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PubMed1999

Validation of the HumDXS6807 short tandem repeat polymorphism for forensic application.

This paper presents sequence and population genetic data of the HumDXS6807 short tandem repeat (also known as CHLC.GATA52B03) which is a tetranucleotide repeat polymorphism representing seven alleles of 251-275 bp in length. HumDXS6807 is located at Xpter-Xp22.2, i.e., at a genetic distance of more than 87 and 151 cM from the well-known markers HumARA and HumHPRTB, respectively. Kinship tests in 157 family trios revealed a typical X-linked codominant inheritance; mutations were not found. Population genetic data were obtained by analyzing a Caucasian population sample comprising 308 females and 209 males: polymorphism information content (PIC) = 0.640; Heterozygosity (Het) = 0.668; Mean exclusion chance (MEC) = 0.414. The HumDXS6807 allele distribution met the Hardy-Weinberg expectations.

DNA↗
PubMed1997

Variation at three short tandem repeat (STR) loci in Australians: forensic and ethnic considerations.

We report the results of typing three short tandem repeat (STR) polymorphisms by a multiplex system in three forensically relevant populations of Australia; (i) a general Australian, (ii) a Caucasian, and (iii) an Asian sample. The STRs are tetranucleotide repeats in the following autosomal genes; CSF1PO, TPOX and THO1, and collectively comprise the CTT multiplex (Promega). In all three population samples, each of the loci exhibited genotype frequencies consistent with those expected under Hardy-Weinberg equilibrium, and, further, there was no significant deviation from random association of alleles across separate loci. These two characteristics, plus the high discrimination power values, demonstrate that the CTT multiplex system is a powerful tool for DNA profiling in Australian jurisdictions. Australian Asians and Caucasians exhibit frequencies of alleles at these three STR loci very similar to those in other Asian and Caucasian samples. While most of the variation exists within any single population, there are still considerable differences between Asians and Caucasians. This difference between the two groups is minimal with respect to TPOX and greatest for THO1 alleles.

Alleles↗
PubMed1994

Mapping of short tandem repeat polymorphisms on human chromosome 3.

Linkage analysis was used to determine map positions for 18 short tandem repeat polymorphisms that continuously span 186 cM of human chromosome 3. Mapping was based on the genotyping of 40 CEPH reference families. Loci order from pter-qter was D3S1252-D3S1235-D3S1234-D3S1233- D3S1254-D3S1251-D3S1215-RHO-ACPP- D3S1238-D3S1206-D3S196-D3S1237- (D3S1253,D3S1439)-D3S1243-D3S1232-SST. Odds against inversion of adjacent markers in all cases were 700:1 or better, except for the marker pair at D3S1253,D3S1439 that was not separated by any recombinants and therefore could not be ordered. Only one gap greater than 25 cM on the sex-equal map was observed.

Base Sequence↗
PubMed1999

A variable-number-tandem-repeat of the serotonin transporter gene and anxiety disorders.

1. A polymorphism of the variable-number-tandem-repeat (VNTR) in the second intron of the serotonin transporter (ST) gene, which has been reported to be associated with major depression, was studied in anxiety disorders. 2. The VNTR of the human ST gene was compared between 103 patients with anxiety and 106 controls. 3. The frequency of the allele containing 12 copies of the VNTR element (STin2.12) was significantly higher in the combined patient group (p = 0.027), and among patients with OCD (p = 0.0326), and GAD (p = 0.0123), in comparison with in controls. 4. The presence of the STin2.12 allele was significantly associated with the risk of combined anxiety disorders (odds ratio = 2.06, 95% CI 1.09-3.90), OCD (10.2, 1.34-77.4), and GAD (3.61, 1.23-10.6).

Adolescent↗
PubMed2002

Genomic diversity at 15 fluorescent labeled short tandem repeat loci in few important populations of State of Uttar Pradesh, India.

Genomic diversity at 15 short tandem repeat loci is studied in four major endogamous populations of Uttar Pradesh (UP), India. The studied populations included Thakur, Khatri, Kurmi and Jat; all of whom belong to Hindi speaking linguistic group of UP State of India. All the STR loci of Powerplex 16 System have been found highly significant in showing genomic diversity among the addressed populations. Homozygosity test values for all the 15 loci in studied population range between 0.053 and 0.999, following Hardy-Weinberg equilibrium. Distribution of allele pattern at fluorescent labeled 13 tetranucleotide repeat loci and two pentanucleotide repeat loci of Powerplex 16 System portrays that these markers are highly polymorphic, and thus, suitable in human identity testing and human genetic studies.

Gene Frequency↗
PubMed1997

A genetic study of the short tandem repeat systems VWA and TH01 in an Austrian population.

