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PubMed1995

Three short tandem repeat loci in Japanese population.

Allele frequencies of three short tandem repeat loci, vWF, TH and GCG, were examined for 210 unrelated Japanese individuals. Eight alleles were identified with PCR and gel electrophoresis for vWF, 7 for TH and 13 for GCG, indicating that these loci are highly polymorphic. Combined discrimination power of the 3 STRs was 0.995. These results imply that the loci are useful as probes for the identification of Japanese individuals. Thus, we applied the probes to the identification of a forensic specimen that was decomposed severely. The vWF and TH probes successfully gave clear bands in gel electrophoresis, but GCG failed to be typed because of a lot of shadow bands. The results suggests the usefulness of at least the former two probes in forensic studies.

Alleles↗

PubMed1995

[Evaluation of bone marrow grafts and hemopoietic chimerism using PCR hypervariable sequencing with variable number tandem repeat sequences].

PCR amplification of highly polymorphic variable number of tandem repeat (VNTR) sequences could be particularly useful in documentation of engraftment and characterization of chimerism following allogeneic bone marrow transplantation (BMT). We have monitored a 31-year old male patient treated with allogeneic BMT for chronic myeloid leukaemia. The recipient's DNA samples were obtained before the transplant and on day 28, 100 and 150 after BMT. The donor's DNA (patient's sister) was also obtained as a reference. ACT B2 locus on chromosome 6 was chosen for the analysis. In addition a deletion polymorphism locus within the pseudoautosomal region of chromosome X and Y (amelogenin gene) was also analysed. On day 28 after BMT both donor and recipient specific alleles were detected in the recipient's sample. However, on day 100 and 150 the recipient specific alleles were no longer detectable. The aforementioned pattern was observed for both markers analysed. The disappearance of recipient specific alleles correlated with clinical symptoms of chronic graft-versus host disease.

Adult↗

PubMed1996

Analysis of the short tandem repeat systems HUMF13B and HUMvWF in Chinese (Liaoning).

The short tandem repeat (STR) systems HUMF13B and HUMvWF were investigated in 200 healthy Chinese individuals living in Liaoning (The northeast of China). The HUMF13B allele frequencies were 6 = 0.0025, 8 = 0.1825, 9 = 0.1750, 10 = 0.6325 and 11 = 0.0075; and the HUMvWF allele frequencies were 13 = 0.0300, 14 = 0.2475, 15 = 0.0450, 16 = 0.1750, 17 = 0.2600, 18 = 0.1525, 19 = 0.0725 and 20 = 0.0175. The distribution of genotypes corresponded to the Hardy-Weinberg equilibrium. The distinguishing probabilities (D.P) were calculated as 0.7318 and 0.9366; the polymorphism information content (PIC) were calculated as 0.4827 and 0.7822; and the heterozygosity (h) were calculated as 0.5378 and 0.8128, respectively. The HUMF13B and HUMvWF systems provide a useful genetic marker for human genetics, anthropological studies, and forensic science in the chinese population.

Alleles↗

PubMed1997

Analysis of allele distribution for six short tandem repeat loci in the French Canadian population of Québec.

Short tandem repeat (STR) loci represent a rich source of highly polymorphic markers in the human genome which are useful for the purposes of forensic identification and determination of biological relatedness of individuals. Here, as a part of an ongoing extensive study, we report the analysis of a multilocus genotype survey of 642 to 870 chromosomes in the French Canadian Caucasian population of Québec at six STR loci. The loci HUMCSF1PO, HUMTPOX, HUMTH01, HUMF13A01, HUMFESFPS, and HUMvWA were typed using two multiplex polymerase chain reactions (PCR). Amplified DNA samples were subsequently analyzed by polyacrylamide gel electrophoresis followed by silver staining. The heterozygote frequencies of the loci range from 0.614 to 0.820 (0.661 to 0.818 expected) and the number of alleles from 7 to 12 per locus. Although statistically significant deviation from Hardy-Weinberg expectations of genotype frequencies was noted at some loci by one or more tests, in general, the genotype frequencies are well estimated from the product of allele frequencies at all loci. The most frequent six-locus genotype is expected to occur in the French Canadian population with a frequency of 3.50 by 10(-5) and together, these six loci have an average probability of discrimination of 0.9999985. The study presented here indicates that these six STR loci are informative genetic markers for identity testing purposes in the French Canadian Caucasian population of Québec.

