary determining region 3 (CDR3) in the VH region of MAb MUSE11 consisted of a unique sequence that may be important in defining the specificity of MAb MUSE11.

Amino Acid Sequence↗

PubMed1994

The validation of short tandem repeat (STR) loci for use in forensic casework.

A quadruplex reaction has been developed which amplifies the short tandem repeat (STR) loci HUM-VWA31/A, HUMTHO1, HUMF13A1 and HUMFES/FPS. Detection of the PCR products employs denaturing polyacrylamide gels coupled with fluorescent-based technology. This system has been evaluated for use in routine forensic casework and has been shown to be both robust and reproducible. The quadruplex reaction is as sensitive as the commercially available HLA DQ alpha Amplitype typing system and can be used on both degraded and aged material. The problems of environmental contamination have been shown to be limited provided strict procedural practices are followed-i.e. physical separation of sample extraction and amplified products; the use of dedicated equipment such as pipettes; the separation of amplification preparation area. The ability of the system to detect mixtures and the successful analysis of case stains has shown that this system is well suited as a tool for forensic investigation.

Alleles↗

PubMed1995

Structural variation of novel alleles at the Hum vWA and Hum FES/FPS short tandem repeat loci.

This paper reports the sequences of novel alleles identified during population databasing studies on the short tandem repeat loci HumvWA and HumFES/FPS. Two HumFES/FPS alleles follow the simple repeat pattern (ATTT)7 and (ATTT)15. Sequence variation corresponding to an A to C transversion occurred in the 5' flanking region in two individuals possessing the designated allele 7. Two HumvWA alleles exhibited compound repeat regions comprising TCTA and TCTG repeat units. Sequence analysis confirmed the putative designation of 11 for a 127 base pair allele. However, a 131 base pair allele, putatively designated as 12, exhibited a more complex sequence. Two different types of repeat unit structures were identified which also exhibited sequence variation in the 3' flanking region.

Alleles↗

PubMed1997

Short tandem repeat HumACTBP2 (SE33) and HumVWA: population genetic study on a north Italian population.

Allele frequencies at the short tandem repeat (STR) loci HumACTBP2 and HumVWA were determined in 118 unrelated individuals from Northern Italy (Milan area). For locus HumACTBP2 (SE33) a total of 39 alleles was observed. Furthermore, two interalleles (N18m+N19m) and one allele (> N35) were found which were not observed in a wider German population survey (n = 560). For the STR system HumVWA, 7 alleles could be detected. Both systems showed no significant deviation from Hardy-Weinberg equilibrium. A comparison of Italian and German population data revealed no significant differences for locus HumVWA, while significant differences were observed for locus HumACTBP2.

Actins↗

PubMed1999

Variable number tandem repeat dopamine transporter gene polymorphism and Parkinson's disease: no association found.

We studied a variable number of tandem repeat polymorphisms in the dopamine transporter gene in search of an association with Parkinson's disease in a French population. Five alleles were detected, consisting of 7, 8, 9, 10 and 11 copies of the 40-base pair repeat sequence, of which the 10-copy allele was the most common. There was no significant difference between the patients and the control subjects in the distribution frequencies of the alleles or genotypes, or in ages at onset in patients between the main allelic classes.

Adult↗

PubMed2002

A variable number of tandem repeats in the serotonin transporter gene does not affect the antidepressant response to fluvoxamine.

A variable number of tandem repeats (VNTR) in the second intron of the serotonin transporter gene (STin2) has been studied in association with the susceptibility to affective disorders. Recently, it was reported that selective serotonin reuptake inhibitors were more effective in patients with major depressive disorder having the homozygous allele pair (12-copy/12-copy) of VNTR in the STin2 than in ones having other allele combinations. As the study had methodological problems, further studies are needed to confirm the above finding. Therefore, the authors investigated whether the allelic variation of VNTR in the STin2 was associated with the antidepressant response to fluvoxamine in 66 patients with major depressive disorder. Fluvoxamine was prescribed up to 200 mg/day in the dosing protocol for 6 weeks. The present study showed no significant association between the polymorphism of VNTR in the STin2 and the treatment response to fluvoxamine.

Adult↗

PubMed1998

The INS 5' variable number of tandem repeats is associated with IGF2 expression in humans.

