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At least 613 records · Page 34Linked to original sources
PubMed2005

Evaluation of sieving polymers for fast, reproducible electrophoretic analysis of short tandem repeats (STR) in capillaries.

Efficient capillary electrophoretic STR analysis requires rapid, reproducible and robust separation of DNA fragments with reasonable capillary longevity--this is currently accomplished using proprietary commercial polymeric sieving matrices specifically developed for this separation. These matrices, while effective, are costly and do not provide adequate resolution of STR DNA fragments in capillaries with shorter effective separation lengths, increasing the time required to accomplish the separation and minimizing the potential extrapolation to other miniaturized platforms. As the forensic community looks toward next generation microchip technology as a means of processing casework more rapidly, new sieving polymers need to be evaluated for utilization in this platform. The research presented here describes the assessment of commercially-available polymeric sieving matrices for STR analysis, with consideration given to feasibility of incorporation into a microdevice. Polymer composition, molecular weight, and concentration were evaluated, along with an assessment of the effects of buffer composition, separation temperature, and capillary length. These variables were evaluated individually or collectively on the ability to resolve STR DNA fragments and the reproducibility of the separations and the results compared to a proprietary commercial product. A 600,000 Da MW poly(ethylene oxide) (PEO) solution at a 3% (w/v) concentration was determined to be the most suitable matrix for these separations. This polymer, in coated capillaries, provided highly robust and reproducible separations, with near baseline resolution of fragments having single base differences. Reductions in the temperature of the separation, from 60 degrees C to 40 degrees C, and the urea concentration of the buffer, from 7 M to 3.5 M, provided increased longevity of the PEO polymer for repeated separations. Comparison of this polymer with currently specified commercial products used for STR analysis showed that the optimized PEO matrix provided superior separations under all conditions tested. In addition, PEO could be utilized in shorter capillary systems, with a concurrent decrease in analysis time, highlighting its potential for use in shortened capillary or microdevice systems.

Buffers↗
PubMed2005

Optimization of a simple, automatable extraction method to recover sufficient DNA from low copy number DNA samples for generation of short tandem repeat profiles.

AIM: To develop an automated, high throughput extraction protocol in order to produce database eligible profiles from fingerprints and other low copy number (LCN) DNA sources. METHODS: Extraction of either purified control DNA or buccal cells, for example, with commercial kits was compared to extraction with a simple digestion buffer and a subsequent concentration and purification. Results were evaluated based on the amount of DNA recovered and the completeness of the DNA profiles produced. RESULTS: Simple procedures with fewer steps were superior to commercial kits, such as DNA IQ (Promega, Madison, WI, USA) and QiaAmp (Qiagen, Valencia, CA, USA), and other protocols with many manipulations. The optimized protocol included a thirty-minute incubation with 0.01% SDS and proteinase K at 56 degrees C, followed by an incubation at 100 degrees C for 10 minutes. Concentration of the extract and removal of the SDS was accomplished with a Microcon 100 (Millipore, Bedford, MA, USA), which can be assembled into a 96 well plate, the Microcon-96 Retentate Assembly Plate (Millipore) for automation. The addition of 1 ng Poly A RNA to the Microcon significantly improved DNA recovery. CONCLUSION: A one-step sample digestion followed by sample concentration/purification minimized sample loss and maximized amplification input. Moreover, this methodology can be easily adapted for automation. Implementation of this protocol, due to the numerous potential sources of LCN DNA samples, will enhance the recovery of biological evidence from crime scenes and may be a source of database profiles.

Automation↗
PubMedDate not supplied

Polymorphic short tandem repeats for PCR-based diagnosis of the Charcot-Marie-Tooth 1A duplication in Ukraine.

Charcot-Marie-Tooth neuropathy (CMT) is one of the most common hereditary disorders, affecting 1:2500 individuals. The major mutation--microduplication of 1.4 megabases in 17p11.2 region, which is responsible for 68-90 % of cases of CMT1, results in CMT1A. In the present article we provide the population genetic study in 52 unrelated non-CMT volunteers from population of Ukraine in three STRs (D17S921, D17S1358 and D17S122) from the 17p11.2 chromosomal region to determine their ability for the CMT1A-duplication detection using STR-PCR method in Ukraine. The informativity for the CMT1A detection in current use STR panel is calculated to be 93,6%. It has been shown that current use STR panel analysis is important for CMT1A duplication detection, early differential diagnosis of CMT including prenatal diagnosis and genetic consulting in high risk families.