Adult↗

PubMed1996

Tandem repeating of the expression cartridge--a novel strategy to enhance the expression efficiency of cloned gene in Escherichia coli.

A novel strategy to enhance the expression efficiency of cloned target gene in Escherichia coli was developed. The whole expression cartridge, consisting of promoter, SD sequence, target gene and transcription terminator, was tandem repeatedly engineered into a expression plasmid. Consequently, the copy number of specific gene was increased substantially, leading to the improvement of expression efficiency. Using this approach, a recombinant plasmid, designed as pLYD, was constructed and transformated into the Escherichia coli strain DH5 alpha. Upon induction, the desired protein was synthesized in a considerable level and accumulated up to 63% of the total cell proteins. The present study revealed that tandem repeating of expression cartridge provided a convenient means to improve expression level efficiently.

DNA, Recombinant↗

PubMed2005

[Significance of polymorphisms in variable number of tandem repeat region of interleukin-4 gene in recurrence of childhood steroid sensitive nephrotic syndrome].

OBJECTIVE: Recent studies suggest that T cell dysfunction, especially IL-4, may be involved in the pathogenesis of steroid sensitive nephrotic syndrome (SSNS). The aim of this study was to investigate the association between the polymorphisms in variable numbers of tandem repeat region (VTR) of IL-4 gene and childhood SSNS. METHOD: The polymorphism in the IL-4 gene was identified by using the polymerase chain reaction and direct sequencing methods in 55 Chinese children with SSNS, who were followed-up for at least 1 year, and 115 healthy Chinese adult blood donors as controls. A variable number of tandem repeat (VNTR) region polymorphisms of IL-4 gene were detected, and alleles were designated as IL-4 B1 and B2, corresponding to 2 and 3 repeats, respectively. The serum IgE was also examined in 48 patients before the steroid treatment. RESULT: (1) There were no significant differences in the genotype and allele frequencies between patients with SSNS and normal controls (P > 0.05). (2) The frequencies of B1B1 (96.4%) were significantly higher in SSNS children with frequent relapses (28 patients had more than 3 relapses during the first year of the disease) than in 27 patients without frequent relapses (P < 0.05). (3) Twenty-three patients with frequent relapses showed higher levels of serum IgE (1.98 +/- 0.23 g/L) than 25 patients (IgE: 1.05 +/- 0.19 g/L) without frequent relapses (P < 0.05), and the patients with B1B1 (38 patients) also had higher serum IgE levels than patients with B1B2 and B2B2 (10 patients) (P < 0.05). CONCLUSION: The results suggest that IL-4 VNTR B1B1 genotype might be a predictor for the frequent relapse in childhood SSNS in Chinese.

Adolescent↗

PubMed1999

Population genetics of nine short tandem repeat (STR) loci - DNA typing using the AmpFlSTR profiler PCR amplification kit.

Frequency data for nine short tandem repeat (STR) loci were collected from 130 unrelated Caucasians from North Bavaria using the AmpFlSTR Profiler multiplex system. The loci D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820 and the sex test amelogenin were investigated. Allele frequencies, rates of heterozygosity and the discrimination power of the combined systems were calculated by statistical analysis. Except for D5S818 all loci met Hardy-Weinberg expectations.

DNA↗

PubMed1995

Tandem repeats of the 5' non-transcribed spacer of Tetrahymena rDNA function as high copy number autonomous replicons in the macronucleus but do not prevent rRNA gene dosage regulation.

