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Results for “Multiplex PCR”

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PubMed2006

[A minisequencing technique for genotyping 12 Y-SNP and its genetic polymorphisms].

OBJECTIVE: The aim of the present study was to establish a rapid and robust assay used to simultaneously genotype SNPs by the single nucleotide primer extension (minisequencing) with the SNaPshot Kit and obtain the population genetic data in Chinese population in Sichuan. The analysis of single nucleotide polymorphisms (SNPs) is a promising application in forensic casework. METHODS: 12 Y-SNPs, which were SRY2627, SRY1532, M13, M20, SRY8299, Tat, M69, M9, 92R7, M17, M19 and M112, were multiple amplificated and the PCR products were pooled, Purified, and then used as templates for the minisequencing reaction with the commol/Lercially available SNaPshot Kit. Then the products of minisequencing reaction were detected by capillary elcetrophoresis. RESULTS: 78 genomic DNA individual samples from Sichuan, China and 5 semen stain samples from sexal criminal scene were analyzed and two haplotypes could be identified. CONCLUSION: A rapid method has been established to analyze the 12 Y-SNPs by multiplex PCR and minisequencing. It can be applied in forensic casework successfully.

Base Sequence↗

PubMed2006

Fluorescent multiplex amplification of three X-STR loci.

This study was carried out to evaluate the value of three X-STR loci (DXS6803, DXS981and DXS6809) in forensic application and thereby investigate their polymorphism. The primer for each locus was labeled with fluorochrome 6-FAM. A fluorescent multiplex PCR for simultaneously amplifying three X-STR loci was set up. The PCR products that were obtained were analyzed using capillary electrophoresis and ABI PRISM 3100 Genetic Analyzer, with GENESCAN Analysis Software. When 340 male and 195 female individuals of Han population in China were tested, 13, 12, and 11 alleles were observed for DXS6803, DXS981 and DXS6809, respectively. One hundred and eighty three haplotypes were detected in the male individuals. The haplotype diversity reached 0.9926. The results show that the three loci of the multiplex system provide significant information on polymorphism for forensic identification and paternity testing, particularly for complicated paternity deficient cases.

Chromosomes, Human, X↗

PubMed2004

[Value of the polymerase chain reaction in the diagnosis of herpes infections of the nervous system].

OBJECTIVE: To assess the performance of a polymerase chain reaction (PCR) method in cerebrospinal fluid (CSF) for the diagnosis of nervous system infections caused by herpesvirus, and to estimate the incidence of encephalitis due to herpes simplex virus type 1 in the adult population of the island of Gran Canaria. METHODS: We studied 330 CSF specimens from 312 patients (281 HIV-negative and 31 HIV-positive) remitted to investigate clinically suspected encephalitis or meningitis, or to study neuropathy or demyelinating disease. A multiplex PCR technique was used to detect herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), varicella-zoster virus (VZV), human cytomegalovirus (CMV), Epstein-Barr virus and human herpesvirus type 6. The patients' clinical records were reviewed to establish the definite diagnosis. RESULTS: Nine samples from eight patients (2.6%) showed positive results (9.7% of patients with pathological CSF and none with normal CSF). The eight patients had clinical and analytic findings of herpesvirus nervous system infection: HSV-1 DNA in four patients with encephalitis, HSV-2 DNA in one patient with meningitis, VZV DNA in two patients with meningitis and CMV DNA in one HIV-positive patient with encephalitis. Herpesvirus was the cause of 50% of encephalitis cases and 10% of meningitis cases. The incidence of HSV-1 encephalitis was five cases per million inhabitants per year. CONCLUSIONS: Diagnosis of herpesvirus nervous system infections by PCR in CSF is not appropriate when CSF parameters are normal. We found a higher incidence of herpesvirus encephalitis than has been reported in other studies.

Adult↗

PubMed2004

New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci.