Allele- and genotype frequencies of the two short tandem repeat (STR) systems VWA and TH01 were determined in an Austrian population sample by polymerase chain reaction (PCR) analysis. A total of 9 alleles for VWA and 6 alleles for TH01 could be observed in a population of 278 (VWA) and 276 (TH01) individuals. Both systems are in accordance with Hardy-Weinberg equilibrium. They are highly informative for individualization from stain analysis and, in addition, they are very useful for paternity testing. The data presented here allow the statistical interpretation of PCR results for an Austrian population.

Alleles↗
PubMed1995

Rapid sizing of short tandem repeat alleles using capillary array electrophoresis and energy-transfer fluorescent primers.

Genetic typing of the short tandem repeat (STR) polymorphism HUMTHO1 has been performed using capillary array electrophoresis and energy-transfer fluorescent dye-labeled polymerase chain reaction primers. Target alleles were amplified by use of primers labeled with one fluorescein at the 5' end and another fluorescein at the position of the 15th (modified) base to produce fragments that fluoresce in the green (lambda max = 525 nm). Unknown alleles were electrophoretically separated together with a standard ladder made up of alleles having 6, 7, 8, and 9 four-base pair repeats, each of which was amplified with an energy-transfer primer having a donor fluorescein at the 5' end and a rhodamine acceptor at the position of the 7th (modified) base to produce standard fragments fluorescing in the red (> 590 nm). Separations were performed on arrays of hollow fused-silica capillaries filled with a replaceable sieving matrix consisting of 0.8% hydroxyethyl cellulose plus 1 microM 9-aminoacridine to enhance the resolution. The labeled DNA fragments were excited at 488 nm, and the fluorescence was detected with a two-color confocal fluorescence scanner. Separations are complete in less than 20 min and allow sizing with an average absolute error or accuracy of less than 0.4 base pair and an average standard deviation of approximately 0.5 base pair with no correction for mobility shift and cross-talk between the fluorescence channels. This work establishes the feasibility of high-speed, high-throughput STR typing of double-stranded DNA fragments using capillary array electrophoresis.

Alleles↗
PubMed1993

Variation of short tandem repeats within and between populations.

Using the polymerase chain reaction (PCR) the frequency distributions of three short tandem repeats (STR) were investigated in five populations: North European, Cypriot, Pakistani, Gujarati and Vietnamese. Each STR is situated within an intron; the markers are in the genes for human coagulation factor XIII (4bp repeat), lipoprotein lipase (4bp repeat) and CD4 (5bp repeat). Population data were generated for each STR and allele frequencies calculated. A calculation of the level of population substructuring for the three systems was also made. The lipoprotein lipase STR data showed no evidence for population substructuring, but there was a significant level of substructuring in the other two systems. This initial pilot study demonstrates the need to validate each marker used for DNA profiling in different human populations, and that some markers (such as LPL) can be used with confidence in widely differing ethnic groups, while others (such as CD4 and F13A) may be of value in distinguishing sub-groups.

Alleles↗
PubMed2002

Stability of variable-number tandem repeats of mycobacterial interspersed repetitive units from 12 loci in serial isolates of Mycobacterium tuberculosis.

Variable number tandem repeats (VNTRs) of elements named mycobacterial interspersed repetitive units (MIRUs) have previously been identified in 12 minisatellite loci of the Mycobacterium tuberculosis genome. These markers allow reliable high-throughput genotyping of M. tuberculosis and represent a portable approach to global molecular epidemiology of M. tuberculosis. To assess their temporal stability, we genotyped 123 serial isolates, separated by up to 6 years and belonging to a variety of distinct IS6110 restriction fragment length polymorphism (RFLP) families, from 56 patients who had positive sputum cultures. All 12 MIRU VNTR loci were completely identical within the groups of serial isolates in 55 out of 56 groups (98.2%), although 11 pairs of isolates from the same patients with conserved MIRU VNTRs displayed slightly different IS6110 RFLP profiles. In a single case, serial isolates with an unchanged IS6110 RFLP profile showed a change in 1 out of 12 MIRU VNTR loci. These results indicate that MIRU VNTRs are stable over time and therefore are suitable for reliable follow-up of patients chronically infected with tuberculosis over long periods. Moreover, they support MIRU VNTR genotyping as a powerful first-line method followed by subtyping by IS6110 RFLP to define ongoing transmission clusters.

Antitubercular Agents↗
PubMed2004

Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore.

Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The Hunter-Gaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.

Alleles↗
PubMed1985

Structure and evolution of two related transcription units of Epstein-Barr virus carrying small tandem repeats.

