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PubMed1998

Genotyping of forensic short tandem repeat (STR) systems based on sizing precision in a capillary electrophoresis instrument.

Automated fluorescence analysis of polymerase chain reaction (PCR)-amplified short tandem repeat (STR) systems by capillary electrophoresis (CE) is becoming an established tool both in forensic casework and in the implementation of both state and national convicted offender DNA databases. A new capillary electrophoresis instrument, the ABI Prism 310 Genetic Analyzer, along with the Performance Optimized Polymer 4 (POP-4) provides an automated and precise method for simultaneously analyzing ten fluorescently labeled STR loci from a single PCR amplification kit, which provides a power of discrimination of approximately one in five billion from a single PCR amplification. Data are presented on sizing precision, sizing accuracy, and resolution for the STR loci in the AmpFlSTR Profiler kit. Sizing accuracy is highly dependent on the electrophoresis system, and therefore the reporting of alleles based on the nucleotide size obtained from an electrophoresis system is not recommended for forensic work. The precision of the 310 capillary electrophoresis system, coupled with software developed for automated genotyping of alleles based on the use of an allelic ladder, allows for accurate genotyping of STR loci. Sizing precision of < or = 0.16 nucleotide standard deviation was obtained with this system, thus allowing for accurate genotyping of length variants that differ in length by a single nucleotide.

Alleles↗
PubMed1998

Glycosylation of the tandem repeat unit of the MUC2 polypeptide leading to the synthesis of the Tn antigen.

A synthetic peptide corresponding to the human MUC2 tandem repeat domain containing 14 Thr residues was glycosylated in vitro using UDP-GalNAc and microsomal membranes of the colorectal cancer cell line, LS180. The products were fractionated by reverse phase HPLC, which gave seven glycopeptide fractions. Their molecular weights were estimated by matrix-assisted laser desorption/ionization mass spectrometry, the values obtained corresponding to glycopeptides containing from one to ten GalNAc residues. On solid phase radioimmunoassaying involving a monoclonal anti-Tn antibody (MLS128), it was found that the glycopeptides containing nine or ten GalNAc residues were strongly immunoreactive, whereas the glycopeptides containing less than six GalNAc residues were inactive, indicating that a cluster of GalNAc-Thr is essential for the Tn antigenicity.

Acetylgalactosamine↗
PubMed1995

Swiss population data and forensic efficiency values on 3 tetrameric short tandem repeat loci-HUMTH01, TPOX, and CSF1PO-derived using a STR multiplex system.

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci were determined in a Swiss population sample (n = 100) using the GenePrint STR Multiplex System, electrophoresis of the PCR products in DNA sequencing gels and subsequent detection of allelic fragments by silver staining. The loci are HUMTH01, TPOX, and CSF1PO. The observed heterozygosities are 83.0%, 60.0%, and 72.0%, respectively. The discrimination power determined for the individual loci is 0.914, 0.780, and 0.860, respectively, and the combined discrimination power for the triplex is 0.997. All loci meet Hardy-Weinberg expectations and after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence. Moreover, independence of alleles at these STR loci with other PCR-based loci derived from the same Swiss population sample, previously reported, were considered. These loci were DQA1, LDLR, GYPA, HBGG, D7S8, GC and D1S80. Again, after Bonferroni correction there was no evidence that the population sample deviates from expectations of independence among alleles at the 10 different PCR-based loci. Thus, the allelic frequency data can be used in human identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Swiss population.

Alleles↗
PubMed1994

Swiss population data on three tetrameric short tandem repeat loci--VWA, HUMTHO1, and F13A1--derived using multiplex PCR and laser fluorescence detection.

Allele and genotype frequencies for 3 tetrameric short tandem repeat loci VWA, HUMTHO1, and F13A1 were determined in a Swiss population sample using multiplex PCR and subsequent electrophoresis in DNA sequencing gels processed by automated laser fluorescence detection. The technique allows single base pair resolution and rapid typing, with a concomitant reduction in the potential for human transcriptional typing errors. All loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the 3 loci. The allelic frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a multiple STR locus DNA profile in the Swiss population.