The minisatellite DNA polymorphism consisting of a variable number of tandem repeats (VNTR) at the human INS (insulin gene) 5'-flanking region has demonstrated allelic effects on insulin gene transcription in vitro and has been associated with the level of insulin gene expression in vivo. We now show that this VNTR also has effects on the nearby insulin-like growth factor II gene (IGF2) in human placenta in vivo and in the HepG2 hepatoma cell line in vitro. We show that higher steady-state IGF2 mRNA levels are associated with shorter alleles (class I) than the longer class III alleles in term placentae. In vitro, reporter gene activity was greater from reporter gene constructs with IGF2 promoter 3 in the presence of class I alleles than from those with class III. Taken together with the documented transcriptional effects on the insulin gene, we propose that the VNTR may act as a long range control element affecting the expression of both INS and IGF2. The localization of a type 1 diabetes susceptibility locus (IDDM2) to the VNTR itself suggests that either or both of these genes may be involved in the biologic effects of IDDM2.

Alleles↗

PubMed1993

Automated DNA profiling employing multiplex amplification of short tandem repeat loci.

We have employed automated fluorescence-based technology to detect amplified tri-, tetra-, and pentanucleotide short tandem repeat (STR) loci electrophoresed on denaturing polyacrylamide sequencing gels. The system described incorporates an internal size standard in each sample, allowing the STR-PCR products to be sized automatically with a high degree of precision. By utilizing different fluorescent dye markers for loci that have overlapping allele size ranges, we have developed three multiplex STR systems containing a total of 14 different loci. These multiplex systems were then used to evaluate the usefulness of the 14 loci for the identification of individuals. Allele frequency data were collected from a minimum of 50 individuals from each of three different racial groups: Caucasians, Afro-Caribbeans, and Asians. Of the resulting 42 locus population sets, deviation from Hardy-Weinberg equilibria was detected in only the STR HUMCYARO3-Caucasian data. The probabilities of two unrelated individuals matching by chance (pM) at all 14 loci in the three multiplex reactions was < 1 x 10(14). The combination of multiplex STR-PCR and automatic fluorescence-based detection is thus a rapid and powerful technique for individual identification.

Autoanalysis↗

PubMed1998

'Epitope fingerprinting' using overlapping 20-mer peptides of the MUC1 tandem repeat sequence.

The ISOBM TD-4 Workshop antibodies 122-177 were tested for reactivity with 20 overlapping MUC1 tandem repeat 20-mer peptides by an ELISA, in order to determine the complete amino acid sequences of the epitopes. Of the 56 antibodies studied, 30 showed specific binding and thus the epitopes were characterized. The epitopes appear to be 'broader' when compared to those deduced from studies using smaller peptides. Interassay variation is remarkably small, allowing for precise grouping of clusters with very similar epitope patterns. Five groups of antibodies show remarkable similarity: BC3 and VU-4-H5; BC4W154, C595 and Mc5; MF06 and B27.29; VU-11-D1 and VU-11-E2; Ma552, VU-3-C6, 7540MR and BC4E549. We have used the term 'epitope fingerprinting' to refer to the 'fine structure' of the epitope with all its essential and flanking amino acids. We believe this method is more precise than the usual epitope mapping with short peptides.

Amino Acid Sequence↗

PubMed2005

Analysis of multiple data sets reveals no association between the insulin gene variable number tandem repeat element and polycystic ovary syndrome or related traits.

CONTEXT: Variation at the insulin gene VNTR (variable number tandem repeat) minisatellite has been reported to be associated with polycystic ovary syndrome (PCOS), but findings have been inconsistent and all studies have featured small sample sizes. OBJECTIVE: To gain a robust understanding of the role of the INS-VNTR in PCOS susceptibility. DESIGN: Case-control, family-based association and quantitative trait analyses. SETTING AND PARTICIPANTS: A UK population comprising 255 parent-offspring trios, 185 additional cases, and 1062 control subjects (cases and controls all British/Irish) as well as 1599 women from a northern Finland population-based birth cohort characterized for PCO symptomatology and testosterone levels. VNTR class was inferred from genotyping of the -23HphI variant. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): INS-VNTR genotype frequencies between subject groups, body mass index, and testosterone levels by genotype. RESULTS: Case-control analyses in both UK and Finnish samples failed to confirm previously reported class III allele associations with PCOS (UK, P = 0.43, Finnish, P = 0.31; Kruskal-Wallis chi2). Transmission analysis in trios showed no excess transmission of either allele (P = 0.62), regardless of parent of origin (maternal: P = 0.73; paternal: P = 0.66). No association between genotype and testosterone levels was seen in any sample (UK PCOS subjects, P = 0.95; Finnish symptomatic cases, P = 0.38; Finnish control women, P = 0.58). CONCLUSIONS: Despite the strong biological candidacy and supportive data from previous studies, we conclude that variation at the INS-VNTR has no major role in the development of PCOS.

