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PubMed2003

Short tandem repeat typing in exon 1 of the androgen receptor gene.

Exon 1 of the androgen receptor (AR) gene on the X chromosome contains a polymorphic CAG trinucleotide short tandem repeat. We describe here the rapid and reliable method of typing CAG repeats using electrophoresis, with denaturing polyacrylamide gel and an allelic ladder marker. Twenty-one alleles (the repeat number ranges from 13 to 35) were found using CAG repeat typing in normal Japanese individuals (83 males and 82 females). The allelic diversity (h) calculated was h=0.889, illustrating that CAG repeats at the AR locus is a highly polymorphic system.

Chromosomes, Human, X↗
PubMed2006

The tandem-repeat polymorphism of the DC-SIGNR gene in HCV infection.

The C-type lectin DC-SIGNR has been shown to bind hepatitis C virus (HCV). Here, we analysed the tandem-repeat polymorphism of the DC-SIGNR gene with respect to intraindividual HCV replication. In a cross-sectional comparison HCV-infected patients (n = 430) and healthy subjects (n = 100) were genotyped for the DC-SIGNR polymorphism using PCR. The distribution of DC-SIGNR alleles did not differ significantly between the two groups. However, HCV-infected patients with 5-, 6-, and 7-repeat alleles had higher HCV-RNA levels when compared with carriers of 4- and 9-repeat alleles (P < 0.05). Thus, the DC-SIGNR polymorphism might affect HCV loads supporting the concept that DC-SIGNR contributes to HCV replication efficacy.

Adult↗
PubMed1994

Genetic linkage studies in antithrombin-deficient kindreds using a highly polymorphic trinucleotide short tandem repeat (STR) within the human antithrombin gene.

PCR amplification and analysis of short tandem repeats (STR) have provided a useful tool for genetic linkage studies and for the diagnosis of genetic disorders. We have recently identified a novel trinucleotide STR, (ATT).(TAA), in the fifth intron of the human antithrombin gene (AT3) located on chromosome 1q23. PCR amplification, cloning, and sequence analysis revealed this AT3-STR to be highly polymorphic with repeat units ranging in size from (ATT)5 to (ATT)18. Ten distinct alleles were found in 81 unrelated Caucasian individuals (162 alleles) with an observed heterozygosity of 81%. Genetic linkage studies using the AT3-STR in two previously described antithrombin (AT)-deficient kindreds, AT-Hamilton (Ala 382 Thr) and AT-Amiens (Arg 47 Cys), demonstrate, in a given kindred, that a specific AT3-STR polymorphism is strongly associated with a particular AT mutation. Thus, this highly polymorphic AT3-STR should be very useful in performing linkage studies in AT-deficient kindreds as well as in investigating other chromosome 1-related genetic disorders.

Antithrombins↗
PubMed1995

Expression and characterization of a single recombinant proteoglycan tandem repeat domain of link protein that binds zinc and hyaluronate.

The first proteoglycan tandem repeat (PTR) of bovine link protein has been cloned in the pMAL-c vector and overexpressed in fusion with maltose-binding protein (MBP) in Escherichia coli. The fusion protein can be isolated from the soluble phase of the bacterial lysate by amylose affinity chromatography. The PTR domain can be cleaved from the MBP domain with factor Xa protease. Evidence using zinc affinity chromatography is presented which indicates that at least one of the zinc-binding sites of bovine link protein is contained within the first PTR domain. Zinc affinity chromatography was then incorporated as the final purification step of the MBP/PTR protein. Evidence for the binding of MBP/PTR to hyaluronic acid (HA) is demonstrated by coprecipitation with HA using cetylpyridinium chloride. Binding is specific since MBP/PTR does not coprecipitate with chondroitin sulfate. Binding is also demonstrated in an ELISA assay on HA-coated plates. In this assay, binding could be inhibited by the addition of HA or HA oligosaccharides.

Amino Acid Sequence↗
PubMed1995

Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers.