Alleles↗
PubMed1996

PCR typing of DNA fragments of the two short tandem repeat (STR) systems upstream of the human myelin basic protein (MBP) gene in Danes and Greenland Eskimos.

DNA from the double short tandem repeat (STR) system MBP (locus 18q23-pter) was amplified by the polymerase chain reaction (PCR) and the two polymorphic repeat systems were separated by cutting with the restriction enzyme NlaIII. The lengths of the DNA fragments of the two MBP STR systems MBP-A and MBP-B were analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 112 unrelated Danes, 140 unrelated Greenland Eskimos, and 88 Danish mother/child pairs were analyzed. The distributions of MBP phenotypes were in Hardy-Weinberg equilibrium in both the Eskimo and Danish populations. Significant differences were observed between the distribution of fragments ('alleles') in Greenland Eskimos and in Danes. The allele MBP-A7 was considerably more frequent in Eskimos (0.2214) than in Danes (0.0775) and also the allele MBP-B9 was considerably more frequent in Eskimos (0.225) than in Danes (0.06). Strong gametic associations were found between fragments from MBP-A and MBP-B series in both Danes and Eskimos. Some of the associations were different in Danes and Eskimos. In the 88 Danish mother/child pairs, the segregation of the MBP genotypes were in accordance with a genetic model of co-dominant inheritance and no mutation was found. Two MBP STR regions with irregular structures were sequenced. One fragment had a single base G to A transition at position 124 in the primer binding region between the MBP-A and MBP-B regions. In the other fragment, a deletion starting at position 117 and including the primer binding region between MBP-A and MBP-B regions was found.

Alleles↗
PubMed2001

Genotyping of dinucleotide tandem repeats by MALDI mass spectrometry of ribozyme-cleaved RNA transcripts.

We describe a method for high-throughput typing of short tandem repeat (STR) polymorphisms. Current gel electrophoresis techniques allow only moderate throughput with long hands-on and analysis time, and the output is on a relative scale of electrophoretic mobility, prone to artifacts. Matrix-assisted laser- desorption/ionization mass spectrometry (MALDI-MS) enables an automated high throughput and delivers accurate data directly depicting the molecular nature of the analyte. Analysis of large DNA fragments, however, is limited by adduct formation and fragmentation, which result in peak broadening and low signal intensity. MALDI typing of polymorphic STRs has been reported for tri- and tetranucleotide repeats with sufficient resolution to distinguish alleles. For dinucleotide repeats, essential in animal genome studies, an enhanced resolution is necessary. Increased mass resolution was reported for RNA (ref. 7) and modified DNA (refs 8-10) due to substituents that disfavor intramolecular reactions leading to fragmentation. RNA transcripts can be synthesized enzymatically from PCR products containing a promoter sequence, requiring no specialty reagents or primer labels. Furthermore, RNA transcripts are single-stranded, a prerequisite for high-resolution mass spectrometry of nucleic acids. The 3' heterogeneities produced by viral RNA polymerases, however, impede exact sizing of RNA runoff transcripts. Non-templated multiple-base extensions as well as premature termination have been reported. PCR of dinucleotide repeats tends toward the deletion of repeat units, generating a complex pattern of interleaved extensions (from RNA polymerase) and deletions (from PCR) that obscure the true allele size. We overcome this obstacle by adding a 3' sequence encoding a catalytic RNA sequence, the so-called hammerhead ribozyme, that cleaves itself co-transcriptionally, creating a homogeneous 3' end.

Alleles↗
PubMedDate not supplied

Short tandem repeat (STR) variation in eight village populations of the island of Korcula (Croatia).

