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PubMed1999

Incorporation of N-acetylgalactosamine into consecutive threonine residues in MUC2 tandem repeat by recombinant human N-acetyl-D-galactosamine transferase-T1, T2 and T3.

An oligopeptide containing three consecutive Thr residues mimicking the tandem repeat portion of MUC2 (PTTTPLK) was investigated for the acceptor specificity to UDP-N-acetyl-D-galactosamine:peptide N-acetylgalactosaminyltransferase isozymes, UDP-N-acetyl-D-galactosamine:peptide N-acetylgalactosaminyltransferase-T1, T2 and T3. The enzymatic reaction products were fractionated by the reversed-phase high performance liquid chromatography, then characterized by matrix-assisted laser desorption ionization time of flight mass spectrometry and by a peptide sequencing analysis. A maximum of two, one or three N-acetyl-D-galactosamine residues was transferred by UDP-N-acetyl-D-galactosamine:peptide N-acetylgalactosaminyltransferase-T1, T2 or T3, respectively. The preferential orders of N-acetyl-D-galactosamine incorporation were Thr-2, then Thr-4 for UDP-N-acetyl-D-galactosamine:peptide N-acetylgalactosaminyltransferase-T1, Thr-2 for UDP-N-acetyl-D-galactosamine:peptide N-acetylgalactosaminyltransferase-T2 and Thr4, Thr-3, then Thr-2 for UDP-N-acetyl-D-galactosamine:peptide N-acetylgalactosaminyltransferase-T3.

Acetylgalactosamine↗
PubMed1997

Analysis of short tandem repeat polymorphisms in human DNA by matrix-assisted laser desorption/ionization mass spectrometry.

The analysis of an important class of human genetic polymorphisms, short tandem repeats (STRs), using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) is described. Several model STR systems have been investigated to evaluate MALDI-TOFMS as a realistic alternative to established electrophoresis procedures, and to develop rapid and generally applicable approaches to polymerase chain reaction (PCR) product purification for MALDI-TOFMS analysis. A purification/preconcentration method for PCR product preparation based on affinity capture of biotin-labeled PCR products is demonstrated to be directly compatible with MALDI-TOFMS analysis. The entire sample preparation for MALDI-TOFMS analysis immediately following PCR amplification from human DNA extracts can be accomplished routinely in under 12 min in a single Eppendorf tube. The simplicity of this approach essentially eliminates the sample preparation bottleneck encountered with MALDI-TOFMS analysis of PCR products using existing methods. Using this method, encouraging genotyping results are demonstrated for the THO1 and TPOxx STR systems using subpicomole quantities that represent a fraction of the original dsDNA from a single PCR reaction. The technique is also demonstrated to facilitate rapid sizing of PCR fragments larger than 200 bases using MALDI-TOFMS. As described here, the analysis of DNA can be accomplished in a manner that takes advantage of the rapid and accurate analysis capabilities offered by MALDI-TOFMS.

DNA↗
PubMed2000

Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry.

The application of electrospray ionization (ESI) ion trap mass spectrometry (MS) to the analysis of short tandem repeats (STRs or microsatellites) is described. Several equine dinucleotide STR loci were chosen as a model system to evaluate ESI ion trap as a routine instrument for rapid and reliable genoytping. With the use of specific primers STR loci were amplified from different blood samples having allele sizes between 60 and 100 bp. A new purification method based on reversible binding of PCR products to magnetic particles has proven to be directly compatible with ESI ion trap MS analysis. The sense and antisense strands of the PCR products with concentrations of approximately 100 fmol/microliter were measured with a mass accuracy of 0.01%. The simplicity of the purification method and the capability for automated handling together with the precise sizing of PCR products by ESI ion trap MS facilitate the large scale analysis of polymorphic STRs. Moreover, mixtures of different allele length as obtained for heterozygous samples could accurately be assigned as well as a C-->G switch between the two strands of a PCR product.

Animals↗
PubMed1996

Structure of a variable number tandem repeat of the serotonin transporter gene and association with affective disorder.