Two regions of the Epstein-Barr virus (EBV) genome carrying partially homologous clusters of short tandem repeats (NotI and PstI repeats) flanked by 1044 and 1045 base pairs with almost complete homology (DL and DR, left and right duplication, respectively) were most abundantly transcribed into poly(A)+ mRNA after induction with the tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate. The nucleotide sequence of both repeat clusters and the conserved upstream regulatory sequences from the M-ABA EBV strain are presented. Nearly the whole part of the sequences coding for the RNAs is covered by the NotI and PstI repeats, respectively. The regulatory sequences for these genes are located in the homologous regions of 1044 and 1045 base pairs (DL and DR, respectively). A CAAT box, a TATA box, and other herpes simplex virus-like elements were identified for both transcription units. The initiation points and the 3' ends of both inducible RNAs were mapped by S1 nuclease analysis. Both genes have open reading frames and may potentially code for proteins with repetitive amino acid compositions. The structure of these two inducible EBV genes is discussed, and an evolutionary model is proposed for the generation of gene duplication in the M-ABA strain of EBV.

Biological Evolution↗
PubMed2005

The variable number of tandem repeats element in DAT1 regulates in vitro dopamine transporter density.

BACKGROUND: A 40-bp variable number of tandem repeats (VNTR) polymorphism exists in the 15th exon of DAT1, the gene encoding the human dopamine transporter (DAT). Though the VNTR resides in a region encoding the 3' untranslated region (UTR) and does not alter the protein's amino acid sequence, the prevalent 10-repeat variant has shown both linkage and association to Attention Deficit Hyperactivity Disorder (ADHD). In this study, we examined the effects of the DAT1 VNTR on measures of in vitro DAT expression and pharmacology. A series of four DAT1 constructs, each containing the DAT1 coding region, but varying with respect to the downstream presence or content of the 3'UTR, were engineered and stably transfected into an HEK-293 variant using Flp-In integration, an enzyme-mediated, site-specific recombination technology. RESULTS: [3H] Win 35,428 saturation binding assays and DAT immunoblots revealed statistically significant differences in DAT expression attributable to DAT1 genotype. Cells harboring the 10-repeat DAT1 variant were characterized by a Bmax approximately 50% greater than cells with the 9-repeat VNTR; those containing only the DAT1 coding region or the coding region flanked by a truncated 3' UTR resulted in greater DAT density than either of the naturalistic 9- and 10-repeat variants. Competition binding assays showed no statistically significant DAT1 genotype effects on the DAT affinity for methylphenidate, a finding consistent with the positional location of the VNTR. CONCLUSION: This study identified the DAT1 VNTR as a functional polymorphism and provides an interpretive framework for its association with behavioral phenotypes.

Attention Deficit Disorder with Hyperactivity↗
PubMed2005

[Genetic polymorphism of 5 short tandem repeat loci in Hui population in Ningxia area].

OBJECTIVE: To analyze the genetic polymorphism of 5 short tandem repeat(STR) loci in Hui population in Ningxia area. METHODS: The genetic polymorphisms of five selected STR loci(D11S1984, D14S306, D14S617, D17S1290 and D19S433) in chromosomes 11, 14, 17 and 19 in 144 unrelated individuals in Hui population in Ningxia area were analyzed by PCR amplification, denaturing polyacrylamide gel electrophoresis(PAGE) and silver staining. RESULTS: 10, 8, 11, 13 and 8 alleles, 30, 25, 33, 40 and 23 genotypes of the 5 STR loci in Hui population in Ningxia were detected. The measured values of the heterozygosity of the 5 STR loci were 0.8413, 0.8033, 0.8331, 0.8369 and 0.7703; of the polymorphism information content were 0.8217, 0.7746, 0.8121, 0.8174 and 0.7332; of the discrimination power (DP) were 0.9516, 0.9257, 0.9611, 0.9660 and 0.9135. The calculated discrimination power was 0.9999995. The measured values of paternity exclusion were 0.7046, 0.6367, 0.6911, 0.7012 and 0.5801; the calculated paternity exclusion was 0.9958. The genotype distributions were in accordance with Hardy-Weinberg equilibrium. CONCLUSION: The 5 STR loci have better polymorphism in Hui population in the Ningxia area, and thus could serve as useful markers for population genetics research and for individual identification and paternity test in forensic medicine.

Asian People↗
PubMed2005

[Analysis on allele frequencies of 7 short tandem repeat loci of Kashing-Beck disease patients on].