The aim of this study was to analyse short tandem repeat (STR) variation using the data on nine loci (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, D7S820) in the populations from eight villages on the island of Korcula, Croatia, in order to analyse its genetic and population structure. The analysis of STR data in this study indicated an appreciable degree of genetic homogeneity among the studied village populations on the island, even though a so-called 'east-west dichotomy' and differentiation between the inhabitants of the most recent settlement and the remaining ones was indicated with respect to the loci CSF1PO and TPOX, respectively. The validity of STR markers in assessing genetic structure of small populations and especially in determining the relationships among geographically closely related but reproductively isolated groups remains to be further evaluated, especially in terms of a larger number of studied loci in order to possibly find specific markers useful for resolving genetic patterns of variability at regional levels.

Croatia↗
PubMed1989

A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. I. Conformational predictions for the tandemly repeated peptide (Asn-Ala-Asn-Pro)9.

A search for low-energy helical and near-helical conformations of the tandemly repeated peptide (Asn-Ala-Asn-Pro)9 was undertaken by minimization of the CHARMM potential energy function from eight starting conformations; the latter were obtained from the two low-energy conformations of this repeated peptide found by Gibson & Scheraga, Proc. Natl. Acad. Sci. USA 83, 5649-5653 (1986), and the single conformation found by Brooks et al., Proc. Natl. Acad. Sci. USA 84, 4470-4474 (1987), and from modifications of these three conformations. The same eight starting conformations, as determined by dihedral angles, were used for minimizations of the AMBER and ECEPP potentials. Comparison of the final conformations by least-squares superposition of their C alpha atoms, and by inspection of the parameters of the ideal helix or coiled coil that most closely matched the coordinates of their C alpha atoms in a least-squares sense, showed that: (1) energy minimization, starting from the same conformation but using any two different potentials, could lead to final conformations whose resemblance to each other varied from acceptable to highly unsatisfactory; (2) the ordering of the final energy-minimized conformations, and the energy differences between them, were quite different for all three potentials; (3) the extent of agreement or disagreement between pairs of conformations generated using CHARMM and AMBER, CHARMM and ECEPP, or AMBER and ECEPP, respectively, was not significantly different. The lowest-energy conformation generated using each of the potentials was a left-handed helix, whose pitch and number of residues per turn were similar to those of the left-handed helix found by Gibson & Scheraga. Although the starting conformation which led to the lowest-energy conformation was different for all three potentials, pairwise superposition of the C alpha atoms in the final conformations showed root-mean-square deviations of only 1.0-1.3 A. It is concluded that energy minimizations starting from a large enough sample of initial conformations might on occasion lead to essentially the same conformational prediction whichever potential is used; however, if the sample of starting points is small, predictions based on the three potentials will usually diverge.

Amino Acid Sequence↗
PubMed2001

In vivo glycosylation of mucin tandem repeats.

The biochemical and biophysical properties of mucins are largely determined by extensive O-glycosylation of serine- and threonine-rich tandem repeat (TR) domains. In a number of human diseases aberrant O-glycosylation is associated with variations in the properties of the cell surface-associated and secreted mucins. To evaluate in vivo the O-glycosylation of mucin TR domains, we generated recombinant chimeric mucins with TR sequences from MUC2, MUC4, MUC5AC, or MUC5B, which were substituted for the native TRs of epitope-tagged MUC1 protein (MUC1F). These hybrid mucins were extensively O-glycosylated and showed the expected association with the cell surface and release into culture media. The presence of different TR domains within the chimeric mucins appears to have limited influence on their posttranslational processing. Alterations in glycosylation were detailed by fast atom bombardment mass spectrometry and reactivity with antibodies against particular blood-group and tumor-associated carbohydrate antigens. Future applications of these chimeras will include investigations of mucin posttranslational modification in the context of disease.

Amino Acid Sequence↗
PubMed1990

Structural instability of human tandemly repeated DNA sequences cloned in yeast artificial chromosome vectors.

