Results for “Short tandem repeat” — Page 3

PubMed1997

A dedicated internal standard in fragment length analysis of hyperpolymorphic short tandem repeats.

Some of the most polymorphic short tandem repeats (STRs) have alleles differing in size by as little as one basepair. Since sizing precision with commercially available internal standards ordinarily does not allow safe discrimination at this level, typing is accomplished through comparisons with allelic ladders run on each gel. Here we introduce the use of optimally spaced sequenced alleles as a dedicated internal standard for measurement and typing of hyperpolymorphic STRs. We have constructed such a dedicated internal standard for HUMACTBP2 ([1]; Moos and Gallwitz, EMBO I., 5 (1983) 757-761) typing, including 25 sequenced, ROX labelled HUMACTBP2 alleles spanning the size range for alleles at this locus (233-333 basepairs (bp)). Comparisons of inter-gel runs of selected alleles with this dedicated standard and the commercial GS500 internal standard demonstrate that only the presently described internal standard is suited for direct typing based on fragment length measurements only. Obvious advantages of this typing procedure are that fragment measurements are precise and in accordance with sequenced lengths, and that the typing procedure via an external allelic ladder is avoided. Sequences of the alleles used in the internal standard as well as of selected alleles for allelic ladders in two other hyperpolymorphic AAAG-repeat STRs, D11S554 (Phromchotikul et al., Hum. Mol. Genet., 3 (1991) 21) and HUMAPOA11 (Kimpton et al., PCR Methods Appl., 3 (1993) 13-22) are also presented. To allow fragment length analysis of these two STRs, five D11S554 alleles, spanning from 176 to 225 basepairs, were added to the dedicated internal standard. Performing similar comparisons as for HUMACTBP2, it is demonstrated that even if sizing accuracy is not as good as with HUMACTBP2, typing based on measured fragment size only may be achieved with both other STRs as well. Selecting different colours for the three STRs, triplex electrophoretic runs were performed of a Norwegian population database of 300 unrelated individuals. The probability that two unrelated individuals have the same type in all three STRs is 5 x 10(-7), and the combined paternity exclusion power 99.77%, indicating that this STR selection may represent a good choice for forensic genetic casework.

Base Composition↗

PubMed1998

Development and population study of an eight-locus short tandem repeat (STR) multiplex system.

Amplification of short tandem repeat (STR) loci has become a useful tool for human identification applications. To improve throughput and efficiency for such uses, the polymorphic STR loci CSF1PO, TPOX, TH01, vWA, D16S539, D7S820, D13S317, D5S818, F13A01, FESFPS, F13B, and LPL have been evaluated, developed, and configured into fluorescently labeled multiplex systems. Eight of these STR loci were combined to generate the PowerPlex System, a two-color multiplex system that supports rapid, accurate, reliable analysis and designation of alleles. The remaining four loci comprise the FFFL System, a one-color multiplex system. The PowerPlex System may be evaluated alternatively as two one-color, four-locus multiplex systems, CTTv Multiplex and GammaSTR Multiplex. The products of multiplex amplification may be analyzed with a variety of fluorescence detection instruments. Determination of genotypes of over 200 individuals from each of three different population/ethnic groups revealed independence of inheritance of the loci and allowed calculation of matching probability, typical paternity index, and power of exclusion for each multiplex.

Alleles↗

PubMed2007

Polymorphisms of short tandem repeat of genes and breast cancer susceptibility.

AIM: To explore the relationship of short tandem repeat polymorphisms and breast cancer susceptibility. METHODS: We searched the MEDLINE database (up to June 2006) with the keywords of tandem repeat sequences, gene polymorphisms, breast cancer, cancer susceptibility and microsatellite instability. We reviewed the literature on gene polymorphisms, especially the relationship of short tandem repeat and breast cancer risk. RESULTS: We focused on the candidate genes sex hormones, steroid hormone and receptors, carcinogen metabolism, cell proliferation regulation and other genes. CONCLUSIONS: The functional effects of short tandem repeat polymorphisms on cancer susceptibility, especially on breast cancer risk, are identified. The importance of short tandem repeat polymorphisms on development and progression of breast cancer are discussed.