Alleles↗
PubMed2006

[Analysis of allele frequencies of 6 short tandem repeat loci on chromosome 12 in patients with Kashing-Beck disease].

OBJECTIVE: To analyze the allele frequencies of 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S16725 and D12S1613) on chromosome 12 among KBD patients and residents in the KBD and non-KBD areas. METHODS: EDTA-blood samples were collected from 146 unrelated Chinese Han individuals in Shaanxi Province including 57 KBD patients, 48 control subjects living in the Kashing-Beck disease(KBD) area and 48 in the non-KBD area. The DNA samples were extracted and amplified by PCR, and the PCR products were analyzed by ABI 3100 Genetic Analyzer. RESULTS: In KBD patients, the allele number for the 6 STR loci (D12S358, D12S1675, D12S1663, D12S1697, D12S16725 and D12S1613) was 7, 7, 7, 10, 12 and 8, and the genotype number were 13, 12, 9, 17, 19 and 10, respectively; in the residents in KBD area, the allele number was 7, 5, 7, 9, 13 and 9, and the genotype number 12, 10, 12, 19, 16 and 8; in residents in non-KBD area, the allele number was 7, 5, 5, 12, 8 and 9, and the genotype number 17, 16, 8, 22, 14 and 8. There were significant differences in the allele frequencies in the D12S1725 loci between KBD patients and residents living in KBD area (P=0.0119) and the non-KBD area (P=0.0050), but no significant difference in other 5 loci among the 3 groups. CONCLUSION: KBD patients have significantly different allele distribution patterns in the D12S1725 loci from the control subjects.

Adult↗
PubMed2006

A combination of five short tandem repeats of chromosome 15 significantly improves the identification of Prader-Willi syndrome etiology in the Argentinean population.

Prader-Willi syndrome (PWS) is a multisystemic disorder caused by the loss of expression of paternally transcribed genes in the PWS critical region of chromosome 15. Various molecular mechanisms are known to lead to PWS: deletion 15q11-q13 (75% of cases), maternal uniparental disomy (matUPD15) (23%) and imprinting defects (2%). FISH and microsatellite analysis are required to establish the molecular etiology, which is essential for appropriate genetic counseling and care management. We characterized an Argentinean population, using five microsatellite markers (D15S1035, D15S11, D15S113, GABRB3, D15S211) chosen to develop an appropriate cost-effective method to establish the parental origin of chromosome 15 in nondeleted PWS patients. The range of heterozygosity for these five microsatellites was 0.59 to 0.94. The average heterozygosity obtained for joint loci was 0.81. The parental origin of chromosome 15 was established by microsatellite analysis in 19 of 21 non-deleted PWS children. We also examined the origin of the matUPD15; as expected, most of disomies were due to a maternal meiosis I error. The molecular characterization of this set of five microsatellites with high heterozygosity and polymorphism information content improves the diagnostic algorithm of Argentinean PWS children, contributing significantly to adequate genetic counseling of such families.

Argentina↗
PubMed2006

[How to draw a conclusion in motherless parentage testing using short tandem repeats as genetic makers].

OBJECTIVE: To calculate the exclusion power of STR loci in motherless parentage testing and to discuss how to draw a conclusion if there are inconsistent loci. METHODS: Based on the law of inheritance and allele frequency, the powers of exclusion of STR loci in motherless parentage testing (PE(M)) were calculated. Based on the mean PE(M) and mutation rate of 13 CODIS loci. The probabilities of inconsistence under paternity and non-paternity were calculated respectively according to binomial theorem. RESULTS: The PE(M) of locus having co-dominate alleles could be calculated as: PE(M) = (i = 1)sigma (n) p i 2(1-p (i))2+ (i < j)sigma (n) 2p (i)p (j)(1-p (i)-p (j))2. According to the formula, the average PE(M) of 13 CODIS was 0.411. Based on the mean PE(M) and mutation rate, the likelihood ratio of true father to random man (paternity index) was got using binomial theorem. CONCLUSION: The conclusion in motherless parentage testing could be drawn based on the likelihood ratio (paternity index) derived from mean PE(M) and mutation ratio.

Algorithms↗
PubMed1994

Instability of short tandem repeats (microsatellites) in human gliomas.

