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PubMed1990

Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code".

This review is based on a thorough description of the structure and sequence organization of tandemly organized repetitive DNA sequence families in the human genome; it is aimed at revealing the locus-specific sequence organization of tandemly repetitive sequence structures as a highly conserved DNA sequence code. These repetitive so-called "super-structures" or "higher-order" structures are able to attract specific nuclear proteins. I shall define this code therefore as a "chromatin folding code". Since locus-specific superstructures of tandemly repetitive sequence units are present not only in the chromosome centromere or telomere region but also on the arms of the chromosomes, I assume that their chromatin folding code may contribute to, or even organize, the folding pathway of the chromatin chain in the nucleus. The "chromatin folding code" is based on its specific "chromatin code", which describes the sequence dependence of the helical pathway of the DNA primary sequence (i.e., secondary structure) entrapping the histone octamers in preferential positions. There is no periodicity in the distribution of the nucleosomes along the DNA chain. The folding pathway of the nucleosomal chromatin chain is however still flexible and determined by e.g., the length of the DNA chain between the nucleosomes. The fixation and stabilization of the chromatin chain in the space of the nucleus (i.e., its "functional state") may be mediated by additionally unique DNA protein interactions that are dictated by the "chromatin folding code". The unique DNA-protein interactions around the centromeres of human chromosomes are revealed for example by their "C-banding". I wish to stress that it is not my aim to relate each block of repetitive DNA sequences to a specific "chromatin folding code", but I shall demonstrate that there is an inherent potential for tandem repeated sequence units to develop a locus-specific repetitive higher order structure; this potential may create a specific chromatin folding code whenever a selection force exists at the position of this repetitive DNA structure in the genome.

Chromatin↗
PubMed2004

Variable number of tandem repeats in Salmonella enterica subsp. enterica for typing purposes.

The genomic sequences of Salmonella enterica subsp. enterica strains CT18, Ty2 (serovar Typhi), and LT2 (serovar Typhimurium) were analyzed for potential variable number tandem repeats (VNTRs). A multiple-locus VNTR analysis (MLVA) of 99 strains of S. enterica supsp. enterica based on 10 VNTRs distinguished 52 genotypes and placed them into four groups. All strains tested were independent human isolates from France and did not reflect isolates from outbreak episodes. Of these 10 VNTRs, 7 showed variability within serovar Typhi, whereas 1 showed variability within serovar Typhimurium. Four VNTRs showed high Nei's diversity indices (DIs) of 0.81 to 0.87 within serovar Typhi (n = 27). Additionally, three of these more variable VNTRs showed DIs of 0.18 to 0.58 within serovar Paratyphi A (n = 10). The VNTR polymorphic site within multidrug-resistant (MDR) serovar Typhimurium isolates (n = 39; resistance to ampicillin, chloramphenicol, spectinomycin, sulfonamides, and tetracycline) showed a DI of 0.81. Cluster analysis not only identified three genetically distinct groups consistent with the present serovar classification of salmonellae (serovars Typhi, Paratyphi A, and Typhimurium) but also discriminated 25 subtypes (93%) within serovar Typhi isolates. The analysis discriminated only eight subtypes within serovar Typhimurium isolates resistant to ampicillin, chloramphenicol, spectinomycin, sulfonamides, and tetracycline, possibly reflecting the emergence in the mid-1990s of the DT104 phage type, which often displays such an MDR spectrum. Coupled with the ongoing improvements in automated procedures offered by capillary electrophoresis, use of these markers is proposed in further investigations of the potential of MLVA in outbreaks of salmonellosis, especially outbreaks of typhoid fever.

Alleles↗
PubMed2005

[Distribution of genotype and allele frequencies of dopamine D4 receptor gene 48 bp variable number tandem repeat polymorphism in Chinese Han population in Hunan].