Breast Neoplasms↗

PubMed1993

A polymorphic X-linked tetranucleotide repeat locus displaying a high rate of new mutation: implications for mechanisms of mutation at short tandem repeat loci.

We report a high rate of new mutation at a short tandem repeat sequence polymorphism (STR, microsatellite) at locus DXS981 on the proximal long arm of the human X chromosome. Among individuals of the CEPH pedigrees, new allele lengths are detected at this tetranucleotide repeat with a frequency of approximately 1.5%. In cases where the origin of the new allele was traceable, new mutant alleles at DXS981 varied by exactly one repeat length (4 bp) relative to that on the originating parental chromosome. Complete linkage disequilibrium between two additional insertion/deletion polymorphisms which closely flank the variation at the tetranucleotide repeat suggests that, to the extent that these new mutants are germline in origin, they are not generated by unequal exchange between homologues. Considered in light of the types of new mutations detected and the substantial linkage disequilibrium at this locus, these data have implications for the mechanism of variation at other loci containing short tandemly repeated sequences.

Alleles↗

PubMed1999

Numerous length polymorphisms at short tandem repeats in human cytomegalovirus.

We show the presence of numerous short tandem repeats in the human cytomegalovirus (HCMV) genome and assess their usefulness as molecular markers. The genome is shown to contain at least 24 microsatellite regions that exhibit length polymorphisms. Insertion-deletion polymorphisms at these short tandem repeats are common (80% of repeats examined are polymorphic among two laboratory strains and 10 clinical isolates). This is the first report of widespread microsatellite length polymorphism in a viral genome. Some regions are highly polymorphic: one was revealed by DNA sequencing to contain length variants at five closely linked sites, which combined resulted in 10 variants for this region among the 12 strains and isolates examined. This study not only provides a new molecular marker system for this virus but also extends our understanding of microsatellite polymorphism in two important ways. First, variable-length repeats in HCMV can be considerably shorter than polymorphic repeats previously found in other organisms. Second, highly variable microsatellite repeats are not confined to prokaryotes and eukaryotes, as previously assumed. This variation provides a useful marker system for distinguishing viral isolates, and similar markers are also likely to be found in other large-genome DNA viruses.

Cytomegalovirus↗

PubMed1992

Continuous linkage map of human chromosome 14 short tandem repeat polymorphisms.

Nine moderately to highly informative short tandem repeat polymorphisms were assigned to chromosome 14 using somatic cell hybrids and were mapped using linkage analysis. The nine markers formed a continuous linkage map covering almost the entire long arm from 14q11.2 to q32. The markers filled a large gap within previously reported linkage maps for this chromosome. Best order of the new loci from q11.2 to q32 was D14S50, D14S54, D14S49, D14S47, D14S52, D14S53, D14S55, D14S48, and D14S51. The order shown for all adjacent pairs of loci was very strongly favored with the exception of loci pair D14S55 and D14S48, for which the order was moderately favored. Map lengths for the nine loci were 142 cM in females and 72 cM in males. Female recombination frequencies exceeded male recombination frequencies in the middle and distal portions of the map.

Alleles↗

PubMed2005

Validation of a male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex.

Y chromosome-specific short tandem repeat (Y-STR) analysis has become another widely accepted tool for human identification. The PowerPlex Y System is a fluorescent multiplex that includes the 12 loci: DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. This panel of markers incorporates the 9-locus European minimal haplotype (EMH) loci recommended by the International Y-STR User Group and the 11-locus set recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Described here are inter-laboratory results from 17 developmental validation studies of the PowerPlex Y System and include the following results: (a) samples distributed between laboratories and commercial standards produced expected and reproducible haplotypes; (b) use of common amplification and detection instruments were successfully demonstrated; (c) full profiles were obtained with standard 30 and 32 cycle amplification protocols and cycle number (24-28 cycles) could be modified to match different substrates (such as direct amplification of FTA paper); (d) complete profiles were observed with reaction volumes from 6.25 to 50 microL; (e) minimal impact was observed with variation of enzyme concentration; (f) full haplotypes were observed with 0.5-2x primer concentrations; however, relative yield between loci varied with concentration; (g) reduction of magnesium to 1mM (1.5 mM standard) resulted in minimal amplification, while only partial loss of yield was observed with 1.25 mM magnesium; (h) decreasing the annealing temperature by 2-4 degrees C did not generate artifacts or locus dropout and most laboratories observed full amplification with the annealing temperature increased by 2 degrees C and significant locus dropout with a 4 degrees C increase in annealing temperature; (i) amplification of individual loci with primers used in the multiplex produced the same alleles as observed with the multiplex amplification; (j) all laboratories observed full amplification with >or = 125 pg of male template with partial and/or complete profiles observed using 30-62.5 pg of DNA; (k) analysis of < or = 500 ng of female DNA did not yield amplification products; (l) the minor male component of a male/female mixture was observed with < or =1200-fold excess female DNA with the majority of alleles still observed with 10,000-fold excess female; (m) male/male mixtures produced full profiles from the minor contributor with 10-20-fold excess of the major contributor; (n) average stutter for each locus; (o) precision of sizing were determined; (p) human-specificity studies displayed amplification products only with some primate samples; and (q) reanalysis of 102 non-probative casework samples from 65 cases produced results consistent with original findings and in some instances additional identification of a minor male contributor to a male/female mixture was obtained. In general, the PowerPlex Y System was shown to have the sensitivity, specificity and reliability required for forensic DNA analysis.

