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Results for “Short tandem repeat”

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At least 577 records · Page 32Linked to original sources
PubMed2002

Determination of the donor:host blood cell ratio after haematological stem cell transplant by means of semiquantitative detection of short tandem repeat polymorphisms.

An improved method of quantifying the donor:host blood cell ratio after haematological stem cell transplantation (PBSCT) using a variable number of tandem repeat (VNTR) markers is presented. The post-transplant DNA is extracted from the patient's blood and amplified by semiquantitative polymerase chain reaction (PCR) without prior mock transplant and plotting of a standard curve. The amplification products are then analysed by ABI PRISM 310 capillary electrophoresis apparatus. The resultant peak areas are correlated with the corresponding microsatellite allele by GeneScan software and the donor:host cell ratio is calculated. Improvements to PCR amplification conditions are essential for the outcome of the quantification since preferential amplification of alleles in the PCR process can account for the marked deviation found between the results gained by measurement of different microsatellite loci. To assess the accuracy of the method, the post-transplant blood samples of 6 patients who had undergone either myeloablative or non-myeloablative transplantation regimens were analysed retrospectively (median observation time 298 days). By analysing 3 or 4 microsatellite loci we were able to detect full engraftment or mixed chimaerism after transplant with a measurement precision of < or = 4.5 (standard deviation). Sensitivity for different primers ranges from 2% to 5%. The results of the microsatellite analysis correlated well with the corresponding clinical findings. We conclude that post-transplant analysis of microsatellite loci using semiquantitative PCR without standard is suitable for clinical purposes.

Humans↗
PubMed1999

Maine Caucasian population DNA database using twelve short tandem repeat loci.

A population study of Caucasians residing in Maine was conducted using the AmpF1STR Profiler PCR Amplification Kit and the AmpF1STR Profiler Plus PCR Amplification Kit (Applied Biosystems Division (ABD) of Perkin Elmer, Foster City, CA). The kits contain the reagents necessary to amplify 12 different STR loci and the gender marker Amelogenin using two multiplex PCR, each containing nine STR loci. Thus, there is an overlap of six STR loci. The 12 STR loci are TH01, TPOX, CSF1PO, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820. These loci represent 12 of the 13 core loci selected by the CODIS STR standardization project. Dye-labeled amplification products were separated and detected using the capillary electrophoresis instrument ABI Prism 310 Genetic Analyzer. Allele frequencies were determined for the 12 STR loci. Statistical analysis of the data included Hardy-Weinburg equilibrium (HWE) analysis, pairwise independence testing, power of discrimination (PD), and probability of exclusion (PE).

DNA↗
PubMed1999

Variation at 4 short tandem repeat loci in 8 population groups of India.

We have determined the nature and extent of variation at 4 STR loci (CSF1P0, TPOX, TH01, VWA) in 8 caste and tribal population groups of eastern and northern India. Large differences in allele frequencies among the groups were found. Average heterozygosities in all populations were high (approximately 80%). The overall extent of gene differentiation among the 8 groups was high (GST = 0.04). The nature of genomic affinities based on these 4 STR loci does not completely agree with our earlier finding based on classical genetic markers that geographic proximity of habitat has a greater influence on genetic similarity between populations than sociocultural proximity does.

Developing Countries↗
PubMed2000

Population data on the X chromosome short tandem repeat locus HumHPRTB in two regions of Germany.

This report contains the results of two population studies on the X chromosome STR HumHPRTB carried out in a Northern and a Southern region of Germany. The numbers of unrelated individuals were 443 and 335, respectively. Eight alleles (alleles 9 to 16) were found. In female individuals 29 different genotypes were encountered. In German populations the HumHPRTB STR was characterized by the following data: PIC = 0.750; HET = 0.769: MEC = 0.556. Allele distribution met the Hardy-Weinberg expectations. The Northern and Southern populations did not show any significant differences.

Alleles↗
PubMed2000

Diversity of two short tandem repeat loci (CD4 and F13A1) in three Brazilian ethnic groups.

Two microsatellites (CD4 and F13A1) were investigated in seven Brazilian populations: one group each of European- and African-derived subjects from Porto Alegre, southern Brazil, and five Amerindian tribes (three Tupi-Mondé speaking [Gavião, Surui, and Zoró], one Macro-Gê [Xavante], and one Carib [Wai-Wai]). For both markers, neo-Brazilians presented with a high diversity, but Amerindians showed a low level of variability. Genotype frequency distributions were heterogeneous among populations, the only exception being similar CD4 frequencies in Afro- and Euro-Brazilians. Gene diversity analysis revealed that most of the total variation is due to intrapopulational diversity in all populations. Because of the high information content of these markers in Afro- and Euro-Brazilians, these systems are most appropriate for forensic analyses. The comparison among Brazilian and other world populations revealed high similarity among populations of the same ethnic group, indicating a high discriminative power for these markers.