The rRNA genes in the somatic macronucleus of Tetrahymena thermophila are normally on 21 kb linear palindromic molecules (rDNA). We examined the effect on rRNA gene dosage of transforming T.thermophila macronuclei with plasmid constructs containing a pair of tandemly repeated rDNA replication origin regions unlinked to the rRNA gene. A significant proportion of the plasmid sequences were maintained as high copy circular molecules, eventually consisting solely of tandem arrays of origin regions. As reported previously for cells transformed by a construct in which the same tandem rDNA origins were linked to the rRNA gene [Yu, G.-L. and Blackburn, E. H. (1990) Mol. Cell. Biol., 10, 2070-2080], origin sequences recombined to form linear molecules bearing several tandem repeats of the origin region, as well as rRNA genes. The total number of rDNA origin sequences eventually exceeded rRNA gene copies by approximately 20- to 40-fold and the number of circular replicons carrying only rDNA origin sequences exceeded rRNA gene copies by 2- to 3-fold. However, the rRNA gene dosage was unchanged. Hence, simply monitoring the total number of rDNA origin regions is not sufficient to regulate rRNA gene copy number.

Animals↗

PubMed1997

A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

Animals↗

PubMed2005

Multiple-locus variable-number tandem repeat analysis for strain typing of Clostridium perfringens.

Clostridium perfringens is ubiquitous in the environment and causes diseases in man and animals, with syndromes ranging from enteritis, enterotoxemia, and sudden death to food poisoning and gas gangrene. Understanding the epidemiology of these infections and of the evolution of virulence in C. perfringens necessitate an efficient, time and cost effective strain typing method. Multiple-locus variable-number tandem repeat analysis (MLVA) has been applied to typing of other pathogens and we describe here the development of a MLVA scheme for C. perfringens. We characterized five variable tandem repeat (VNTR) loci, four of which are contained within protein encoding genes and screened 112 C. perfringens isolates to evaluate typability, reproducibility, and discriminatory power of the scheme. All the isolates were assigned a MLVA genotype and the technique has excellent reproducibility, with a numerical index of discrimination for the five VNTR loci of 0.995. Thus MLVA is an efficient tool for C. perfringens strain typing, and being PCR based makes it rapid, easy, and cost effective. In addition, it can be employed in epidemiological, ecological, and evolutionary investigations of the organism.

Journal Article↗

PubMed1999

Population genetic studies on nine tetrameric short tandem repeat loci using fluorescence dye-labeled primers and capillary electrophoresis in the Austrian population.

The short tandem repeats (STR) D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 and a locus allowing sex discrimination (amelogenin) can be coamplified by the polymerase chain reaction using a commercially available kit, and subsequently typed using capillary electrophoresis. To establish databases for these loci for Austrian Caucasians, 115 unrelated persons were typed. All loci were in Hardy-Weinberg equilibrium. The combined mean paternity exclusion chance (MEC) was 0.999891 and the combined discriminating power (DP) was 3.08 x 10(-11). The allelic distributions showed no differences to those found for other Caucasian populations. Our data differed significantly from an Afro-American population at 5 loci and from a Chinese population at 4 loci. Linkage disequilibrium between any of the coamplified loci was not evident. Thus the combination of multiplex PCR and capillary electrophoresis can save time and yield excellent results for paternity testing and stain analysis.

Austria↗

PubMed2000

Improved haplotype analysis of human myelin basic protein short tandem repeat loci.