OBJECTIVE: Microsatellite instability implying multiple replication errors (RER) characterizes a proportion of familial and sporadic carcinomas. The purpose of this report is to analyze whether microsatellite instability occurred during the development of human gliomas. EXPERIMENTAL DESIGN: We checked prospectively 16 central nervous system tumors, including 10 glioblastomas and 6 astrocytomas of different malignancy grades, for genetic microsatellite instability. Fifteen different microsatellites, located on 6 different chromosomes, were investigated. All microsatellites are dinucleotide CA, repeats except for D11S956,P23 (CTAT) and CYP 19, which are tetranucleotide repeats and P23 (GTTTT) which is a pentanucleotide repeat. The repeats were analysed by PCR amplification, followed by electrophoresis on denaturing 6% polyacrylamide gels. MEASURES: We looked for all kinds of microsatellite alterations. Only microsatellite shifts were considered to represent microsatellite instability. RESULTS: Three out of 10 glioblastomas showed mobility shifts on gel electrophoresis in tumor, compared to corresponding normal DNA samples. In contrast, no microsatellite instability was found in any of the astrocytomas. Besides the presence of larger or smaller alleles, an imbalance in the ratio between alleles was noticed in one astrocytoma and in one glioblastoma multiforme. In addition, loss of heterozygosity (LOH) is observed without a fixed pattern in 3 glioblastomas. CONCLUSIONS: We conclude that genetic instability of microsatellites may be demonstrated in high grade gliomas rather than in their low grade precursors and should be regarded as an evolution in tumor progression rather than as a new mechanism for tumor initiation in gliomas.

Astrocytoma↗
PubMed1995

Deletion of chromosome 1p loci and microsatellite instability in neuroblastomas analyzed with short-tandem repeat polymorphisms.

We have analyzed DNA from 46 neuroblastoma tumors of all clinical stages and five ganglioneuroma tumors together with corresponding control DNA for loss of heterozygosity (LOH) on the distal 1p chromosomal region (1p-LOH). The markers used for the analyses were genetically mapped DNA polymorphisms detectable with PCR analysis. In general, there was concordance among aggressive tumor stage, 1p deletion, and N-myc amplification, although exceptions were found. Twelve (26%) of the 46 neuroblastoma tumors displayed 1p-LOH, 11 being stage 4 and 1 stage 2 (which progressed subsequently to stage 4), whereas 10 stage 4 tumors showed no 1p-LOH. Of 12 neuroblastomas shown to have N-myc amplification, 10 had 1p-LOH. In 8 cases it was possible to test for parental origin of the chromosome involved in 1p-LOH. No significant correlation between LOH and paternal or maternal allele was found. Commonly deleted loci in the distal 1p region in the neuroblastoma tumors indicated that the region for a tentative neuroblastoma tumor suppressor gene is defined proximally by marker D1S244 and distally by marker D1S80. One striking feature of three stage 2 neuroblastomas and one of the stage 3 tumors was the presence in the tumor DNA of alleles not present in the constitutional DNA of the patients, i.e., microsatellite instability. The significance of this phenomenon in localized neuroblastoma tumors remains to be clarified. Aggressive neuroblastoma in young children (younger than 2 years of age) seems to be a homogenous disorder consistently showing concomitant 1p-LOH and N-myc amplification. In the majority of unfavorable neuroblastoma in older children, however, neither 1p-LOH nor N-myc amplification could be detected. This indicates that neuroblastoma in older children is a biologically more heterogenous disorder in which genetic alterations other than deletions of chromosome 1p and amplification of N-myc also may contribute to tumorigenesis.

Child↗
PubMed1998

[Parental origin of extra chromosome 21 in Down syndrome detected by using short tandem repeat DNA polymorphisms after PCR amplification].

OBJECTIVE: To detect the parental origin of extra chromosome 21 in Down syndrome, using two (GT)n polymorphic markers-D21S215 and D21S120. METHODS: The alleles of D21S215 and D21S120 were amplified by polymerase chain reaction and identified with denaturing polyacrylamide gel electrophoresis followed with Ag-staining. The parental origin of extra chromosome 21 was determined by comparing genotypes of probands with their parents. RESULTS: The parental origin of extra chromosome 21 was determined in 17 Down syndrome out of 24, with 12 and 5 inherited from mother and father respectively. CONCLUSION: The parental origin of extra chromosome 21 in Down syndrome can be determined by analyzing the polymorphisms of D21S215 and D21S120. Etiological study of trisomy 21 should be focused on maternal meiosis.