The use of short tandem repeat polymorphisms (STRPs) as marker loci for linkage analysis is becoming increasingly important due to their large numbers in the human genome and their high degree of polymorphism. Fluorescence-based detection of the STRP pattern with an automated DNA sequencer has improved the efficiency of this technique by eliminating the need for radioactivity and producing a digitized autoradiogram-like image that can be used for computer analysis. In an effort to simplify the procedure and to reduce the cost of fluorescence STRP analysis, we have developed a technique known as multiplexing STRPs with tailed primers (MSTP) using primers that have a 19-bp extension, identical to the sequence of an M13 sequencing primer, on the 5' end of the forward primer in conjunction with multiplexing several primer pairs in a single polymerase chain reaction (PCR) amplification. The banding pattern is detected with the addition of the M13 primer-dye conjugate as the sole primer conjugated to the fluorescent dye, eliminating the need for direct conjugation of the infrared fluorescent dye to the STRP primers. The use of MSTP for linkage analysis greatly reduces the number of PCR reactions. Up to five primer pairs can be multiplexed together in the same reaction. At present, a set of 148 STRP markers spaced at an average genetic distance of 28 cM throughout the autosomal genome can be analyzed in 37 sets of multiplexed amplification reactions. We have automated the analysis of these patterns for linkage using software that both detects the STRP banding pattern and determines their sizes. This information can then be exported in a user-defined format from a database manager for linkage analysis.

Chromosome Mapping↗
PubMed1989

Enzymatic synthesis of DNA probes complementary to a human variable number tandem repeat locus.

Both cloned and synthetic DNA probes complementary to human variable number tandem repeat (VNTR) loci have been used to detect restriction fragment length polymorphism. In this report, we describe an approach for the enzymatic synthesis of a DNA probe complementary to one VNTR locus. The probe is produced by annealing short synthetic oligonucleotides comprising single repeat units and enzymatically ligating them into a polymeric DNA probe. In HinfI digests of human genomic DNA separated by agarose gel electrophoresis, this ligated oligonucleotide probe (LOP) detects multiple polymorphic loci in the range of 3-23 kb producing highly informative DNA fingerprint patterns when different individuals are compared. The hybridization pattern is very stable even under high-stringency wash conditions. The LOP is more easily generated than cloned VNTR probes and is totally synthetic, avoiding problems associated with cloned probes including bacterial growth and maintenance as well as in vitro labeling.

Autoradiography↗
PubMed1994

PCR typing of DNA fragments of the short tandem repeat (STR) system HUMTH01 in Danes and Greenland Eskimos.

DNA from the short tandem repeat (STR) system HUMTH01 was amplified by the polymerase chain reaction (PCR) and analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 100 unrelated Danes, 147 unrelated Greenland Eskimos, and 89 Danish mother/child pairs were analyzed. Significant differences were observed between the distribution of fragments ('alleles'), whereby allele number 7 was considerably more frequent in Eskimos (0.687) than in Danes (0.201). The distributions of HUMTH01 phenotypes were in Hardy-Weinberg equilibrium in both the Eskimo and Danish populations. In the 89 Danish mother/child pairs, the segregation of the HUMTH01 genotypes was in accordance with the genetic model of co-dominant inheritance and no mutations were found. In a blind trial, DNA samples from 40 unrelated Danes were investigated by one of us in Copenhagen, at the FBI Forensic Science Research and Training Center (FSRTC), Quantico, and at the Institut für Rechtsmedizin, Münster, Germany. Concordant HUMTH01 types were found in 39 out of 40 individuals. The allele which led to discrepant typing results was assigned type 9.3 in two laboratories and type 10 in one laboratory.

Alleles↗
PubMed1991

The use of synthetic tandem repeats to isolate new VNTR loci: cloning of a human hypermutable sequence.

Synthetic tandem repeats (STRs) of oligonucleotides have previously been shown to detect polymorphic loci in the human genome. Here, we report results from the use of three such probes to screen a human cosmid library. Nine of the 45 positive clones that were analyzed appear to contain highly polymorphic minisatellite or VNTR loci. The degree of enrichment for minisatellite sequences varied with the choice of STR: one provided a 15- to 20-fold enrichment (4 polymorphic loci among 10 clones), whereas 2 others gave a 3- to 5-fold enrichment (5 polymorphic probes in a total of 35 clones) compared to random screening. The 9 VNTR markers have been localized by linkage analysis in the CEPH panel and/or by in situ hybridization. Eight probes identify new loci, one of which maps to an interstitial region. One of the VNTR loci (identified by probe CEB1) was found to be hypermutable, with 52 mutation events identified among 310 children characterized in 40 CEPH families. The parental origin of the mutation could be identified in all instances, and only one mutation was found to be of maternal origin. The mutation rate in males was estimated to be approximately 15%. Segregation analysis of flanking markers suggests that mutations are not associated with crossing over. As the only previously described hypermutable minisatellite loci in humans have equal rates of male and female mutations, these observations establish that a second type of hypermutable minisatellite exists in the human genome. In neither case does the generation of new alleles appear to be associated with unequal crossing over.

Base Sequence↗
PubMed2006

Divergence of ape and human monoamine oxidase A gene promoters: comparative analysis of polymorphisms, tandem repeat structures and transcriptional activities on reporter gene expression.