The suitability of yeast artificial chromosome vectors (YACs) for cloning human Y chromosome tandemly repeated DNA sequences has been investigated. Clones containing DYZ3 or DYZ5 sequences were found in libraries at about the frequency anticipated on the basis of their abundance in the genome, but clones containing DYZ1 sequences were under-represented and the three clones examined contained junctions between DYZ1 and DYZ2. One DYZ3 clone was quite stable and had a long-range structure corresponding to genomic DNA. All other clones had long-range structures which either did not correspond to genomic DNA, or were too unstable to allow a simple comparison. The effects of the transformation process and host genotype on YAC structural stability were investigated. Gross structural rearrangements were often associated with re-transformation of yeast by a YAC. rad1-deficient yeast strains showed levels of instability similar to wild-type for all YAC clones tested. In rad52-deficient strains, DYZ5 containing YACs were as unstable as in the wild-type host, but DYZ1/DYZ2 or DYZ3 containing YACs were more stable. Thus the use of rad52 hosts for future library construction is recommended, but some sequences will still be unstable.

Chromosomes, Fungal↗
PubMed1993

Identification of a simple tandem repeat DNA polymorphism in the human glycogen synthase gene and linkage to five markers on chromosome 19q.

We have identified a simple tandem repeat DNA polymorphism in the human glycogen synthase gene of the form (TG)n. This DNA polymorphism has 10 alleles and a heterozygosity of 0.82 and can be easily typed using the polymerase chain reaction. It has been localized within the framework genetic map of chromosome 19 and is located in the region of the apolipoprotein C-II and histidine-rich calcium-binding protein genes. This DNA polymorphism will facilitate genetic studies of the role of the glycogen synthase gene in the development of insulin resistance and NIDDM.

Base Sequence↗
PubMed2004

Maternal-fetal interactions and birth order influence insulin variable number of tandem repeats allele class associations with head size at birth and childhood weight gain.

Polymorphism of the insulin gene (INS) variable number of tandem repeats (VNTR; class I or class III alleles) locus has been associated with adult diseases and with birth size. Therefore, this variant is a potential contributory factor to the reported fetal origins of adult disease. In the population-based Avon Longitudinal Study of Pregnancy and Childhood birth cohort, we have confirmed in the present study the association between the INS VNTR III/III genotype and larger head circumference at birth (odds ratio [OR] 1.92, 95% CI 1.23-3.07; P = 0.004) and identified an association with higher cord blood IGF-II levels (P = 0.05 to 0.0001). The genotype association with head circumference was influenced by maternal parity (birth order): the III/III OR for larger head circumference was stronger in second and subsequent pregnancies (OR 5.0, 95% CI 2.2-11.5; P = 0.00003) than in first pregnancies (1.2, 0.6-2.2; P = 0.8; interaction with birth order, P = 0.02). During childhood, the III/III genotype remained associated with larger head circumference (P = 0.004) and was also associated with greater BMI (P = 0.03), waist circumference (P = 0.03), and higher fasting insulin levels in girls (P = 0.02). In addition, there were interactions between INS VNTR genotype and early postnatal weight gain in determining childhood BMI (P = 0.001 for interaction), weight (P = 0.005), and waist circumference (P = 0.0005), such that in the approximately 25% of children (n = 286) with rapid early postnatal weight gain, class III genotype-negative children among this group gained weight more rapidly. Our results indicate that complex prenatal and postnatal gene-maternal/fetal interactions influence size at birth and childhood risk factors for adult disease.

Birth Order↗
PubMed2004

Variation at the insulin gene VNTR (variable number tandem repeat) polymorphism and early growth: studies in a large Finnish birth cohort.