OBJECTIVE: To analyze the allele frequencies of 7 short tandem repeat (STR) loci (D12S1718, D12S1675, D12S358, D12S367, D12S1638, D12S1646 and D12S1682) on chromosome 12 among Kashing-Beck disease (KBD) patients and the control population living in the KBD areas and non-KBD area. METHODS: EDTA-blood specimens were collected from 102 unrelated individuals of Chinese Han population in Shaanxi province including 29 KBD patients,30 controls living in the KBD area and 43 living in the non-KBD area. DNA samples were extracted using the Wizard Genomic DNA purification kit (http://www. Promega. com) and were amplified by polymerase chain reaction (PCR) technique. The PCR products were analyzed by ABI 3100 Genetic Analyzer. RESULTS: (1) In KBD patients group, the allele number for 7 STR loci were 4,7,7,8,5,5 and 7, the genotype number were 5,12,13,11,10,9 and 13; (2) In the control population living in KBD area, the allele number for 7 STR loci were 4,9,7,6,6,6 and 8,t he genotype number were 5,10,12,14,12,9 and 13;(3) In the control population living in the non-KBD area, the allele number for 7 STR loci were 7,9,7,7,5,8 and 11, the genotype number were 9,16, 17,16,12,15 and 20;(4) Compared with the allele frequencies among three groups, there were significant differences between KBD patients and the controls living in the KBD area (D12S367: P = 0.034; D12S1638: P = 0.041) and the controls living in the non-KBD area (D12S367: P = 0. 029; D12S1638: P= 0 .028) in the D12S367 and D12S1638 loci; (5) There were significant differences among KBD patients (P = 0.036), controls living in the KBD area (P = 0.039) and controls living in the non-KBD area in the D12S1646. CONCLUSION: There was significant difference between KBD patients and the controls in the D12S367 and D12S1638 loci.

Adult↗
PubMed2001

Detection of maternal DNA in umbilical cord plasma by fluorescent PCR amplification of short tandem repeat sequences.

Recently, maternal DNA was detected in umbilical cord blood using PCR amplification of minisatellite sequences. The presence of maternal DNA was demonstrated in 1% to 100% of umbilical cord blood samples. The objective of this study was to determine the frequency of cord blood contamination by maternal genetic material. We used fluorescent PCR amplification of highly polymorphic short tandem repeat (STR) markers to detect maternal DNA in umbilical cord plasma.

DNA↗
PubMed2006

Molecular crowding increases the amplification success of multiple displacement amplification and short tandem repeat genotyping.

Multiple displacement amplification (MDA) can generate large quantities of genomic DNA product from small amounts of template. We investigated the ability of MDA to amplify samples containing very small amounts of target DNA (5 pg to 1 ng) in the presence of a second, larger DNA sample for downstream short tandem repeat (STR) multiplex genotyping. We observed that STR amplification success of the minor fraction was increased in these mixed samples when compared with standard PCR only or MDA containing only the single trace DNA sample. Increased numbers of alleles were detected, with less amplification bias between loci than in single source samples undergoing the same protocol. To improve the STR genotyping accuracy, animal DNA was substituted for the additional human DNA, maintaining the increase in the number and quality of human-specific STR loci amplified. Polyethylene glycol 400, a commonly used crowding agent, was used as a replacement for the added genomic DNA in the MDA reaction and produced very similar results. Therefore, we suggest that additional DNA is acting as a molecular crowding agent during MDA. Performing MDA on trace amounts of DNA under crowded conditions results in greater numbers of alleles being amplified and more balanced amplification occurring between alleles.

Alleles↗
PubMed2003

Association of a functional tandem repeats in the downstream of human telomerase gene and lung cancer.

Chemoprevention has been widely explored as a promising strategy for controlling the incidence of lung cancer, the leading cause of cancer-related death. To maximize the benefit of lung cancer chemoprevention, it is important to identify individuals at high risk for the disease. The genetic background has been shown to play an important role in one's risk of developing lung cancer. We report here the identification of a polymorphic tandem repeats minisatellite (termed MNS16A) in the downstream region of the human telomerase gene. This minisatellite is located upstream of an antisense transcript from the human telomerase gene locus and was demonstrated to have promoter activity. The promoter activity was significantly lower in the construct containing the shorter repeats, suggesting that the MNS16A variant may have a relevance of functionality. To explore the role of this novel polymorphism in lung cancer, we conducted a pilot hospital-based case-control study by identifying the MNS16A genotype with genomic DNA from 53 lung cancer patients and 72 cancer-free controls. We found four different alleles and classified them as shorter (S) or longer (L) on the functional basis of the length of the repeats in the controls. The MNS16A genotype distributions of the SS, SL, and LL genotypes were 11, 32, and 57%, respectively, in the cases, and 14, 40, and 46%, respectively, in the controls. Compared with the SS+SL genotype, the LL genotype was associated with greater than twofold increased risk of lung cancer (odds ratio=2.18; 95% confidence interval=0.92, 5.20) after adjustment for age, sex, ethnicity, and smoking status, suggesting a potential role of MNS16A in lung cancer susceptibility. Larger studies are needed to verify our findings.

Base Sequence↗
PubMed2002

Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats.

The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S.25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

Centromere↗