Molecular methods for the rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) are generally based on the detection of an S. aureus-specific gene target and the mecA gene. However, such methods cannot be applied for the direct detection of MRSA from nonsterile specimens such as nasal samples without the previous isolation, capture, or enrichment of MRSA because these samples often contain both coagulase-negative staphylococci (CoNS) and S. aureus, either of which can carry mecA. In this study, we describe a real-time multiplex PCR assay which allows the detection of MRSA directly from clinical specimens containing a mixture of staphylococci in <1 h. Five primers specific to the different staphylococcal cassette chromosome mec (SCCmec) right extremity sequences, including three new sequences, were used in combination with a primer and three molecular beacon probes specific to the S. aureus chromosomal orfX gene sequences located to the right of the SCCmec integration site. Of the 1,657 MRSA isolates tested, 1,636 (98.7%) were detected with the PCR assay, whereas 26 of 569 (4.6%) methicillin-susceptible S. aureus (MSSA) strains were misidentified as MRSA. None of the 62 nonstaphylococcal bacterial species or the 212 methicillin-resistant or 74 methicillin-susceptible CoNS strains (MRCoNS and MSCoNS, respectively) were detected by the assay. The amplification of MRSA was not inhibited in the presence of high copy numbers of MSSA, MRCoNS, or MSCoNS. The analytical sensitivity of the PCR assay, as evaluated with MRSA-negative nasal specimens containing a mixture of MSSA, MRCoNS, and MSCoNS spiked with MRSA, was approximately 25 CFU per nasal sample. This real-time PCR assay represents a rapid and powerful method which can be used for the detection of MRSA directly from specimens containing a mixture of staphylococci.

Bacterial Proteins↗

PubMed2001

New tests for syphilis: rational design of a PCR method for detection of Treponema pallidum in clinical specimens using unique regions of the DNA polymerase I gene.

A sensitive and specific PCR method to detect Treponema pallidum in clinical specimens was developed. PCR primers were designed based on two unique features of the DNA polymerase I gene (polA). The first distinctive characteristic is that the region codes for a high cysteine content and has low homology with similar regions of DNA polymerase I gene from known microorganisms. The second unique feature is the presence of four insertions in the gene. PCR tests using primers designed on the basis these regions reacted with various pathogenic T. pallidum subspecies but did not react with nonpathogenic treponemal species or other spirochetes. An additional 59 species of bacteria and viruses, including those that cause genital ulcers, tested negative. This PCR method is extremely robust and sensitive. The detection limit is about 10 to 25 organisms when analyzed on gel. However, the analytic sensitivity can be increased by at least 1 log, to a detection limit of a single organism, when the ABI 310 Prism Genetic Analyzer is used to detect fluorescence-labeled amplicons. We further used this test in a clinical setting and compared the results with results from a previously reported multiplex-PCR test (for T. pallidum, Haemophilus ducreyi, and herpes simplex virus). We tested 112 genital ulcer specimens by the polA PCR, obtaining a sensitivity of 95.8% and a specificity of 95.7%. These results suggest that the polA PCR is applicable as a routine clinical diagnostic test for syphilis.

Amino Acid Sequence↗

PubMed2006

An internal amplification control system based on primer-dimer formation for PCR product detection by DNA hybridization.

The detection of PCR products by DNA hybridization techniques can suffer from inhibition of the amplification process by sample matrix components. We have designed a simple internal control system for PCR based on the incorporation of a primer pair with complementary 3' ends, resulting in the generation of a unique "primer-dimer" detectable by hybridization with a specific capture probe immobilized on polyester cloth as part of an array of amplicon-specific probes. The inclusion of this primer pair did not adversely affect the amplification and subsequent detection of target gene sequences by hybridization with immobilized probes in either single gene amplification or multiplex PCR systems. The failure to amplify target gene sequences because of the presence of inhibitors was mirrored by a failure to amplify the internal control primer-dimer, demonstrating the efficacy of this system in identifying the presence of DNA amplification inhibitors.

Bacteriological Techniques↗

PubMed2006

Development of an improved species specific PCR test for detection of Haemophilus parasuis.

A PCR test for identification of Haemophilus parasuis was optimized using the 16S rDNA sequences of the 15 serotype reference strains of H. parasuis. The test was evaluated on a collection of 218 Danish field isolates as well as on 81 representatives of 27 other species, including genetically affiliated species within Pasteurellaceae. In addition, DNA preparations from 56 H. parasuis isolates from North America were included. To obtain a test that was specific for H. parasuis, a multiplex PCR using 3 different primers was developed. The PCR test produced an amplicon of approximately 1090 bp only with representatives of H. parasuis. The test was further evaluated on 55 clinical samples from 16 Danish pigs suspected for being infected with H. parasuis, showing polyserositis or septicemia at autopsy as well as on 492 nasal swabs. The test was compared with the performance of a PCR test earlier published by Oliveira et al. [Oliveira, S., Galina, L., Pijoan, C., 2001. Development of a PCR test to diagnose Haemophilus parasuis infections. J. Vet. Diagn. Invest. 13, 495-501]. The sensitivity of the present PCR test was found to be slightly lower when applied on clinical samples from diseased pigs and 10-fold lower when tested on pure cultures of H. parasuis (5CFU and 0.5CFU/PCR reaction, respectively). Addition of 1.4 x 10(5) Escherichia coli to each PCR tube did not alter the sensitivity of the tests. No difference in sensitivity of the tests was observed when tested on purified DNA. On the other hand, the present PCR test was found to be 100% species specific for H. parasuis, in contrast to the PCR test of Oliveira et al., which also tested positive for strains belonging to A. indolicus, A. porcinus, and A. minor, species commonly occurring in the upper respiratory tract. However, when the PCR test of Oliveira et al. is used on samples from systemic locations the chances for false positive results are apparently low. The present PCR test represents a rapid and reliable method for genetically based identification of H. parasuis. The high species specificity of the test makes it suitable for detection of H. parasuis in clinical samples, regardless of the presence of affiliated species and contaminating flora. As the two PCR tests differ in sensitivity and specificity, the use of both PCR tests for different purposes is a possibility.