A variable number of tandem repeats (VNTR) polymorphism based on a 30-bp unit have been reported in the promoter region of the human monoamine oxidase A gene (MAOA). Human VNTRs have been shown to affect transcriptional activity, and some reports suggest that VNTR polymorphisms are associated with psychoneurological disorders. VNTR polymorphism has also been reported in the ape MAOA promoter but the transcriptional activities of the alleles remain to be determined. In the present study, we sequenced the 1.3-kb promoter region of ape MAOA and compared the transcriptional activities of ape MAOA promoter sequences with those of humans. All apes examined were polymorphic in the region corresponding to the human VNTR and two, four, three, and two alleles were found in chimpanzees, gorillas, orangutans, and gibbons, respectively. VNTR repeat structures in gorillas, orangutans, and gibbons were considerably different from those in humans and chimpanzees. In a human neuroblastoma cell line, most of the ape sequences that had a short repeat length (12bp or 18bp) exhibited higher promoter activity than a human 3-repeat sequence with a 30-bp repeat length. However, an intra-species difference dependent on the repeat number was not observed among the ape alleles examined.

Animals↗
PubMed1995

Analysis of short tandem repeat (STR) allele frequency distributions in a Balinese population.

Genotypes for 53 short tandem repeat (STR) markers distributed at an average of 39 cM intervals throughout the genome were determined for 46 individuals from the village of Bengkala, Bali. This village of approximately 2200 individuals has an oral and written tradition suggesting genetic bottlenecks. The allele frequency distributions in Bengkala were compared with distributions obtained by typing individuals in the CEPH data base using a Kolmogorov-Smirnov two sample test. Twenty-eight of the 53 markers showed differences (P < 0.05) in distribution between the two populations. Allele frequencies of tetranucleotide STRs were much more similar between the two populations than were those of dinucleotide STRs (P < 0.043). Population heterogeneity in Bengkala was indicated by an excess of observed homozygosity, deviations from Hardy-Weinberg equilibrium at seven loci, and significant allelic associations between physically unlinked loci. In addition to providing information pertinent to the issue of genetic diversity of STRs in the human population, these analyses serve as a resource to map a gene causing non-syndromal autosomal recessive deafness in Bengkala, and to corroborate the anthropological study of the history and social structure of the village.

Alleles↗
PubMed2001

Highly polymorphic short tandem repeat analyses clarify complex molecular test results.

Judicious application of highly polymorphic short tandem repeat (STR) analyses and modification of assay conditions readily distinguished nonparentage from true parentage, with occasional failure to transmit one parentally derived allele. These categories were resolved with a reliability of >99.9%, the standard applied to most DNA evidence presented in a U.S. court of law. While completing a single prenatal diagnosis submitted at 19 weeks gestation, the authors found that one polymorphic grandpaternal allele did not amplify, a duplicate control propositus' DNA sample had been switched by an outside laboratory, and recombination occurred in maternal meiosis within the mutant gene region. In two parentage cases with one available parent, a Y-linked STR or an autosomal STR was modified when transmitted to the offspring. In contrast, some apparently inconsistent results between parental DNA and offspring were resolved by purifying or diluting the original extracted DNA samples. Thus, the source of each complex molecular test result was characterized unambiguously by testing a sufficient number of highly polymorphic STR loci and by purifying or diluting troublesome DNA samples to diminish polymerase chain reaction amplification artifact.

Adult↗
PubMed2005

Mutations of 15 short tandem repeat loci in Chinese population.

OBJECTIVE: To explore the mutations of 15 short tandem repeat (STR) loci in PlowerPlex16 System which are world-widely used in parentage testing. METHODS: Mutations of 15 STR loci in PlowerPlex16 System were investigated in 1921 parentage testing cases from Chinese population. RESULTS: In 1921 parentage cases, seventy cases (3.644%) were found to have mutations. Among these were one case with double mutations (D21S11 and PentaD) and another case with two different mutations (D7S820 and D16S539) in two children. The total number of mutated STR loci observed was 72 over 3764 meiosis with a mutation rate of 0.128% +/- 0.1104% x 10(-3). The highest mutation rate was 0.292% at vWA and D21S11. No mutation was observed at TH01 or at TPOX. The mutated alleles coming from father were five times more than those from mother. The majority (98.611%) of mutated alleles were the results of one-step mutation. The ratio of one-step gain versus loss was 1.826:1. There was only one multiple-step mutation with a double-repeat gain observed at PentaD locus. In the PlowerPlex16 System, nine loci, namely D8S1179, Penta D, D13S317, D16S539, D7S820, D5S818, D3S1358, TH01 and TPOX, have lower mutation rates and are more suitable for parentage testing. CONCLUSION: Mutation of STR is relatively common and often makes parentage testing more complicated. Selecting stable STR locus with low mutation rate is more important in parentage testing.