Chromosomes, Human, Pair 21↗
PubMed1998

Unnecessary surgical operation confirmed by individual identification by analyses of several short tandem repeat (STR) loci.

A 60-year-old man who was diagnosed as having hepatic cell carcinoma by needle punch biopsy from the liver, underwent right hepatic lobectomy. However, no malignant components were detected in the removed tissue. It was suspected that he was the wrong patient and had undergone the operation unnecessarily. Individual identification was performed using paraffin blocks of his liver tissue taken by needle punch biopsy, that of liver tissue taken at surgery and his peripheral blood by genotyping several STR loci. All of these specimens had the same genotypes. Histological re-examination revealed that the biopsied sample contained no malignant component. The end result was that the initial biopsied liver specimen was misdiagnosed as hepatic cancer and the patient underwent an unnecessary operation due to misdiagnosis.

Biopsy, Needle↗
PubMed1999

Analysis of 6 short tandem repeat loci in Navarre (northern Spain).

A genetic study was performed on a sample of 146 autochthonous individuals from the province of Navarre (northern Spain) to test for 6 STR systems: CSF1PO, TPOX, TH01, F13A1, FES/FPS, and VWA31/A. The Navarre population has a series of allele frequencies that are at the extreme end of the European range of variation and that are in most cases similar to those found in the Basque population of the provinces of Alava, Biscay, and Guipuzcoa. This similarity is corroborated by correspondence analysis, in which the population of Navarre is at one end of the first axis with the Basque sample close to it and the remaining European populations far removed. In tree-type representations the Navarre population is grouped with the Basque series at 1 end. Even so, the comparison of allele frequency distributions by the chi-square heterogeneity test indicates that these 2 groups are statistically different. Our results together with the cultural relationship that exists between all the Basque-speaking provinces and the genetic heterogeneity described in earlier studies between the Basque provinces of Alava, Biscay, and Guipuzcoa (Aguirre et al. 1989; Manzano, Orue et al. 1996; Manzano, Aguirre et al. 1996) lead us to believe that the Navarre population lies within the heterogeneous Basque genetic map.

Chi-Square Distribution↗
PubMedDate not supplied

Detection of single and multiple polymorphic loci by synthetic tandem repeats of short oligonucleotides.

Loci containing tandem repeats of short sequences are sometimes associated with a high level of polymorphism due to variations in the number of repeats. The different variants can be easily characterized by Southern blotting when the repeats span a range from a few hundred bases to a few kilobases, and probes derived from such tandem repeats constitute convenient genetic markers. These structures, usually called minisatellites, are best documented in the human genome, where their number has been estimated to be at least 1500. However, their role and mode of evolution are poorly understood. We are developing tools to evaluate the number of such redundant sequences in a genome and to gain access to new polymorphic loci. Our strategy is based on the use of polymers of oligonucleotides as DNA probes for hybridization on Southern blots. In a previous report, we made polymers with random units of 14 bp and showed that they detect multiple polymorphic loci on human genomic DNA. At present, we are testing the effect of an increase in the complexity of the polymer, as obtained by the use of a longer random unit, and the effect of slight sequence modifications to a particular tandem repeat sequence. In addition, some of these synthetic probes can detect a single polymorphic locus and directly provide new genetic markers.

Base Sequence↗
PubMed2002

Analysis of HLA-DRB1*-A* and -B* alleles in prenatal diagnosis for determination of maternal contamination in fetal DNA.

During chorionic villi sampling for prenatal diagnosis with molecular biology techniques, contamination by maternal decidua frequently occurs and can lead to misinterpretation of the test results. To avoid such problems, we present a new method for appraising maternal contamination of fetal DNA, based on genomic typing of the highly variable human leukocyte antigen (HLA) locus-DRB1*, locus A* and locus B* regions by genetic amplification with sequence-specific primers and PCR. Fetal DNA samples obtained for beta-thalassemia diagnosis were analysed after artificial contamination with increasing maternal DNA concentrations ranging from 0.5 to 10% (0.5, 1, 3, 5 and 10%). The approach was found to be rapid, specific, reproducible and highly sensitive and permits recognition of 1-3% contamination by maternal DNA concentrations. The system currently used for detecting maternal DNA contamination in fetal samples is the analysis of polymorphic loci by variable number of tandem repeats and/or short tandem repeats. We propose that the analysis of HLA alleles may provide a valid alternative or complement to this system.

Alleles↗