Animals↗

PubMed1999

Molecular characterization of femA from Staphylococcus hominis and Staphylococcus saprophyticus, and femA-based discrimination of staphylococcal species.

The femA gene encodes a protein precursor which plays a role in peptidoglycan biosynthesis in Staphylococcus aureus and is also considered as a factor influencing the level of methicillin resistance. A femA homologous gene was recently characterized in S. epidermidis, entailing the possibility of femA phylogenetic conservation in staphylococcal species. Accordingly, we assessed the presence of femA homologous genes in S. hominis and S. saprophyticus. Strategy for identification relied upon alignment of S. aureus and D. epidermidis femA sequences and upon identification of potentially conserved regions. Amplifications of portions of the femA genes were performed under permissive annealing conditions, by using several sets of primers designed to match the consensus regions. DNA sequencing of overlapping PCR fragments led to the characterization of the entire femA genes of S. hominis and S. saprophyticus, and provided more precise information on the femA start codon for all five species. The genomic organization of all these femA genes appeared highly conserved, with alternance of homologous and variable regions. On this basis, a consensus sequence of the femA gene was defined and interspecies variations were exploited to design strategies for staphylococci species-specific identification, including multiplex PCR amplification and a reverse hybridization assay.

Amino Acid Sequence↗

PubMedDate not supplied

Quantification of PCR products using microparticles and flow cytometry.

The analysis of genetic biomarkers has become an important tool in clinical diagnostics. This includes the identification of disease-related genetic alterations, the detection of pathogenic infective germs on DNA or RNA level and the quantification of the expression of marker genes indicating an altered physiological status. It has been previously described that the combination of polymerase chain reaction (PCR), microparticles and flow cytometry represents a universal platform technology for the routine analysis of such biomarkers. Here we demonstrate the applicability and flexibility of this technology by means of various applications. The quantification of interferon gamma (IFNG) mRNA in irradiated white blood cells is shown as well as the detection of latent infections with cytomegalovirus (CMV). Besides the quantification of single amplification products, the flow cytometric assay is also capable of analysing products of a multiplex PCR. As an example, we describe the identification of spontaneous deletions in the genome of a hybrid cell line using a co-amplified gene (RAB1) essential for the cell survival as an internal control. Furthermore, we show that the use of a green laser (532 nm, 50 mW) substantially increased the sensitivity of the assay compared to conventional flow cytometers using a 488 nm (25 mW) laser. We conclude that the analysis of PCR products using microparticles and flow cytometry fulfils the criteria of clinical routine diagnostics regarding (i) sensitivity, (ii) specificity, (iii) reproducibility and (iv) automatibility.

Animals↗

PubMed2006

Development and assessment of a rapid method to detect Escherichia coli O26, O111 and O157 in retail minced beef.

A molecular-based detection method was developed to detect Escherichia coli O26, O111 and O157 in minced (ground) beef samples. This method consists of an initial overnight enrichment in modified tryptone soya broth (mTSB) and novobiocin prior to DNA extraction and subsequent serogrouping using a triplex PCR. This method has a low limit of detection and results are available within 24 hours of receipt of samples. Once optimized, this rapid method was utilized to determine the prevalence of these E. coli serogroups in six hundred minced beef samples all of which were previously examined by immunomagnetic separation (IMS) and selective plating for E. coli O26 and O111. Using IMS, two E. coli O26 isolates were detected. No E. coli O111 were recovered. The multiplex PCR technique described here did not detect E. coli O111 nor O157 in any of the samples, however six minced beef samples were positive for E. coli O26 using our method, only two of these were previously detected by IMS and culture. Application of molecular methods are useful to support culture-based approaches thereby further contributing to risk reduction along the food chain.