Alleles↗
PubMed2006

[Structure analysis of apolipoprotein B 3' variable number of tandem repeats].

OBJECTIVE: To study the distribution, frequency and structure of variable number of tandem repeats (VNTR) in 3' region of apoB gene in Chinese population. METHODS: Genomic DNA was extracted from peripheral blood obtained under consent from randomly-chosen 522 individuals who came to the hospital for physical examination, and used to screen for polymorphisms of 3' VNTR of the apoB gene by employing polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), gradient polyacrylamide gel electrophoresis, cloning and sequencing. RESULTS: Sixteen types of alleles of apoB 3oVNTR were identified, among which heterozygotes were more than homozygotes. The biggest allele is HVE58, and the smallest one is HVE22. HVE34 had the highest frequency (40.4%), followed by HVE32 (34.7%). This showed significant difference from the allelic distribution of other populations (Caucasian and Swedish). Through sequencing of 60 alleles, a new isomer (Y-A=ATAATTAAATATTT) and four new types of alleles were found. CONCLUSION: The Chinese population we studied had a higher frequency of small alleles and showed a difference in allelic structure and frequency distribution from European and American in this populations.

Adult↗
PubMed1995

Accurate size comparison of short tandem repeat alleles amplified by PCR.

A strategy is presented for classifying complex short tandem repeat (STR) alleles by size. Such alleles can differ in length by only 1 bp. The HUMACTBP2 locus was used as a model. Dye-labeled, PCR-amplified alleles were analyzed on an automated DNA sequencer with laser-induced fluorescence detection and fragment-sizing software. Between-gel allele sizes calculated against an in-lane allelic ladder or viral DNA size standard were too imprecise to distinguish a 1-bp difference. However, the size difference between a sample allele and its matching ladder allele provided a reliable criterion for size classification. The mean size difference +/- 3 SDs was 0.5 bp, and so an individual result within this interval signified a match. Statistically, 99.7% of the results should lie within +/- 3 SDs with virtually no chance of encountering the 9-SD difference from the mean necessary to misclassify an allele by 1 bp. The method was valid for sample alleles sized against the allelic ladder and for both sample and ladder alleles sized against the viral DNA standard. A correction for the effect of different dye labels on mobility was included in the calculations.

Alleles↗
PubMed1996

[Population genetics of short tandem repeat locus HUMTH01].

The distributions of genotypes and allele frequencies for the short tandem repeat locus HUMTH01 in Chinese and German populations were studied by amplified fragment length polymorphism analysis. The PCR amplification products with different primers were compared by coelectrophoresis and the population data from different laboratories were evaluated. Based on the allele frequencies of HUMTH01, the genetic distances among 25 populations were computed and a phylogenetic tree was constructed accordingly. Some new implications for population genetics were obtained from this phylogenetic tree.

Chromosome Mapping↗
PubMed2005

Use of PCR amplification of tRNA gene-linked short tandem repeats for genotyping Entamoeba histolytica.

We have developed a reliable method for PCR-based genotyping of Entamoeba histolytica based on variation in the numbers of short tandem repeats that are linked to tRNA genes in this species. Species-specific primer pairs were designed that differentiate E. histolytica from E. dispar as well as that reveal intraspecies PCR product length polymorphisms. The primers were tested with samples from different parts of the world, and DNA was extracted from cultured cells as well as liver abscess pus and feces by various methods. We now have the tools necessary to investigate a possible link between parasite genotype and the outcome of infection with Entamoeba histolytica, as well as other aspects of the organism's epidemiology.

Animals↗
PubMed2005

Short tandem repeat (STR) genotyping of keratinised hair. Part 1. Review of current status and knowledge gaps.

We present a review of the literature on procedures for obtaining short tandem repeat (STR) genotypes from keratinised hair, being either hair shaft or telogen phase (naturally shed) hairs without associated scalp, follicle or sheath cells. Both the hair shaft and the telogen hair club have been subjected to the DNA-degrading keratinisation process and are more likely to be found at a crime scene than anagen (plucked) or catagen phase hairs. We discuss human hair structure, the human hair growth cycle, the keratinisation process and their implications for DNA extraction procedures, PCR amplification strategies and the interpretation of STR genotypes. Knowledge gaps and areas requiring research are identified and are the subject of a second article in this series.

DNA↗