OBJECTIVE: To investigate the distribution of genotype and allele frequencies of the dopamine D4 receptor(DRD4) gene exon 3 48 bp variable number of tandem repeats polymorphism in Hunan Han population. METHODS: The genotype and alleles of 304 healthy persons were examined with polymerase chain reaction, denaturing polyacrylamide gel electrophoresis and silver staining. RESULTS: Seven alleles and twelve genotypes were found. The most common allele was allele 5 with a frequency of 70.6%. There was statistically significant difference in allele distribution between the Hunan Han population and the Han population of other regions such as Shanghai, Beijing and Sichuan in China (P< 0.05). Different allele frequency distributions were observed when compared to other ethnic populations such as Japanese, American, Mexican, and Italian (P< 0.05). CONCLUSION: The distributions of allele of DRD4 gene exhibit regional and ethnic heterogeneity.

Adult↗
PubMed1996

Amplification of human short tandem repeats from medieval teeth and bone samples.

The suitability of typing hypervariable DNA loci for the genetic analysis of prehistoric populations is demonstrated for the first time. Alleles of the human short tandem repeat locus VWA31/A have been amplified from ancient teeth and bone samples derived from an early medieval burial site at Weingarten, Germany, using the polymerase chain reaction. The DNA results for 76 individuals reveal remarkable similarity of the allelic frequencies between the past and modern populations. A surplus of apparent homozygotes in the ancient population is most likely due to a stochastic problem of amplification of degraded DNA. Therefore technical obstacles for the application to ancient DNA were evaluated. The substantial perspectives of using microsatellite typing for the analysis of heritable diseases, determination of relatedness, and establishment of genealogies in prehistoric populations are outlined.

Alleles↗
PubMed2004

Variable number of tandem repeat of the 5'-flanking region of type-C human natriuretic peptide receptor gene influences blood pressure levels in obesity-associated hypertension.

The gene for natriuretic peptides receptor C (NPRC), which is a candidate susceptibility gene for essential hypertension (EH) or obese hypertension, plays a key role in the regulation of plasma levels and biological effects of natriuretic peptides. The aims of the present study were to find new genetic markers in the 5'-flanking region of the NPRC gene and to assess relationships between variants and phenotypes of EH, including EH in obese patients. Using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis, we discovered a novel six-nucleotide repeat polymorphism located 4 base pairs (bp) upstream of the major transcriptional initiation site. We performed association analysis of this variable number of tandem repeat (VNTR) in 242 EH patients and 212 normotensive controls (NT). Although no significant difference in overall frequency of VNTR was found between NT and EH groups, the blood pressure level of EH patients with the 5/6 genotype was significantly higher in obese subjects. This suggests that the VNTR of the 5'-flanking region of the NPRC gene influences blood pressure levels in obesity-associated hypertension.

5' Flanking Region↗
PubMed1993

Isolation and identification of a novel tandemly repeated DNA sequence in the centromeric region of human chromosome 8.

EcoRI subclones, designated as 50E1 and 50E4, were independently obtained from a cosmid clone previously mapped to the centromeric region of human chromosome 8. Southern blot hybridization analyses suggested that both subclones contain repetitive DNA sequences different from the chromosome 8 specific alphoid DNA. DNA sequence analysis of the 704 bp insert of 50E1 and the 1,962 bp insert of 50E4 revealed that both inserts contained tandemly repeated units of approximately 220 bp. Fluorescence in situ hybridization studies confirmed these two subclones to be specifically located on the centromeric region of chromosome 8. A 220 bp consensus sequence, derived from nine monomeric repeats, showed no significant homology to alphoid consensus sequences or to other currently known human centromeric DNA sequence. Furthermore, no significant homology was found with any other DNA sequence deposited in the EMBL or GenBank databases, indicating that this chromosome 8 specific repetitive DNA sequence is novel. From slot blot experiments it was estimated that 0.013% of the human genome comprises 1,750 of these monomeric repeats, residing on the centromeric region of chromosome 8 in tandem array(s).

Base Sequence↗
PubMed1994

Fluorescent-based typing of the two short tandem repeat loci HUMTH01 and HUMACTBP2: reproducibility of size measurements and genetic variation in the Swedish population.