Animals↗

PubMed2004

Real-time PCR for single-cell genotyping in sickle cell and thalassemia syndromes as a rapid, accurate, reliable, and widely applicable protocol for preimplantation genetic diagnosis.

Sickle-cell and beta-thalassemia syndromes are priority genetic diseases for prevention programs involving population screening with the option of prenatal diagnosis for carrier couples. Preimplantation genetic diagnosis (PGD) represents a specialized alternative to prenatal diagnosis and is most appropriately used for couples with an unsuccessful reproductive history and/or undergoing assisted reproduction. However, clinical application of PGD has been hindered by difficulties in reliably transferring molecular diagnostic protocols to the single-cell level. We standardized and validated a protocol involving first-round multiplex PCR, amplifying the region of the beta-globin gene containing most of the common disease mutations world-wide and two unlinked microsatellite markers (GABRB3 and D13S314), followed by: 1) analysis of beta-globin genotypes with real-time PCR and 2) microsatellite sizing to exclude chance contamination. The protocol was standardized on 100 single lymphocytes from a beta-thalassemia heterozygote, including 15 artificially contaminated samples, the latter demonstrated through microsatellite analysis. PCR failure and allele drop-out (ADO) were observed in one (uncontaminated) sample each (1.2%). A pilot study in six clinical PGD cycles with five different beta-globin genotype interactions achieved results (in 5-6 hr) in 46 out of 50 single blastomeres (92%), all concordant with results from an established PGD method applied simultaneously; microsatellite analysis detected only parental alleles, excluding contamination. Beta-globin genotypes were also confirmed in two blastomeres through prenatal diagnosis (twin pregnancy), and in 11 out of 12 spare embryos, revealing one incident of ADO. Overall, the protocol proved to be sensitive, accurate, reliable, rapid, and applicable for many genotype interactions, with internal monitoring of contamination, thus fulfilling all requirements for clinical PGD application.

Anemia, Sickle Cell↗

PubMed1999

Application of capillary nongel sieving electrophoresis for gene analysis.

Capillary electrophoresis (CE) has proved to be a strong tool for DNA analysis and has found abundant applications in the fields of restriction fragment sizing, mutation screening, polymerase chain reaction (PCR) product characterizing and forensic identifying. CE may be the main alternative to slab gel electrophoresis. Capillary nongel electrophoresis is the most favorable mode when aiming for this purpose because of its advantages of long lifetime, easy operation, good reproducibility, and low expense. In this paper, a new kind of sieving matrix, with mannitol as the additive for capillary electrophoresis, as well as related methods and their application for gene analysis were reported. Nine DNA fragments amplified by multiplex PCR from a normal dystrophin gene were well separated by this system. Three different deletions were found in Duchenne muscular dystrophy (DMD) patients. Three to four copies of the sex-determination region of the Y chromosome (SRY) gene, as well as the phenylalanine hydroxylase (PAH) gene, could be detected in mixed samples. The frequencies of short tandem repeats (STR) in PAH genes was analyzed in 61 normal Chinese individuals and 6 phenylketonuria families. One case of prenatal gene diagnosis was performed. By using this matrix, CE coupled with reverse transcription PCR (RT-PCR), the analysis of the alternative splicing expression pattern of the fragile X mental retardation 1 (FMR1) gene in adult lung tissue was achieved.

Adult↗

PubMed2004

Allelic drop-out in the STR system ACTBP2 (SE33) as a result of mutations in the primer binding region.

In the course of routine genotyping of forensic reference samples by multiplex PCR, an allelic drop-out due to mutations in the primer binding regions of the highly polymorphic STR marker ACTBP2 was observed in 17 samples. The variation rate was estimated to be 0.0014 (95% confidence interval: 0.0006-0.003). The most frequently found mutation was an G to A transition in the reverse primer binding region which was present in 14 out of 17 cases. To overcome the problem we have added a modified reverse primer to different multiplex kits that led to the correct genotype.

Binding Sites↗

PubMed1995

p53 gene alterations in special types of breast carcinoma: a molecular and immunohistochemical study in archival material.