Animals↗

PubMed2005

Validation of male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex.

Y chromosome-specific short tandem repeat (Y-STR) analysis has become another widely accepted tool for human identification. The PowerPlex Y System is a fluorescent multiplex that includes the 12 loci: DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439. This panel of markers incorporates the 9-locus European minimal haplotype (EMH) loci recommended by the International Y-STR User Group and the 11-locus set recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Described here are inter-laboratory results from 17 developmental validation studies of the PowerPlex Y System and include the following results: (a) samples distributed between laboratories and commercial standards produced expected and reproducible haplotypes; (b) use of common amplification and detection instruments were successfully demonstrated; (c) full profiles were obtained with standard 30 and 32 cycle amplification protocols and cycle number (24-28 cycles) could be modified to match different substrates (such as direct amplification of FTA paper); (d) complete profiles were observed with reaction volumes from 6.25 to 50 microL; (e) minimal impact was observed with variation of enzyme concentration; (f) full haplotypes were observed with 0.5-2x primer concentrations; however, relative yield between loci varied with concentration; (g) reduction of magnesium to 1mM (1.5 mM standard) resulted in minimal amplification, while only partial loss of yield was observed with 1.25 mM magnesium; (h) decreasing the annealing temperature by 2-4 degrees C did not generate artifacts or locus dropout and most laboratories observed full amplification with the annealing temperature increased by 2 degrees C and significant locus dropout with a 4 degrees C increase in annealing temperature; (i) amplification of individual loci with primers used in the multiplex produced the same alleles as observed with the multiplex amplification; (j) all laboratories observed full amplification with >or = 125 pg of male template with partial and/or complete profiles observed using 30-62.5 pg of DNA; (k) analysis of < or = 500 ng of female DNA did not yield amplification products; (l) the minor male component of a male/female mixture was observed with < or =1200-fold excess female DNA with the majority of alleles still observed with 10,000-fold excess female; (m) male/male mixtures produced full profiles from the minor contributor with 10-20-fold excess of the major contributor; (n) average stutter for each locus; (o) precision of sizing were determined; (p) human-specificity studies displayed amplification products only with some primate samples; and (q) reanalysis of 102 non-probative casework samples from 65 cases produced results consistent with original findings and in some instances additional identification of a minor male contributor to a male/female mixture was obtained. In general, the PowerPlex Y System was shown to have the sensitivity, specificity and reliability required for forensic DNA analysis.

Animals↗

PubMed2001

Polar alteration of short tandem repeats (STRs) in mammalian cells.

Instability of short tandem repeats (STRs) in DNA during replication is observed in all organisms examined, and is causatively involved in various human diseases. We explore the mechanisms involved in instability by examining length changes occurring during the replication of [(CA)(20)TA](n) and [(CAG)(20)TAG](n), in human cells. We show that the majority of alterations consist of an insertion or deletion of one repeat unit, and base substitutions or length changes involving many repeat units are rare. We also show that length changes of two-tract STRs are biased toward the 3'-end of the repeat tract, in reference to lagging strand synthesis. There are some differences between our observations and previous observations in microbes, e.g. the orientation effect was not observed in this study. The results of this study are discussed in terms of the molecular mechanisms leading to alterations in repeat tracts.