We have recently reported an association between a polymorphism of a variable number tandem repeat (VNTR) region of the serotonin transporter gene and susceptibility to major depressive disorder. We identified three alleles containing respectively 9 (STin2.9), 10 (STin2.10) and 12 (STin2.12) copies of a repetitive element. We report here the sequences of the three alleles. The repetitive element conformed to the consensus sequence, GGCTGYGACCY(R)GRRTG, where Y = T/C, R = G/A, with loss of the 12th base pair in one of the repeating elements. We have also extended the numbers of cases and controls in the study. The frequencies of the three alleles in 119 individuals with single or recurrent major depressive episodes, 128 individuals with bipolar disorder and a group of 346 controls were compared. There was a significant difference between patients with affective disorder and controls in the proportion of individuals carrying the STin2.9 allele. For the risk of unipolar disorder given a single STin2.9 allele, the odds ratio was 4.44 (95% Cl, 1.65-11.95) and for bipolar disorder 3.22 (95% Cl, 1.15-9.09). The findings support the hypothesis that allelic variation in the serotonin transporter gene may contribute to susceptibility for both major depression and bipolar disorder.

Alleles↗
PubMed1996

The presence of tandem repeats and the initiation of replication in rabbit mitochondrial DNA.

The non-coding region of rabbit mitochondrial DNA (mtDNA) exhibits two sets of tandem repeats between conserved sequence block 1 (CSB1) and the tRNA Phe gene. Both repeated sequences, short repeated (SR) and long repeats (LR), which contain 20 and 153 nucleotides, respectively, are involved in the generation of a high degree of mitochondrial heteroplasmy. Due to the location of these sequences in the regulatory region and their properties in terms of variable conformations, they could affect the initiation of replication of the heavy-strand DNA (H-strand DNA) and subsequently would influence the efficiency of mtDNA replication. The extremities of the displacement loop (D-loop) DNA strand and the 5' ends of RNA primers initiating the H-strand DNA synthesis were characterized in individual rabbits. Mapping at the nucleotide level of the 5' and 3' ends of the D-loop DNA strands indicates that both extremities are heterogeneous. The H-strand replication origin OH is located close to the conserved sequence block CSB1 as in other mammals. In all of the individuals studied so far, DNA molecules with a 5' end 1-2 nucleotides downstream of CSB1 were always present. As H-strand DNA replication is believed to be primed by RNA transcribed from the light-strand promoter (LSP), RNA mapping was carried out to identify the 5' end of H-strand RNA. Neighbouring initiation sites were identified at the nucleotide level in an (A+T)-rich region at nucleotide 1841 and in a stretch of cytosine residues at nucleotides 1849-1852, which are located at the beginning of the first long repeat. A detailed RNA analysis indicates that H-strand RNA molecules are initiated in each long repeat. The amplification of the regulatory region has produced multiple initiation transcription sites and a family of RNA primers of various lengths. These variations in length and the ensuing secondary structures are not critical for their potential function as H-strand DNA replication primers.

Animals↗
PubMed2006

Multiple-locus variable-number tandem repeat analysis for typing of Staphylococcus epidermidis.

We applied a high-resolution PCR-based typing method, multiple-locus variable-number tandem repeat analysis (MLVA), for discrimination of 30 multidrug-resistant clinical isolates of Staphylococcus epidermidis. The results of MLVA were congruent with results obtained by pulsed-field gel electrophoresis (PFGE). MLVA generated discrete character data, and its discriminatory capacity was comparable to that of PFGE.

Bacterial Typing Techniques↗
PubMed1998

Tetranucleotide short tandem repeat polymorphisms and their possible mode of origin.

An analysis of three autosomal, one X-chromosomal, and one Y-chromosomal tetranucleotide short tandem repeat loci in a large southern German population sample (including family studies) and in several nonhuman primate species revealed remarkable similarities in structure of already known and some newly detected alleles and in allele frequency distributions. These similarities, which are briefly discussed, can best be explained by transspecific evolution, followed by gene-conversion-like mutational events.

Alleles↗
PubMed2005

[Study of genetic polymorphism of 6 short tandem repeat loci in Nongqu Mongolian of inner Mongolia Autonomous Region in China].