Variation at the insulin gene (INS-)VNTR (variable number of tandem repeats) minisatellite polymorphism has been reported to be associated with both early growth and adult metabolic phenotypes. However, the samples studied have been small and the relationship between INS-VNTR variation and parameters of early growth inconsistent, with four previous studies producing conflicting results. We have studied the relationship between INS-VNTR class (measured by genotyping the nearby -23HphI variant with which it is in tight linkage disequilibrium) and early growth in 5,646 members of the Northern Finnish Birth Cohort of 1966. Comparing class III homozygotes with other genotypes using multivariate linear regression analysis, we found no significant associations with any early growth measure (birth weight, birth length, ponderal index, and head circumference at 1 year), even after stratifying subjects by growth trajectory during infancy and/or birth order. For example, among infants with limited postnatal growth realignment (n = 2,470), class III/III infants were no heavier at birth (difference [+/-SE] in the means [fully adjusted], 58 +/- 51 g; P = 0.26) than class I/- infants. No significant associations were detected following reanalysis with an additive model (for example, for birth weight, beta = 20 g [95% CI -3 to 44], P = 0.09). Studies of this large population-based cohort have failed to generate convincing evidence that INS-VNTR variation influences early growth.

Birth Order↗
PubMed2005

[Genetic polymorphism of Y-chromosome short tandem repeat in Elunchun ethnic group of China].

OBJECTIVE: To reveal the allelic frequencies and haplotype frequencies of ten Y-chromosome short tandem repeats(STR) loci (DYS392, DYS438, DYS439, DYS456, DYS459, DYS460,DYS461, DYS462, DYS389I and DYS389II systems) in an Elunchun population sample. METHODS: PCR and polyacrylamidegel electrophoresis(PAGE) followed by silver staining were performed to analyze the blood samples from 102 unrelated Elunchun male individuals. RESULTS: The allele diversity values for each locus ranged from 0.418(DYS461) to 0.727(DYS389 I). Gene diversities were higher than 0.5 except DYS462(0.479) and DYS461 (GATAA7.2)(0.418). Furthermore, 101 haplotypes from 10 Y-chromosome STRs loci were found in the sample and a high haplotype diversity 0.99 was determined. CONCLUSION: The above findings suggest that the ten Y-chromosome STR loci are valuable Y-specific markers for establishing Y-STR database, understanding human origin, paternity testing and personal identification.

China↗
PubMed1995

[Analysis of short tandem repeats polymorphism in the phenylalanine hydroxylase gene and its application to prenatal gene diagnosis of phenylketonuria].

There is a polymorphic tetranucleotide short tandem repeats (STR) sequence in the intron 3 of the phenylalanine hydroxylase (PAH) gene. The polymorphism of this STR sequence in Chinese was analysed on 36 normal individuals and 16 PKU families. After PCR amplification, the DNA fragments were separated on polyacrylamide sequencing gel and visualized by silver-staining. Seven alleles were identified with frequencies of 0.028, 0.042, 0.014, 0.138, 0.542, 0.208 and 0.028 in normal populations, and 0.016, 0.078, 0.047, 0.312, 0.375, 0.156 and 0.016 in PKU families, and PICs of 0.585 and 0.693, respectively. This polymorphic marker is very useful in quick prenatal gene diagnosis in PKU families, and prenatal gene diagnosis was performed by linkage analysis in two pregnancies at risk.

Alleles↗
PubMed1985

Short tandem repeats shared by B- and C-hordein cDNAs suggest a common evolutionary origin for two groups of cereal storage protein genes.