The aim of this study was to investigate the reproducibility of genetic typing of two tetrameric short tandem repeat (STR) loci and the extent of genetic variation in the Swedish population. An automated, fluorescent-based Applied Biosystems 373A sequencer was used for typing of the HUMTH01 and HUMACTBP2 loci (also named SE33). The former locus has seven alleles in the size range of 154-174 bp, while the latter is a complex locus with more than 32 alleles in the range of 227-316 bp. Using different fluorescent dyes, polymerase chain reaction (PCR) products from the two STR loci were sized in one lane using an internal size standard. In order to compare within- and between-gel reproducibility of fragment size estimates, a control sample was typed three times on each of 20 gels. Within the gel, the standard deviation (SD) of fragment size variability was less than 0.1 bp for four fragment sizes between 158-291 bp. Standard deviations between gels were slightly higher for the two shorter fragment sizes (HUMTH01), while the larger fragments varied between 0.3 and 0.4 bp (HUMACTBP2). The amount of genetic variation was investigated in samples from three Swedish cities (n = 301). Seven alleles were found at HUMTH01 and the observed heterozygosity was 0.77. At the HUMACTBP2 locus more than thirty alleles were found and the observed heterozygosity was 0.96. The observed genotype frequencies at HUMTH01 and HUMACTBP2 did not deviate significantly from Hardy-Weinberg expectations. No indication of a significant excess of homozygotes was found at any of the loci. We conclude that both HUMTH01 and HUMACTBP2 can be reliably typed using the method described. However, the latter locus requires an allelic ladder to be run on each gel.

Alleles↗
PubMed2000

Y chromosomal short tandem repeat (STR) loci in a representative group of males living in South Württemberg: a database for application in forensic medicine.

In this study, we resolved the allelic distribution of three Y chromosomal short tandem repeats (STRs), DYS19 (n=218), DYS390 (n=257) and DYS393 (n=215), in a population study of 257 unrelated men living in the area of South Wüerttemberg/Hohenzollern. In DYS19 and in DYS393, five different alleles were discovered, and in DYS390, six different alleles. Forty-nine different haplotypes were found in 202 unrelated male individuals. By investigating each of the three STR systems separately, the most powerful results were found in DYS390, with a PE (power of exclusion) of 0.74, followed by DYS19 (PE: 0.65) and DYS393 (PE: 0.47). Using a combination of two systems (n=202), the PEs ranged from 0.79 (DYS19 and DYS393) to 0.89 (DYS19 and DYS390). The combination of all three STR systems revealed a PE of 0.93.

DNA Fingerprinting↗
PubMedDate not supplied

Genetic variation observed at two tetrameric short tandem repeat loci on chromosome 12 (D12S66 and D12S67) among five distinct ethnic groups of India: detection of two new alleles.

OBJECTIVE: The present investigation reports the genetic variation observed at two tetrameric short tandem repeat (STR) loci on chromosome 12 (D12S66 and D12S67) among five anthropologically distinct population groups of India. SUBJECTS AND METHODS: A total of 277 random, normal and healthy volunteers were investigated for the D12S66 locus, and 236 for the locus D12S67, from five ethnic groups of India. Two of these belong to the state of Maharashtra in western India (Konkanastha Brahmins and Marathas) and three from the state of Kerala in South India (Nairs, Ezhavas and Muslims). DNA was extracted from peripheral blood samples, amplified by duplex polymerase chain reaction (PCR) and electrophoresed on 6% denaturing urea (7 M) gel electrophoresis. The analysis was performed on ALF Express DNA sequencer (Amersham Pharmacia Biotech) using Fragment Manager software. Statistical analysis was done by using Arlequin ver. 1.1. RESULTS: At D12S66 locus, a total of nine alleles (8-17 repeats) and 27 genotypes were detected with an observed heterozygosity ranging from 0.55 to 0.91. At the D12S67 locus, nine alleles (36-44 repeats) and 33 genotypes were observed with a heterozygosity ranging from 0.74 to 0.89. Both the loci displayed high Power of Discrimination (PD) which ranged from 0.81 to 0.91 and Polymorphic Information Content (PIC) ranging from 0.68 to 0.84. At D12S66, two alleles were detected for the first time in these population groups which were not reported earlier. The level of gene differentiation (G(ST) value, 0.02) was moderate at these two loci, indicating a close relationship among the population groups. CONCLUSIONS: From this investigation, it is concluded that both the tetrameric loci are highly polymorphic and informative, and can be used for the characterization of the Indian population groups in addition to other well-studied STR loci.