We report an improved haplotype analysis of the human myelin basic protein gene (MBP) short tandem repeat (STR) polymorphism. The polymorphic G-->A transition and 2 conventional STR polymorphisms, MBPA and MBPB, were simultaneously determined by an amplified product length polymorphism technique. After the MBPC fragments containing MBPA and MBPB were amplified, the linkage of these 2 STR loci was determined by a second amplification, using polymerase chain reaction (PCR) technique, of the isolated MBPC fragments. The present haplotype analysis dispensed with family studies for the haplotyping of MBPA and MBPB. Polymorphisms of the MBP loci studied in German and Japanese populations showed a high genomic variation. Haplotype analysis of the MBP loci showed distinct differences between the German and the Japanese populations. Consequently, haplotype analysis of the MBP loci promises to be useful in forensic identification and paternity testing.

Alleles↗

PubMed2003

Allele and haplotype frequencies of Y-short tandem repeat loci in Turkey.

AIM: To assess the frequency distribution of six Y-chromosomal specific short tandem repeat (STR) polymorphisms and frequencies of haplotypes in Turkish population. METHODS: Blood samples were taken from 200 unrelated Turkish men from different regions of Turkey, who were involved in legal proceedings concerning paternity. The DNA was amplified and typed by use of Y-Plex 6 kit containing 6 Y-STR markers (DYS393, DYS19, DYS389 II, DYS390, DYS391, and DYS385). Capillary electrophoresis was carried out on an ABI 310 Genetic Analyzer. RESULTS: Allele frequency profiles of the Turkish men showed no significant differences compared with previously published results for Swiss and German populations. The range of gene diversity was determined between 48.3% for DYS391 and 96.0% for DYS385. Of 184 determined haplotypes, 170 occurred once, and the rest more than once. The most common haplotypes had a frequency of 1.5%. CONCLUSION: High degree of haplotype diversity in Turkish population makes analysis of Y-STRs a useful tool in forensic cases.

Chromosomes, Human, Y↗

PubMed2006

[Usefulness of variable numbers of tandem repeats typing in clinical strains of Mycobacterium avium].

OBJECTIVES: We evaluated the usefulness of Variable Numbers of Tandem Repeats (VNTR) analysis, which was recently reported as a new typing method of Mycobacterium avium strains of animal origin, for strain differentiation of clinical isolates of M. avium in comparison with the standard IS1245-RFLP typing method. In addition, forty M. avium isolates recovered from sputum samples of same patient in different times were analyzed with VNTR typing method. SUBJECTS AND METHODS: The subjects were twenty-four clinical isolates of M. avium stocked at Higashi Nagoya National Hospital and discriminatory power was evaluated with Hunter Gaston Discriminatory Index (HGDI). Furthermore, forty M. avium isolates recovered from sputum samples of one patient obtained at four different times were analyzed by using this VNTR typing method. RESULTS: VNTR typing showed better discriminatory power for twenty-four clinical isolates than IS1245-RFLP method (HGDI: 0.975 vs 0.866). In the second study, polyclonal infection of four genotype strains with different allele profiles were detected. The ratio of mixture of the four different genotype strains varied during clinical course. CONCLUSION: We considered that VNTR typing method was very useful for discriminatory examination of M. avium.

Bacterial Typing Techniques↗

PubMed2002

Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations.

We describe here an online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations, which represents 9-locus Y-STR haplotypes for 1705 African-Americans, European-Americans and Hispanics as of October 2001. This database is available online (http://www.ystr. org/usa/), free to access and was generated in order to supply the U.S. forensic DNA community with a valuable resource for frequencies of complete or incomplete 9-locus Y-STR haplotypes, as well as information about typing protocols and population genetic analyses. Pairwise R(ST)-statistics derived from the Y-STR haplotypes indicate no significant substructure among African-American populations from different regions of the U.S., nor (usually) among European-American and Hispanic populations. Thus, pooling of Y-STR haplotype data from regional populations within these three major groups is appropriate in order to obtain larger sample sizes. However, pooling of different major populations is generally not recommended due to statistically significant differences between African-American populations and all European-American/Hispanic populations, as well as between some European-American and Hispanic populations.

Black People↗

PubMed1998

Multiplexed short tandem repeat polymorphisms of the Weber 8A set of markers using tailed primers and infrared fluorescence detection.