Brazil↗
PubMed2001

Identifying sex chromosome abnormalities in forensic DNA testing using amelogenin and sex chromosome short tandem repeats.

Forensic DNA laboratories worldwide have begun using multiplexed STR systems to decrease analysis time and increase sample throughput. The loci used in these systems are basically "nonsense" regions of human DNA. However, due to the chromosome on which some of these loci are located, various genetic abnormalities can sometimes be detected. This paper will show one such abnormality--Klinefelter's Syndrome--and the process used to show the possibility of this defect in two undiagnosed males using peak height ratios at the Amelogenin locus, and X-Y STRs.

Amelogenin↗
PubMed2001

Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples.

The amplification and typing conditions for the 13 core CODIS loci and their forensic applicability were evaluated. These loci are CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11. Results were obtained using the multiplex STR systems AmpFlSTR Profiler Plus and AmpFlSTR COfiler (Applied Biosystems, Foster City, CA), GenePrint PowerPlex (Promega Corporation, Madison, WI), and subsets of these kits. For detection of fluorescently labeled amplified products, the ABI Prism 310 Genetic Analyzer, the ABI Prism 377 DNA Sequencer, the FMBIO II Fluorescent Imaging Device, and the Fluorlmager were utilized. The following studies were conducted: (a) evaluation of PCR parameter ranges required for adequate performance in multiplex amplification of STR loci, (b) determination of the sensitivity of detection of the systems, (c) characterization of non-allelic PCR products, (d) evaluation of heterozygous peak intensities, (e) determination of the relative level of stutter per locus, (f) determination of stochastic PCR thresholds, (g) analysis of previously typed case samples, environmentally insulted samples, and body fluid samples deposited on various substrates, and (h) detection of components of mixed DNA samples. The data demonstrate that the commercially available multiplex kits can be used to amplify and type STR loci successfully from DNA derived from human biological specimens. There was no evidence of false positive or false negative results and no substantial evidence of preferential amplification within a locus. Although at times general balance among loci labeled with the same fluorophore was not observed, the results obtained were still valid and robust. Suggested criteria are provided for determining whether a sample is derived from a single source or from more than one contributor. These criteria entail the following: (a) the number of peaks at a locus, (b) the relative height of stutter products, and (c) peak height ratios. Stochastic threshold levels and the efficiency of non-templated nucleotide addition should be considered when evaluating the presence of mixtures or low quantity DNA samples. Guidelines, not standards, for interpretation should be developed to interpret STR profiles in cases, because there will be instances in which the standards may not apply. These instances include (a) a primer binding site variant for one allele at a given locus, (b) unusually high stutter product, (c) gene duplication, and (d) translocation.

DNA Fingerprinting↗
PubMed2001

DNA short tandem repeat profiling of three North Indian populations.

POPULATION: Fifty healthy unrelated individuals were randomly chosen from each of the three populations viz., Bhargavas, Chaturvedies, and Brahmins. Three generation pedigree charts were prepared to ensure sirname endogamy in Bhargavas Chaturvedies and group endogamy in Brahmins subjects were chosen from several parts of Uttar Pradesh, a northern state of the Indian republic.

Alleles↗
PubMed2002

Effect of sample preparation and pH-mediated sample stacking on the analysis of multiplexed short tandem repeats by capillary electrophoresis.

An amplification system was used in this study to evaluate the effect of sample preparation and its injection on the electrophoretic separation by capillary electrophoresis using a commercially available capillary electrophoresis instrument. The effect of dilution of amplified samples in water and in different sources of formamide (with conductivity values ranging from 47 to 1000 microS) was evaluated, as was contamination of the sample with high DNA concentrations or buffer salts. Although resolution remained constant in the different solvents tested, the sensitivity increased in samples diluted in water and high-purity formamide. An on-column sample preconcentration method for capillary-based DNA analysis was evaluated to increase the sensitivity of low-quality samples. This technique, pH-mediated sample stacking, is based on the injection of NaOH immediately before sample injection: A neutralization reaction occurs between OH- and tris+ ions so that a low-conductivity zone is created at the head of the capillary. DNA fragments are concentrated at the front of this zone. Using coated capillaries with hydroxycellulose 2% (MW 250,000) as a separation matrix, an improvement in sensitivity was detected in all the solvents studied. The gain in sensitivity was higher for more conductive solvents, and was not correlated with the size of the DNA fragments.

Electrophoresis, Capillary↗