Alleles↗
PubMed2001

Diagnosis of trisomy 21 in fetal nucleated erythrocytes from maternal blood by use of short tandem repeat sequences.

BACKGROUND: The purpose of this study was to determine whether aneuploid fetal nucleated erythrocytes (NRBCs) could be detected in maternal blood through the use of fluorescent PCR amplification with polymorphic short tandem repeat (STR) markers as an alternative or complementary method to analysis by fluorescent in situ hybridization (FISH). METHODS: Peripheral blood samples were obtained from women who had just undergone termination of pregnancy because of fetal trisomy 21 (three cases, 47,XY,+21; four cases, 47,XX,+21). Candidate fetal cells were isolated by flow-sorting by antibodies to the gamma chain of fetal hemoglobin and Hoechst 33342. FISH analysis was performed by the use of chromosome-specific probes for X, Y, and 21. Fetal NRBCs, as defined by the presence of gamma staining, characteristic morphology, and three chromosome 21 signals, along with maternal leukocytes, defined as gamma negative and two chromosome 21 signals, were micromanipulated separately and subjected to fluorescent PCR amplification of chromosome 21 STR markers (D21S11, D21S1411, and/or D21S1412). RESULTS: In five of seven cases analyzed, fetal NRBCs were aneuploid, as determined by the presence of triallelic or diallelic peaks of chromosome 21 sequences when compared with sequences from the maternal leukocytes. CONCLUSIONS: Fluorescent PCR amplification of STRs can detect fetal aneuploidy and may be useful in the setting of poor hybridization efficiency with FISH analysis. These results suggest that combined fetal aneuploidy and single-gene diagnoses by the use of DNA microarrays may be feasible in the near future.

Aneuploidy↗
PubMed1995

A tandemly repeated DNA family originated from SINE-related elements in the European plethodontid salamanders (Amphibia, Urodela).

We have characterized a highly repetitive family, named Hy/Pol III, in the genome of the European salamanders Hydromantes (Plethodontidae). This family consists of short, tandemly repeated sequences organized in clusters, scattered through the genome as shown both by in situ hybridization to chromosomes and by Southern blot hybridization. The repeat unit is about 200 bp in length and it is a composite element since it contains a SINE-like retroposon with a tRNA structure, flanked by two short direct repeats. The whole element itself is bordered by two other direct repeats. The sequence data suggest that two elements, presumably derived from polymerase III transcripts, have been inserted one into the other, giving rise to the observed composite structure. During evolution the Hy/Pol III family was then amplified by tandem duplication at the DNA level. The inferred relationships between Hy/Pol III members from three representative species of the European Hydromantes suggests that a subfamily structure characterizes the evolutionary history of this family.

Animals↗
PubMed2003

The variable number of tandem repeat polymorphism in the P-selectin glycoprotein ligand-1 gene is not associated with coronary heart disease.

Genes involved in inflammatory processes are candidates for predisposition to prothrombotic syndromes. The variable number of tandem repeat (VNTR) polymorphism in the P-selectin glycoprotein ligand (PSGL)-1 gene has been associated with ischemic cerebrovascular disease but not with coronary heart disease (CHD). We assessed the effect of the VNTR polymorphism on CHD in two independent case/control studies. In the first study 281 CHD patients and 397 healthy blood donors were genotyped for the VNTR alleles in PSGL-1. The prevalence of homozygous carriers of the PSGL-1 VNTR allele with 15 repeat units was significantly higher in the CHD patients (5.3% vs. 1.5%) than in controls, suggesting an effect of this marker in CHD. To validate the findings genotyping was performed in a second study including 2,578 CHD patients, 731 patients without CHD, and 1084 healthy blood donors. The larger case control study had a power of 99.9% to detect the initially observed difference but failed to confirm the putative role of PSGL-1 VNTR polymorphism in CHD. Frequencies of the PSGL-1 VNTR 15 repeats for homozygous carriers were 2.2% in healthy blood donors, 2.3% in patients without CHD and 2.7%, in CHD cases, respectively. These results demonstrate that the PSGL-1 VNTR polymorphism is not a genetic risk factor for CHD. Adequately powered studies are prerequisites to obtain reliable results about genotype-phenotype relationships of new candidate genes in complex diseases.