Short tandem repeat polymorphism (STRP) markers have become important reagents for mapping genetic diseases. These markers are available as screening sets, which are located in all chromosomes at discrete intervals, allowing the entire genome to be analyzed. Mapping studies that include many individuals in the analysis necessitate the production of large numbers of genotypes. In an effort to increase the efficiency and lower the cost of using these STRP screening sets, we have divided the amplification primers of the Weber 8A screening set into groups that can be amplified in single polymerase chain reaction (PCR) amplification reactions, resulting in a reduction of both time and cost. Fluorescently-labeled amplification products were produced using a three primer reaction. The forward STRP amplification primer for each marker contained a 19 bp sequence at the 5' end. A fluorescently-labeled primer, with a sequence identical to the 19 bp tail, was added to the amplification reaction as the sole source of fluorescent label. The STRP banding pattern is detected using an automated fluorescent DNA sequencer. Use of this multiplexed genomic screening set should greatly enhance the mapping of human disease loci.

DNA Primers↗

PubMed2002

Role of short tandem repeat DNA in forensic casework in the UK--past, present, and future perspectives.

The analysis of short tandem repeat (STR) DNA sequences is of fundamental importance to forensic science because they have become the recognized standard in constructing national public databases. Consequently, considerable effort has been expended in developing multiplexed (one tube) reactions that analyze several loci in combination. The implementation of STRs in casework cannot take place without a full understanding of the systems used. The purpose of validation is to characterize multiplexes when one is challenged with forensic samples. For example, mixtures are often encountered that may be particularly difficult to interpret against a background of allelic artifacts. By increasing the number of PCR amplification cycles, it is possible to dramatically boost the sensitivity of the system so that just a handful of cells may be successfully analyzed. However, interpretation is much more complex because the origin of DNA profiles may be less certain and complicated by issues such as contamination, the potential for innocent transfer and a predominance of mixtures. This review provides a brief historical background of the development of STRs in forensic casework that culminated in the creation of national DNA databases. The development of guidelines to interpret complex DNA profiles, such as mixtures, is outlined. Finally, the recent innovation of low copy number DNA profiling is explained along with the special considerations needed to report in court.

DNA↗

PubMed2001

Influence of fluorophor dye labels on the migration behavior of polymerase chain reaction--amplified short tandem repeats during denaturing capillary electrophoresis.

The determination of the length of polymerase chain reaction (PCR)-amplified short tandem repeats (STRs) by denaturing capillary electrophoresis (CE) is a standard procedure for purposes of genotyping. We show that dye-specific mobility anomalies exist for 5'-fluorophor-labelled single-stranded DNA (ssDNA) fragments in CE using the performance-optimized polymer 4 (POP4) buffer sieving matrix, containing the entangled poly(N,N-dimethylacrylamide) polymer, urea, and 2-pyrrolidinone. The dye-specific retardation effects relative to coseparated GeneScan-500 [TAMRA] standard fragments can lead to wrong genotyping, even for allele-specific fragments of pentanucleotide STRs, when comparing the relative calculated sizes of identical fragments, labelled with rhodamine (ROX, TAMRA) or fluorescein dyes (FAM, 6-FAM, HEX, JOE, NED, TET): The size of fluorescein dye-labelled fragments of appr. 100 b in length appears to be smaller by up to 6.5 b. This effect becomes more dramatic with decreasing size: a 6-FAM-labelled 24-mer oligonucleotide appeared to be smaller by 11 b. In contrast, in classical urea/polyacrylamide slab-gel electrophoresis only a small dye-specific retardation of identical fragments is observed. The dye-specific effects are superimposed by weaker size and sequence-dependent anomalies of fragment mobility. Therefore, in denaturing CE the coseparation of a defined allele ladder labelled with the same dye as the unknown sample fragments remains the method of choice for accurate genotyping.

DNA, Single-Stranded↗