Animals↗

PubMedDate not supplied

Y-chromosome haplotypes for six short tandem repeats (STRs) in a Mexican population.

BACKGROUND: Short tandem repeats (STRs) on the non-pseudoautosomal region of the Y-chromosome are DNA polymorphic markers able to solve special cases in legal medicine, for instance in paternity testing where the alleged father is not available, and in forensic situations, such as rape cases, where mixtures of male/female DNA are present. METHODS: Six STR polymorphisms from the Y-chromosome (DYS19, DYS385, DYS389/I, DYS390, DYS391, and DYS393) were PCR-typed in 120 males from the northwest region of Mexico by means of native polyacrylamide gel electrophoresis and silver staining. RESULTS: Allele frequencies were estimated for each STR. Their gene diversity ranged from 51.4% for DYS393 to 92.5% for DYS385. Mexican Y-STR allele distributions displayed similarity (p >0.05) with previously reported U.S. Hispanics for DYS19, DYS389/I, DYS390, DYS391, and DYS393. Although Mexicans showed the same modal allele for DYS385 (11/14; 24.4%) with regard to most European populations, differences in allele distributions were observed (p <0.01). The haplotype diversity and the male discriminatory capacity of this six-locus system were 99.3 and 84.1%, respectively. CONCLUSIONS: This knowledge permits the effective use of these six Y-chromosome markers in legal medicine casework in the studied population. This STR-system offers a great potential to identify males and male-lineages, and can be used confidentially in paternity testing and forensic analysis in the Mexican population.

Base Sequence↗

PubMed2001

Turkish population data with the CODIS multiplex short tandem repeat loci.

Allele frequencies for 13 tetrameric short tandem repeat (STR) loci, CSF1PO, D18S51, D3S1358, D21S11, D5S818, FGA, D7S820, HUMTH01, D8S1179, TPOX, D13S317, VWA, and D16S539 were determined on 198 Turkish blood samples.

Gene Frequency↗

PubMed2003

Polymorphism profile of nine short tandem repeat Loci in the Han chinese.

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX, CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amelogenin locus) were amplified with multiplex PCR and were genotyped with a four-color fluorescence method in samples from 174 unrelated Han individuals in North China. The allele frequencies, genotype frequencies, heterozygosity, probability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstrated that the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was 1.05 x 10(-10) within nine STR loci analyzed and the probability of paternity exclusion (EPP) was 0.9998. The results indicate that these nine STR loci and the Amelogenin locus are useful markers for human identification, paternity and maternity testing and sex determination in forensic sciences.

Amelogenin↗

PubMed2001

Case work guidelines and interpretation of short tandem repeat complex mixture analysis.

Interpretation guidelines for short tandem repeat casework analysis are difficult to construct. As soon as a set of guidelines are developed, a new case evolves that does not fit the painstakingly written document. The casework analysts gather and amend the guidelines again, and again. This article seeks to demonstrate that general guidelines can be set and written such that it can be used for any detection format. Guidelines published by the Scientific Working Group for DNA Analysis Methods, a working group of DNA forensic experts in the United States, are used to set the format for the written protocol on interpretations. The rule "the interpretation of results in casework is a matter of professional judgment and expertise. Not every situation can or should be covered by a preset rule" is stressed. Development of minimum and maximum threshold values, heterozygote ratios, stochastic limits, and determination of major and minor components based on validation studies is discussed. The paper travels through setting criteria to evaluate internal lane standards and amplification controls. It continues with establishing ranges for interpretation and defining true alleles versus anomalies. Examples of a variety of profiles are given and the potential interpretation, using signal intensities and genetics. In addition, report writing strategies and wording routinely used by the Pennsylvania State Police DNA Laboratory System are given.

Alleles↗

PubMed1997

Multiplex systems for the amplification of short tandem repeat loci: evaluation of laser fluorescence detection.