Adult↗
PubMed2001

Genotyping of simple and compound short tandem repeat loci using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

The utility of electrospray ionization Fourier transform ion cyclotron resonance (ESI-FIICR) mass spectrometry as a new approach for genotyping short tandem repeats (STRs) is demonstrated. STRs are currently valued as a powerful source of genetic information with repeats that range in structure from simple to hypervariable. Two tetranucleotide STR loci were chosen to evaluate ESI-FTICR mass spectrometry as a tool for genotyping: HUM-TH01, a simple STR with nonconsensus alleles, and vWA, a compound STR with nonconsensus alleles. For HUM-TH01, the genotype (i.e., repeat number of each allele) was determined for each of 30 individuals using mass measurements of double-stranded amplicons. Low-intensity peaks observed in the spectra of amplicons derived from heterozygous individuals were identified by mass as heteroduplexes that had formed between nonhomologous strands. Mass measurement of the double-stranded vWA amplicon was not sufficient for determining whether the individual was homozygous for allele subtype 18 or 18' since the amplicons differ by only 0.99 Da. Therefore, single-stranded amplicons were generated by incorporating a phosphorylated primer, prepared using T4 polynucleotide kinase, into the PCR phase and subsequently digesting the bottom strand using lambda-exonuclease. Accurate mass measurements were obtained for the single-stranded amplicons using internal calibration and the addition of a correction factor to adjust for the natural variation of isotopic abundances, confirming that the individual is homozygous for allele 18. Our results clearly demonstrate that ESI-FTICR mass spectrometry is a powerful approach to characterize both simple and compound STRs beyond the capabilities of electrophoretic technologies.

Cyclotrons↗
PubMed2001

Comparison of variable number tandem repeat and IS6110-restriction fragment length polymorphism analyses for discrimination of high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates.

The present study was designed to evaluate the use of variable number tandem repeat (VNTR) and IS6110-restriction fragment length polymorphism (RFLP) analyses in combination as a two-step strategy for discrimination (as measured by the Hunter-Gaston Discrimination Index [HGDI]) of both high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates compared to IS6110-RFLP alone with an unselected collection of isolates. Individually, IS6110-RFLP fingerprinting produced six clusters that accounted for 69% of the low-copy-number IS6110 isolates (five clusters) and 5% of the high-copy-number IS6110 isolates (one cluster). A total of 39% of all the isolates were clustered (HGDI = 0.97). VNTR analysis generated a total of 35 different VNTR allele profile sets from 93 isolates (HGDI = 0.938). Combining IS6110-RFLP analysis with VNTR analysis reduced the overall percentage of clustered isolates to 29% (HGDI = 0.988) and discriminated a further 27% of low-copy-number isolates that would have been clustered by IS6110-RFLP alone. The use of VNTR analysis as an initial typing strategy facilitates further analysis by IS6110-RFLP, and more importantly, VNTR analysis subdivides some IS6110-RFLP-defined clusters containing low- and single-copy IS6110 isolates.

Cluster Analysis↗
PubMed2002

Strain typing of Borrelia burgdorferi, Borrelia afzelii, and Borrelia garinii by using multiple-locus variable-number tandem repeat analysis.