Adult↗

PubMed2006

[Detection of short tandem repeat (STR) polymorphisms by microchip electrophoresis for individual identification of cattle].

A simple and rapid detection of short tandem repeat (STR) markers was studied as a screening test for individual identification of cattle. DNAs were extracted from eight commercial beef samples by a proteinase K-boil method followed by purification with 2-propanol precipitation. Five STR markers, known to be highly polymorphic, were amplified by PCR and analyzed both by a conventional sequencing analysis (SEQ) and by a proposed microchip electrophoresis (MEP). Every marker revealed high polymorphism, such as 5-9 alleles in SEQ analysis, and 4-6 alleles in MEP analysis. This simple and rapid MEP analysis is expected to be an effective screening tool with use of confirmatory SEQ analysis.

Animal Identification Systems↗

PubMed1999

Genetic susceptibility associated with rare HRAS1 variable number of tandem repeats alleles in Spanish non-small cell lung cancer patients.

The highly polymorphic HRAS1 variable number of tandem repeats (VNTR), which maps 1 kb downstream from the human H-ras1 gene, has been described as an inherited predisposing factor in many human cancers. Here, we investigated the association between the presence of rare HRAS1 minisatellite alleles and lung cancer in the population studied. Four hundred sixty-six HRAS1 VNTR alleles from 233 lung cancer patients and 892 alleles from 446 unaffected controls were typed using PCR-long agarose gel electrophoresis assay of peripheral blood lymphocyte DNA. Rare alleles were differentiated from common alleles (a1, a2, a3, and a4) by shifts in electrophoretic mobility. Odds ratio was calculated to evaluate increased risk of lung cancer associated to the presence of rare HRAS1 alleles. A higher percentage of rare HRAS1 VNTR alleles in lung cancer patients than in unaffected controls (32.7 versus 21.9%) was confirmed. The presence of rare alleles was associated with an increased risk of lung cancer (odds ratio = 1.68; P < or = 0.0001), indicating a genetic predisposition to lung cancer. No differences based on other clinicopathological variables were observed. Furthermore, a meta-analysis showed a higher distribution of rare alleles in our study of Caucasian Spaniards than was found in other studies of American and Northern European Caucasian populations. We conclude that the presence of rare HRAS1 VNTR alleles may be an inherited predisposing factor in lung cancer. This presence can be easily determined from peripheral blood samples by PCR-based methods. Furthermore, interracial variations in allele frequencies and variations between Caucasian subpopulations suggest that genetic variations may be involved in susceptibility to lung oncogenesis, especially in certain ethnic populations.

Alleles↗

PubMed2005

[Gene frequencies and haplotypes of nine Y-short tandem repeat loci in four minority populations of China].

OBJECTIVE: To investigate the polymorphism of nine Y-short tandem repeat loci in 117 male individuals from four minority populations of China, and to obtain the polymorphism information in these populations. METHODS: Nine loci in all samples were amplified by PCR. Products were electrophoresed on ABI PRISM 377 DNA sequencer. The electrophoresis result was analyzed by Genotyper 2.0 software. Allele frequencies, diversities and genetic distance were calculated. RESULTS: Forty-three alleles and 32 haplotypes were found in Manchu population, 43 alleles and 33 haplotypes in Uygur population, 31 alleles and 15 haplotypes in Kirgiz population and 34 alleles and 23 haplotypes in Zhuang population. The closest genetic distance is 0.02530 between Manchu and Uygur, the highest genetic distance is 0.34590 between Kirgiz and Zhuang. CONCLUSION: High haplotype diversities were found in four populations. The study of genetic diversity among different populations is useful in research of their origins, migrations and their relationships.

China↗

PubMed2005

Allele distribution of five X-chromosome short tandem repeat loci in Ewenke population of north China.

OBJECTIVE: To study the allele genetic polymorphism of five short tandem repeat (STR) loci on X-chromosome in Ewenke population of north China and to provide basic data for forensic identification. METHODS: Genomic DNA was extracted from EDTA-whole blood of Ewenke population by Chelex-100. The DNA samples were amplified by PCR and were analyzed by polyacrylamide gel electrophoresis and silver staining. The sequence length variations of DXS6799, DXS8378, DXS101, HPRTB, and DXS6789 loci on X-chromosome in 98 unrelated Ewenke individuals were investigated. RESULTS: All five loci analyzed showed high polymorphism and genetic stability. The data of the five X-chromosome STR loci in Ewenke ethnic group of China was in accordance with Hardy-Weinberg equilibrium by Chi-square test. CONCLUSION: Allele polymorphism of five X-chromosome STR loci can be used as a genetic marker for forensic identification and population genetic research.