OBJECTIVE: To get the genotype and allele frequency distribution of 6 short tandem repeat (STR) loci VWA, FGA, PENTAE, D6S1043, D2S1772, D7S3048 in NongQu Mongolia of China. METHODS: Two hundred and ninety-three unrelated individuals from Nongqu Mongolian were investigated. Polymerase chain reaction and polyacrylamide gel electrophoresis were used. RESULTS: Eighty alleles and 335 genotypes were detected, with frequencies ranging from 0.0017 to 0.2828. All the 6 loci met Hardy-Weinberg equilibrium. The statistical analysis of 6 STR loci showed the heterozygosity (H) >/= 0.7945, the discrimination power (DP) >/= 0.9160, the probability of paternity exclusion (PPE) >/= 0.5919, and the polymorphic information content (PIC) >/= 0.7617. CONCLUSION: These results could serve as valuable data to enrich the Chinese genetic database and play an important role in Chinese population genetic forensic medical application.

Alleles↗
PubMedDate not supplied

Genetic variation observed at three tetrameric short tandem repeat loci HumTHO1, TPOX, and CSF1PO--in five ethnic population groups of northeastern India.

This paper portrays the genetic variation observed at three tetrameric short tandem repeat (STR) loci HumTHO1, TPOX, and CSF1PO in five ethnic population groups from northeastern India. The study also specifies the suitability of use of these markers for forensic testing. The populations studied included three tribal groups (Kuki, Naga and Hmar), one Mongoloid caste group (Meitei), and a religious caste group (Manipuri Muslims). The loci were highly polymorphic in the populations, and all loci met Hardy-Weinberg expectations. No evidence for association of alleles among the loci was detected. The probability of match for the three loci of the most frequent genotype in the five population groups ranged between 2.6 x 10(-4) and 6.6 x 10(-5). The average heterozygosity among the population groups was approximately 70% with the overall extent of gene differentiation among the five groups being high (Gst = 0.046). Genetic affinity among the populations reveal very close association between the Kuki, Hmar, Naga, and Meitei. The Manipuri Muslims, despite being found in the same region, have had no admixture with these populations and maintain a substantial distance with the other groups. The genetic polymorphism data suggest that the studied systems can be used for human identity testing to estimate the frequency of a multiple locus STR DNA profile in population groups of northeastern India.

DNA Fingerprinting↗
PubMed1985

Calmodulin genes in trypanosomes are tandemly repeated and produce multiple mRNAs with a common 5' leader sequence.

In Trypanosoma brucei gambiense, the Ca2+ binding protein calmodulin is encoded by three identical tandemly repeated genes. The transcripts of these genes consist of several RNA species similar in size. A 35-nucleotide spliced leader sequence is present at the 5' end of each mRNA but is not encoded by DNA contiguous to these genes. We have identified two different sites for the fusion of the leader to the mRNA. These results strongly support the idea that a novel, possibly discontinuous, transcription mechanism is used by these parasites.

Amino Acid Sequence↗
PubMed1995

Stability of tandem repeats in the Drosophila melanogaster Hsr-omega nuclear RNA.

The Drosophila melanogaster Hsr-omega locus produces a nuclear RNA containing > 5 kb of tandem repeat sequences. These repeats are unique to Hsr-omega and show concerted evolution similar to that seen with classical satellite DNAs. In D. melanogaster the monomer is approximately 280 bp. Sequences of 19 1/2 monomers differ by 8 +/- 5% (mean +/- SD), when all pairwise comparisons are considered. Differences are single nucleotide substitutions and 1-3 nucleotide deletions/insertions. Changes appear to be randomly distributed over the repeat unit. Outer repeats do not show the decrease in monomer homogeneity that might be expected if homogeneity is maintained by recombination. However, just outside the last complete repeat at each end, there are a few fragments of sequence similar to the monomer. The sequences in these flanking regions are not those predicted for sequences decaying in the absence of recombination. Instead, the fragmentation of the sequence homology suggests that flanking regions have undergone more severe disruptions, possibly during an insertion or amplification event. Hsr-omega alleles differing in the number of repeats are detected and appear to be stable over a few thousand generations; however, both increases and decreases in repeat numbers have been observed. The new alleles appear to be as stable as their predecessors. No alleles of less than approximately 5 kb nor more than approximately 16 kb of repeats were seen in any stocks examined. The evidence that there is a limit on the minimum number of repeats is consistent with the suggestion that these repeats are important in the function of the unusual Hsr-omega nuclear RNA.