Human Lyme borreliosis (LB) is the most prevalent arthropod-borne infection in temperate climate zones around the world and is caused by Borrelia spirochetes. We have identified 10 variable-number tandem repeat (VNTR) loci present within the genome of Borrelia burgdorferi and subsequently developed a multiple-locus VNTR analysis (MLVA) typing system for this disease agent. We report here the successful application of MLVA for strain discrimination among a group of 41 globally diverse Borrelia isolates including B. burgdorferi, B. afzelii, and B. garinii. PCR assays displayed diversity at these loci, with total allele numbers ranging from two to nine and Nei's diversity (D) values ranging from 0.10 to 0.87. The average D value was 0.53 across all VNTR loci. A clear correlation exists between the repeat copy number and the D value (r = 0.62) or the number of alleles (r = 0.93) observed across diverse strains. Cluster analysis by the unweighted pair-group method with arithmetic means resolved the 30 observed unique Borrelia genotypes into five distinct groups. B. burgdorferi, B. afzelii, and B. garinii clustered into distinct affiliations, consistent with current 16S rRNA phylogeny studies. Genetic similarity and diversity suggest that B. afzelii and B. garinii are close relatives and were perhaps recently derived from B. burgdorferi. MLVA provides both phylogenetic relationships and additional resolution to discriminate among strains of Borrelia species. This new level of strain identification and discrimination will allow more detailed epidemiological and phylogenetic analysis in future studies.

Animals↗
PubMed2002

The 27-bp tandem repeat polymorphism in intron 4 of the endothelial nitric oxide synthase gene is not associated with coronary artery disease in a hospital-based Taiwanese population.

We studied whether the 27 base pair (bp) tandem repeat polymorphism in intron 4 of the endothelial nitric oxide synthase (eNOS) gene was associated with coronary artery disease (CAD) in a hospital-based Taiwanese population. We included 219 consecutive patients who underwent coronary angiography at our institution. Two alleles, containing 4 (eNOS4a) and 5 repeats (eNOS4b), were identified after polymerase chain reaction amplifying intron 4 of the eNOS gene. The genotype frequencies for eNOS4b/b, eNOS4a/b and eNOS4a/a were 77.9, 21.5 and 0.6% in CAD subjects, and 80, 20 and 0% in control subjects (Fisher's exact test, p = 0.90), respectively. The odds ratio (OR) for CAD in patients with at least one eNOSa allele was 1.2 (0.5-2.9) after adjustment for classical CAD risk factors. The eNOS4a allele was not associated with the severity of CAD (Fisher's exact test, p = 0.90) and the occurrence of acute myocardial infarction (AMI) or unstable angina (adjusted OR 0.6, 0.3-1.6) in patients with CAD. In conclusion, the 27-bp repeat polymorphism of the eNOS gene was not associated with CAD and the occurrence of AMI or unstable angina in a hospital-based Taiwanese population.

Aged↗
PubMed2006

[The genetic polymorphism of 9 short tandem repeat loci in Yi ethnic group of Yunnan in China].

OBJECTIVE: To study the short teadem repeat(STR) genetics structure of a Chinese Yunnan Yi racial group. METHODS: Genetic distributions for nine STR loci were determined based on STR gene scan marked by fluorescence. RESULTS: Sixty-nine alleles and 164 kinds of genotypes were detected and identified from 84 unrelated Yi racial individuals. The corresponding gene and genotype frequencies were in 0.0060-0.5060 or 0.0119-0.4167 respectively. The expected and observed genotype frequencies of nine STR loci were in accordance with the Hardy-Weinberg equilibrium(P>0.05). The statistical analyses of nine STR loci showed that PIC was distributed in 0.5804-0.8777, H was in 0.6507-0.8002, DP was in 0.7976-0.9558, EPP was in 0.5207-0.8386, except TPOX and THO1 loci. CONCLUSION: Above research data enrich the Chinese genetic database, and play an important role in Chinese genetic study and in forensic application.

Asian People↗
PubMed1995

Short tandem repeat polymorphism linkage studies in a new family with X-linked mental retardation (MRX20).

A family with X-linked recessive mental retardation (XLMR) without other obvious manifestations (MRX20) was studied with 14 short tandem repeat polymorphism (STRP) markers. Two-point lod scores above 3 were obtained with DXS1003, DXYS1, DXS3, and DXS458. A multipoint lod score of 4.25 was obtained with peak at DXS1003. Recombination events identify a 55.6 cM interval between DXS1068 and DXS454, while a one unit support interval identifies 40 cM between MAOA and DXS458.

Genetic Linkage↗