Asian People↗

PubMed1999

Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses.

We sequenced the first ca. 900 bp of the 5'-trnL(UAA)-trnV(UAC)/ndhJ region of the chloroplast DNA of different Microseris accessions in order to resolve homoplasious length variation detected in the trnL(UAA)-trnF(GAA) region. We found two to four tandemly repeated trnF genes in the species of Microseris (Asteraceae, Lactuceae) and two in their sister genus Uropappus. Sequences indicated nonhomologous transitions between two, three, and four trnF genes in different Microseris taxa. Independent origins of similar trnF copy numbers were inferred from a chloroplast phylogeny of Microseris. The taxa involved grow on separate continents, supporting parallel origins of similar length variants. The changes in trnF copy numbers were best explained by interchromosomal recombination with unequal crossing over. The 5' copies of the repeats showed the highest sequence conservation, suggesting that these copies are likely to be functional trnF genes, whereas the other ones probably represent pseudogenes. Our results show that length polymorphisms accumulate once a duplicated sequence has become incorporated. Due to parallel gains of similar trnF copy numbers, homoplasious length variation was introduced into the data matrix. The data demonstrate that length polymorphisms cannot be used as indicators for phylogenetic distance unless they can be analyzed at the sequence level.

Base Sequence↗

PubMed1999

The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs.

The PR65/A subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit, generating functionally diverse heterotrimers. Mutations of the beta isoform of PR65 are associated with lung and colon tumors. The crystal structure of the PR65/Aalpha subunit, at 2.3 A resolution, reveals the conformation of its 15 tandemly repeated HEAT sequences, degenerate motifs of approximately 39 amino acids present in a variety of proteins, including huntingtin and importin beta. Individual motifs are composed of a pair of antiparallel alpha helices that assemble in a mainly linear, repetitive fashion to form an elongated molecule characterized by a double layer of alpha helices. Left-handed rotations at three interrepeat interfaces generate a novel left-hand superhelical conformation. The protein interaction interface is formed from the intrarepeat turns that are aligned to form a continuous ridge.

Adenocarcinoma↗

PubMed2001

The DD5 gene of the decapod crustacean Penaeus japonicus encodes a putative exoskeletal protein with a novel tandem repeat structure.

A gene, named DD5, was identified in the penaeid prawn Penaeus japonicus and its cDNA cloned and sequenced. DD5 is expressed in the epidermal cells underlying the exoskeleton and the transcripts are detected specifically during the postmolt stage of the molt cycle. Sequence analysis of the conceptual protein product suggests that the DD5 protein is a component of the exoskeleton. The bulk of the protein consists of tandem repeats of a unit sequence of approximately 100 amino acids. The repeated sequences are highly homologous to one another and each of them includes a variant of the Rebers--Riddiford consensus sequence.

Amino Acid Sequence↗

PubMed2002

Rapid prenatal detection of down and edwards syndromes by fluorescent polymerase chain reaction with short tandem repeat markers.

Chromosome analysis is the main tool for the prenatal diagnosis of trisomies but requires great technical expertise and time consuming manual procedures. Recently, alternative methods, which provide rapidity and accuracy, without culture, have been developed for pregnant women requiring rapid decisions for termination. In this study, multiplex fluorescent polymerase chain reactions (F-PCRs) were performed by the concurrent use of short tandem repeat (STR) markers specific for the chromosomes 18 and 21. The aims of this investigation were to evaluate the clinical usefulness of this assay for rapid prenatal detection of Down and Edwards syndromes and then to accumulate the basic data for clinical application. F-PCRs were carried out using DNA extracted from amniotic fluid and peripheral blood derived from 47 normal karyotypes, 23 Down and 8 Edwards syndrome patients. Fluorescent intensities of the PCR products were then calculated. Normal samples displayed diallelic peaks for each STR marker. Reference ranges of peak area ratios were 1.0 - 1.4 for D21S11, 1.0 - 1.5 for D21S1412 and 1.0 - 1.3 for D18S535 and D18S51. Down and Edwards syndromes showed characteristic triallelic peaks of similar intensity corresponding to 3 different alleles or characteristic diallelic peaks. The sensitivity, specificity and efficiency of the assay for detecting Down and Edwards syndromes were 96.7%, 93.6% and 94.8%, respectively. In conclusion, these results show that F-PCR rapidly detects Down and Edwards syndromes with high accuracy and provides normal reference ranges of peak area ratios. However, the presence of false results (4 out of 77 cases) and the possibility of anomalies other than trisomies 21 and 18 do not permit F-PCR to substitute for chromosome analysis.

Chromosomes, Human, Pair 18↗