The p53 locus on the short arm of chromosome 17 at 17p13.1 was examined for small genomic deletions and mutations in 23 formalin-fixed, paraffin-embedded cases of special types of breast carcinoma (six medullary, seven apocrine, five differentiated tubular, and five papillary). p53 mutations in the evolutionarily conserved exons 5-9 were detected in 11 cases (four apocrine, two papillary, two medullary, and three differentiated tubular), using the novel non-radioactive PCR-based Hydrolink mutation detection enhancement (MDE) method, and confirmed by direct sequencing of the PCR products. Missense mutations causing amino acid substitutions were evenly distributed among exons. One case of apocrine carcinoma showed a polymorphism at codon 213 (CGA-->CGG). Twelve out of 23 cases were found to express a strong nuclear signal against CM-1 and DO-7, two anti-p53-specific antibodies. Small genomic deletions in the vicinity of the p53 locus were detected in 11 tumours (three papillary, three differentiated tubular, two medullary, and three apocrine carcinomas), using the multiplex PCR method. No statistical correlation was found between deletions at 17p13.1 and p53 mutations (P < 0.5). In addition, p53 mutations and immunoexpression correlated with the c-erbB-2 gene product, an oncogenic protein that has been implicated in cell cycle control (P < 0.001). Our findings suggest that genomic alterations of the p53 gene are quite common events associated with special types of breast carcinoma, particularly of the apocrine subtype, but the prognostic value is unlikely to be of clinical importance.

Base Sequence↗

PubMed1998

Homozygous and frequent deletion of proximal 8p sequences in human prostate cancers: identification of a potential tumor suppressor gene site.

By using tissue microdissection and polymerase chain reaction (PCR) techniques, we examined 85 prostate tumors that were paired with normal tissues from the same patients for allelic loss at 26 highly polymorphic microsatellite sequences, 21 spanning 8p and 5 localized to 8q. Sixty-four tumors (75%) demonstrated loss of at least one 8p locus. Separate distal and proximal regions of deletion were observed as well as an intervening, staggered breakpoint. A novel region of homozygous deletion of sequences at the D8S87 locus was detected both by multiplex PCR and by fluorescence in situ hybridization within this breakpoint region. These data suggest that a tumor-suppressor gene mapping to proximal 8p is deleted frequently and is likely to be important for tumorigenesis in prostate tumors.

Adult↗

PubMedDate not supplied

[Identification of hypervariable and conservative fragments of Listeria genome].

The computer analysis revealed hypervariable and highly conservative fractions in the genes of Gram-positive bacteria of the Listeria genus. As a result of analysis of gene iap coding protein p60, PCR based test systems for detection of 6 Listeria species, L. monocytogenes, L. seeligeri, L. ivanovii, L. innocua, L. grayi and L. welshimeri have been developed. Species-specific and conservative gene fragments coding Listeria pathogenicity factors, listeriolysin and cytolysin, were detected. The sets of primers for detection and gene typing of L. monocytogenes, L. seeligeri and L. ivanovii containing cytolysin have been made. The gene typing of Listeria may be carried out in one reaction with the use of multiplex PCR: amplified fragments for different Listeria species differ in the length of the amplified product. The developed sets of primers have a 95-100% degree of homology and may be recommended for the detection and gene typing of Listeria.

Bacterial Toxins↗

PubMed2006

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments.

Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens.

Algorithms↗

PubMed2006

Occurrence of natural Bacillus thuringiensis contaminants and residues of Bacillus thuringiensis-based insecticides on fresh fruits and vegetables.

A total of 128 Bacillus cereus-like strains isolated from fresh fruits and vegetables for sale in retail shops in Denmark were characterized. Of these strains, 39% (50/128) were classified as Bacillus thuringiensis on the basis of their content of cry genes determined by PCR or crystal proteins visualized by microscopy. Random amplified polymorphic DNA analysis and plasmid profiling indicated that 23 of the 50 B. thuringiensis strains were of the same subtype as B. thuringiensis strains used as commercial bioinsecticides. Fourteen isolates were indistinguishable from B. thuringiensis subsp. kurstaki HD1 present in the products Dipel, Biobit, and Foray, and nine isolates grouped with B. thuringiensis subsp. aizawai present in Turex. The commercial strains were primarily isolated from samples of tomatoes, cucumbers, and peppers. A multiplex PCR method was developed to simultaneously detect all three genes in the enterotoxin hemolysin BL (HBL) and the nonhemolytic enterotoxin (NHE), respectively. This revealed that the frequency of these enterotoxin genes was higher among the strains indistinguishable from the commercial strains than among the other B. thuringiensis and B. cereus-like strains isolated from fruits and vegetables. The same was seen for a third enterotoxin, CytK. In conclusion, the present study strongly indicates that residues of B. thuringiensis-based insecticides can be found on fresh fruits and vegetables and that these are potentially enterotoxigenic.

Bacillus thuringiensis↗