Short tandem repeat (STR) loci are ideal markers for personal identification and for genomic mapping. Two fluorescent multiplex systems, each designed for simultaneous PCR amplification of four polymorphic STR loci (HUMCSF1PO, HUMTPOX, HUMTH01 and HUMVWFA31, and HUMF13A01, HUMFESFPS, HUMBFXIII and HUMLIPOL), were evaluated on three laser fluorescence detection instruments. Concordant DNA typing results were obtained with all three detection methods. These fluorescent multiplex STR systems offer an accurate, reproducible and versatile method of DNA profiling that is well-suited for forensic identity testing and other genetic analyses.

Alleles↗

PubMed2006

[An analysis for genetic polymorphism of twelve Y short tandem repeat loci in Chaoshan populations].

OBJECTIVE: To study the genetic polymorphism of twelve short tandem repeat loci of Y chromosome in Chaoshan Han populations. METHODS: Twelve Y short tandem repeat loci, of which the template DNAs were extracted from blood samples of 121 unrelated Chaoshan Han individuals, were amplified by using the PowerPlex Y system. The PCR products were genotyped with ABI PRISM 3100 genetic analyzer. RESULTS: From the loci DYS19, DYS437, DYS389I, DYS389II, DYS438, DYS439, DYS393, DYS391, DYS390, and DYS392, 4-7 alleles were checked out; from the loci DYS385, 35 alleles were observed. The overall observed haplotype diversity reached 0.9976. DYS391 was the locus with the lowest gene diversity (0.4445), while DYS385 had the highest gene diversity (0.9525). CONCLUSION: The 12 Y-STR loci are highly polymorphic and suitable to forensic casework, population genetics and anthropology studies.

China↗

PubMed1998

Band shift analysis of three base-pair repeat alleles in the short tandem repeat locus D12S391.

Two hundred and sixty UK Caucasian individuals have been typed for the STR locus D12S391. Measurements of absolute band shift, relative to an allelic ladder, allowed fragments differing by one base pair to be consistently distinguished. The intermediate alleles typed from such fragments comprised approximately 5% of the total alleles observed in this study. The existence of intermediate alleles in the D12S391 locus, not included in the allelic ladder, allowed us to assess the efficacy of band shift analysis in detecting intermediate alleles on two different automated fluorescent detection platforms. The results of sequencing a sample of intermediate alleles are also presented.

Alleles↗

PubMed1995

Highly discriminating heptaplex short tandem repeat PCR system for forensic identification.

We describe a highly discriminating multiplex short tandem repeat PCR human identification system that gives a matching probability for Caucasians of European ancestry of 2.94 x 10(-8) or 5.66 x 10(-10) when used in combination with a previously described system. The system produces discrimination equal to or greater than four single locus probes (restriction fragment length polymorphism [RFLP] typing of variable nucleotide tandem repeat [VNTR] loci). The test is robust and reproducible and works with 1-10 ng of template DNA, using fluorescent detection of PCR products from either 4 or 6 short tandem repeat loci and the X-Y homologous gene amelogenin, giving simultaneous sex diagnosis.

Alleles↗

PubMed1996

High-resolution capillary array electrophoretic sizing of multiplexed short tandem repeat loci using energy-transfer fluorescent primers.

Short tandem repeat regions (STRs) from the polymorphic loci VWFA, THO1, TPO and CSF were amplified by the multiplex polymerase chain reaction (PCR) and analyzed by capillary array electrophoresis with fluorescence detection of energy transfer (ET) labels. The fluorescent ET primers are labeled with one fluorescein at the 5' end and a second fluorescein at the position of the 7th or 9th (modified) base to produce fragments that fluoresce in the green (lambda max = 525 nm). M13 A-track sequencing fragments, used as an internal sizing standard, were generated with a universal primer that has a donor fluorescein at the 5' end and a rhodamine acceptor at the position of the 11th (modified) base to produce fragments fluorescing in the red (> 590 nm). The labeled DNA fragments were excited at 488 nm, and the fluorescence was detected with a two-color confocal fluorescence scanner. Separations were performed on arrays of hollow fused silica capillaries filled with denaturing and replaceable hydroxyethyl cellulose sieving matrices. Separations were complete in less than 50 min, and single base resolution as well as reproducible STR sizing was achieved. The relative standard deviation in sizing was below 0.6%. This work establishes the feasibility of high-resolution, high-speed and high-throughput STR typing of single-stranded DNA fragments using capillary array electrophoresis.

Bacteriophage M13↗