Alleles↗
PubMed1993

Mutation of human short tandem repeats.

A total of 20,000 parent-offspring transfers of alleles were examined through the genotyping within 40 CEPH reference families of 28 short tandem repeat polymorphisms (STRPs) located on chromosome 19. Forty-seven initial mutation events were detected in the STRPs using DNA from transformed lymphoblastoid cell lines, but less than half (39%) could be verified using DNA from untransformed cells. None of the cases where three alleles were observed in a single individual could be verified using DNA from untransformed cells. The average mutation rate for the chromosome 19 STRPs after correction for events which would not be detectable as Mendelian errors was 1.2 x 10(-3) per locus per gamete per generation. This rate may have been inflated by somatic as opposed to germline events. Observed mutation rates for individual STRPs ranged from 0 to 8 x 10(-3). The average mutation rate for tetranucleotide STRPs was nearly four times higher than the average rate for dinucleotide STRPs. For determination of the mode of mutation, events involving STRPs on other chromosomes were also examined. Of the events which were verified using DNA from untransformed lymphocytes or which were likely among those for which DNA from untransformed cells was not available: none were located at the sites of meiotic recombination, 91% involved the gain or loss of a single repeat unit, and 15 occurred in the male germline compared to 4 in the female germline (p = 0.01).

Base Sequence↗
PubMed1984

Human satellite I sequences include a male specific 2.47 kb tandemly repeated unit containing one Alu family member per repeat.

A portion of human satellite I DNA is digested by HinfI into three fragments of 775, 875 and 820bp in length which form a tandemly repeated unit 2.47kb in length, specific to male DNA. One Alu family member per repeat is found within the relatively G+C rich 775bp fragment. The 875 and 820bp fragments are highly A+T rich and consist of long stretches of poly dAdT and related sequences.

Base Composition↗
PubMed2006

The insulin gene variable number of tandem repeat: associations and interactions with childhood body fat mass and insulin secretion in normal children.

CONTEXT: Polymorphism at the insulin gene (INS) variable number of tandem repeat (VNTR) shows variable associations with childhood body mass index (BMI) in different populations. OBJECTIVE: The objective of this study was to observe INS VNTR associations with body composition and insulin secretion in children. DESIGN: The study was designed as a prospective birth cohort study. PARTICIPANTS: A total of 947 children genotyped for the INS VNTR participated. MAIN OUTCOME MEASURES: Main outcome measures were whole body dual x-ray emission absorptiometry at 9 yr to estimate height-corrected fat mass index (FMI), truncal FMI, and fat-free mass, and insulin secretion after oral glucose at 8 yr. RESULTS: Homozygous III/III children had higher BMI (P = 0.020), FMI (P = 0.015), and truncal FMI (P = 0.022) at 9 yr than class I bearers, but no difference in fat-free mass (P = 0.23). Gain in weight sd score between birth and 3 yr was associated positively with BMI, FMI, and truncal FMI in class I bearers, but not in III/III children (p-interaction with genotype = 0.009-0.066). INS VNTR genotype was not associated overall with insulin secretion at 8 yr (P = 0.64), but class I bearers showed a stronger positive correlation between insulin secretion and BMI at 8 yr (regression coefficient +/- se, 0.26 +/- 0.05; P < 0.0001) than III/III children (-0.10 +/- 0.07; P = 0.48) (p-interaction = 0.003). CONCLUSION: We clarified that the overall association between INS VNTR class III/III genotype and larger BMI in this population relates to fat mass, but not fat-free mass. In contrast, among the subgroup of children who showed rapid infancy weight gain, class I bearers tended to have larger BMI and fat mass than III/III children. This genetic interaction could relate to insulin secretion, which, in class I bearers, increased more rapidly with overweight and obesity.

Body Composition↗
PubMed2003

The insulin gene variable number tandem repeat class I/III polymorphism is in linkage disequilibrium with birth weight but not Type 2 diabetes in the Pima population.