We have identified cDNA clones coding for the major sulphur-rich and sulphur-poor groups of barley storage proteins (the B- and C-hordeins, respectively). Hybridization studies have revealed unexpected homologies between B- and C-hordein mRNAs. Using a deletion mutant (Risø 56), we have mapped some C-hordein-related sequences within, or closely associated with, B-hordein genes at the Hor 2 locus. Nucleotide sequencing has shown that the primary structure of B-hordein polypeptides can be divided into at least two domains: domain 1 (repetitive, proline-rich, sulphur-poor), which is homologous to C-hordein sequences, and domain 2 (non-repetitive, proline-poor, sulphur rich), which makes up two-thirds of the polypeptide and is partially homologous to a 2S globulin storage protein found in dicotyledons. The coding sequences that are homologous in B- and C-hordein mRNAs have an asymmetric base composition (>80% C-A) and are largely composed of a degenerate tandem repeat based on a 24 nucleotide consensus that encodes Pro-Gln-Gln-Pro-Phe-Pro-Gln-Gln. We discuss the evolutionary implications of the domain structure of the B-hordeins and the unusual relationship between the two groups of barley storage proteins.

Amino Acid Sequence↗
PubMed2005

Rapid prenatal diagnosis of trisomy 21 by real-time quantitative polymerase chain reaction with amplification of small tandem repeats and S100B in chromosome 21.

Trisomy 21 (Down syndrome) is the most common congenital anomaly, and it occurs in one out of 700-1000 births. Current techniques such as amniocentesis and chorionic villi sampling (CVS) require lengthy laboratory culture procedures and high costs. This study was undertaken to establish a rapid prenatal diagnosis of trisomy 21 using real-time quantitative polymerase chain reaction (PCR) of fetal DNA from amniotic fluid. Real-time quantitative PCR was performed with DNA templates obtained from 14 normal blood samples, 10 normal amniotic fluid samples, 14 Down syndrome blood samples, and 7 Down syndrome amniotic fluid samples. Primers for D21S167 and S100B of chromosome 21 were used. Primers that direct the amplification of the 165-bp fragment of the insulin-like growth factor (IGF)-1 gene on chromosome 12 using a PCR primer were included to generate an internal standard for quantitation. The relative levels of D21S167 and S100B were 2.6 and 2.4 times higher in the blood of Down syndrome patients than those in the control group. The differences between these two groups were statistically significant (p-values were 0.0012 and 0.0016, respectively). The relative levels of D21S167 and S100B were 2.1 and 2.7 times higher in the amniotic fluid of Down syndrome fetuses than those in the control group. The difference between these two groups was statistically significant (p-values were 0.0379 and 0.0379, respectively). Prenatal diagnosis of trisomy 21 by real-time quantitative PCR using STR (small tandem repeats) amplification of D21S167 and S100B is a useful, accurate and rapid diagnostic method. Furthermore, it may also be useful for prenatal diagnosis with fetal DNA from maternal blood, and for preimplantation genetic diagnosis and prenatal counseling.

Amniotic Fluid↗
PubMed1997

Variable number of tandem repeats in clinical strains of Haemophilus influenzae.

An algorithm capable of identifying short repeat motifs was developed and used to screen the whole genome sequence available for Haemophilus influenzae, since some of these repeats have been shown to affect bacterial virulence. Various di- to hexanucleotide repeats were identified, confirming and extending previous findings on the existence of variable-number-of-tandem-repeat loci (VNTRs). Repeats with units of 7 or 8 nucleotides were not encountered. For all of the 3- to 6-nucleotide repeats in the H. influenzae chromosome, PCR tests capable of detecting allelic polymorphisms were designed. Fourteen of 18 of the potential VNTRs were indeed highly polymorphic when different strains were screened. Two of the potential VNTRs appeared to be short and homogeneous in length; another one may be specific for the H. influenzae Rd strain only. One of the primer sets generated fingerprint-type DNA banding patterns. The various repeat types differed with respect to intrinsic stability as well. It was noted for separate colonies derived from a single clinical specimen or strains passaged for several weeks on chocolate agar plates that the lengths of the VNTRs did not change. When several strains from different patients infected during an outbreak of lung disease were analyzed, increased but limited variation was encountered in all VNTR sites analyzed. One of the 5-nucleotide VNTRs proved to be hypervariable. This variability may reflect the molecular basis of a mechanism used by H. influenzae bacteria to successfully colonize and infect different human individuals.

Algorithms↗