The insulin gene variable number tandem repeat (INS-VNTR) is proposed to exert pleiotropic genetic effects on birth weight and diabetes susceptibility. In our study, we examined the influence of a polymorphism in tight linkage disequilibrium with INS-VNTR (-23Hph1) on birth weight and type 2 diabetes in the Pima population. A parent-offspring "trio" design was used to assess parent-of-origin effects and population stratification. The presence of the -23Hph1 T-allele was associated with lower birth weight (n = 192; -140 g per copy of the T-allele; P = 0.04), even after adjustment for effects of population stratification (P = 0.03). The effects of paternally transmitted T-alleles were greater than those of maternally transmitted alleles (paternally transmitted: -250 g, P = 0.05; maternally transmitted: -111 g, P = 0.43), but this difference was not statistically significant (P = 0.50). The -23Hph1 T-allele was associated with an increased prevalence of type 2 diabetes (P = 0.009), which family-based association analysis suggested was attributable to population structure (P = 0.04) without significant evidence of linkage disequilibrium between diabetes prevalence and genotype (P = 0.86). Thus allelic variation of the INS gene is associated with lower birth weight and increased prevalence of type 2 diabetes. Significant linkage disequilibrium was found between -23Hph1 and birth weight but not type 2 diabetes, an observation that supports a potential functional role of INS polymorphisms in the regulation of birth weight.

Adult↗
PubMed2003

[Genetic polymorphisms of short tandem repeats loci F13A01, FESFPS, vWA from Han population in Guizhou].

OBJECTIVE: To understand the allele structure and genetic polymorphism at F13A01, FESFPS and vWA short tandem repeats (STRs) loci for Han population in Guizhou province of China, and to construct a preliminary database. METHODS: One hundred sixty unrelated individuals in Han population from Guizhou were analyzed by multiplex polymerase chain reaction. The resultant allele frequencies were compared with those of other population or race database. RESULTS: The genotype distributions of F13A01, FESFPS and vWA were in accordance with Hardy-Weinberg equilibrium. The combined discrimination power and polymorphism information content were 0.9984 and 0.9700 respectively. CONCLUSION: All of the three loci in this study provide useful markers for forensic paternity test and for genetic purposes.

Alleles↗
PubMed1997

A human-specific polymorphism in the coding region of the aggrecan gene. Variable number of tandem repeats produce a range of core protein sizes in the general population.

Aggrecan, one of the major structural genes of cartilage, encodes a proteoglycan core protein composed of an extended central glycosaminoglycan-bearing domain, flanked by globular domains at each end. The central region consists of long stretches of repeating amino acids that serve as attachment sites for glycosaminoglycans such as chondroitin and keratan sulfate; the terminal globular domains interact with other cartilage components. The glycosaminoglycan attachment region is encoded in several species by a single large exon, within which are several different types of repeating sequences. Several species show within this exon a similar block of conserved repeats for attachment of chondroitin sulfate, but in humans this group of repeats is particularly well conserved. Examination of genomic DNA from a population of unrelated individuals by polymerase chain reaction or Southern blot assays shows this block of repeat sequences exists in multiple allelic forms, which differ by the number of repeats at this site in each allele. Thirteen different alleles have been identified, with repeat numbers ranging from 13 to 33. This is an unusual example of an expressed variable number of tandem repeat polymorphism. This polymorphism is apparently restricted to humans, of several species examined. This polymorphism results in individuals with differing length aggrecan core proteins, bearing different numbers of potential attachment sites for chondroitin sulfate. The possibility exists for a molecular understanding of biological variation in cartilage functional properties.

Aggrecans↗
PubMed1994

Simple tandem repeat DNA polymorphism in the human glycogen synthase gene is associated with NIDDM in Japanese subjects.

We investigated the possible association between alleles of a simple tandem repeat DNA polymorphism in the human glycogen synthase gene and non-obese non-insulin-dependent diabetes (NIDDM) in Japanese subjects. Nine alleles (-4G, -3G, -2G, -1G, 0G, 1G, 2G, 3G, and 4G) were identified in the study group of 164 patients with NIDDM and 115 non-diabetic subjects. The overall frequency distribution of the glycogen synthase gene alleles was significantly different between the two groups (p = 0.0316). The 2G allele was found more frequently in patients with NIDDM than in non-diabetic subjects (17.7% vs 8.7%, p = 0.0016). These results suggest that the 2G allele could be a genetic marker of NIDDM in Japanese subjects.

Adult↗