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Results for “Multiplex PCR”

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PubMed1995

Frequent loss of heterozygosity at 7q31.1 in primary prostate cancer is associated with tumor aggressiveness and progression.

Cytogenetic analyses have demonstrated that chromosome region 7q22-32 is commonly altered in prostate adenocarcinomas. In addition, in recent fluorescence in situ hybridization studies, we have observed that aneusomy of chromosome 7 is frequent in prostate cancer and is associated with higher tumor grade, advanced pathological stage, and early prostate cancer death. These findings suggest that genetic alterations of chromosome 7 play a significant role in the development of prostate cancer. To better define the chromosome 7 alterations, PCR analysis of 21 microsatellite loci was performed on 54 paired prostate cancer and control DNAs. Overall, chromosome 7 allelic imbalance was identified in 16 of 54 cases (30%). Allelic imbalances of loci mapped to 7q were observed in 15 of the 16 cases. The allelic imbalances were classified as losses in 15 tumors (28%) and as gains in 1 (2%) by comparative multiplex PCR analysis. The most common site of allelic loss included loci D7S523 and D7S486 at 7q31.1. A comparison with clinicopathological features of the tested tumors revealed that the allelic loss of 7q31.1 correlated with higher tumor grade (P = 0.012) and lymph node metastasis (P = 0.017). These results indicate that 7q31 may be the site of a putative suppressor gene(s) important for the pathogenesis of prostate carcinoma, and that the genetic alterations at 7q31.1 may participate in tumor progression and metastasis.

Alleles↗

PubMed2003

A new PCR-based method for monitoring inoculated wine fermentations.

A new PCR-based method has been developed to monitor inoculated wine fermentations. The method is based on the variation in the number and position of introns in the mitochondrial gene COX1. Oligonucleotide primers homologous to the regions flanking the Saccharomyces cerevisiae COX1 introns have been designed and tested for S. cerevisiae wine yeast strain differentiation. Four primers were selected for their subsequent use in a multiplex PCR reaction and have proved to be very effective in uncovering polymorphism in natural and commercial yeast strains. An important point is that the speed and simplicity of the technique, which does not require the isolation of DNA, allows early detection of the starter yeast strain throughout the fermentation process. The main advantage for the wineries is that the must sample can be used directly for the PCR reaction obtaining very fast results (in approximately 8 h). This allows the wine industries to intervene quickly if necessary.

DNA, Fungal↗

PubMed2005

Multiplexed microsatellite markers for the genetic analysis of Eucalyptus leucoxylon (Myrtaceae) and their utility for ecological and breeding studies in other eucalyptus species.

Eucalyptus leucoxylon is a widespread woodland tree species found in southeastern Australia that has suffered from, and continues to be, threatened by the impacts of habitat clearance and degradation. Populations now consist predominantly of scattered individuals, and their conservation status is of increasing concern. We report the development and characterization of a set of eight highly polymorphic microsatellite loci for E. leucoxylon. The loci can be amplified in three PCR multiplexes and electrophoresed in a single lane, allowing rapid throughput of large numbers of samples. A total of 111 alleles were detected in 68 individuals with an average of 12.3 alleles per locus, a mean expected heterozygosity of 0.83, and a mean observed heterozygosity of 0.72. The combined probabilities of identity and probabilities of paternity exclusion allow an extremely precise level of individual identification, indicating that these microsatellite markers will be ideal for population genetic and parentage-type studies in E. leucoxylon. The markers also exhibited an average of 76% conservation within the subgenus Symphyomyrtus, to which E. leucoxylon belongs, and 53% conservation across other subgenera of Eucalyptus, demonstrating the potential of these markers in ecological and breeding studies in a wide range of Eucalyptus species.

Australia↗

PubMedDate not supplied

Clinical glycopeptide-resistant enterococci isolated from patients after solid organ transplantation.

The aim of this study was to confirm the identification and resistance to vancomycin and teicoplanin of nosocomial enterococcal strains using molecular biology methods. Glycopeptide-resistant enterococci (GRE) strains were isolated from clinical specimens of hospitalized patients. Bacterial identification was performed in an automatic ATB Expression system (bioMérieux SA). Susceptibility to glycopeptides was determined by the disc diffusion method and Etest (AB BIODISK, Sweden). We performed polymerase chain reactions (PCR) for Enterococcus faecium and E. faecalis identification and van genes detection. Fifteen GRE strains were cultured over 2 years (2003-2004). Fourteen isolates were highly resistant to vancomycin (MIC range, 128->256 mg/L) and teicoplanin (MIC range, 32->256 mg/L). Twelve strains harbored van A gene (Van A phenotype). Seven isolates were identified as E. faecium and seven as E. faecalis by the multiplex-PCR method. One strain-E. casseliflavus-showed low resistance to vancomycin (MIC 8 mg/L) with retained susceptibility to teicoplanin (MIC 4 mg/L). It harbored the van C2/C3 gene and was identified as the Van C2/C3 phenotype. GRE strains were more often isolated from hospitalized patients in Poland. Constant monitoring by reliable microbiological methods has become necessary to prevent the spread of these strains in the hospital environment.

Drug Resistance↗

PubMed2002

Abnormal FHIT expression profiles in cervical intraepithelial neoplastic (CIN) lesions.

Abnormal fragile histidine triad transcripts were found in 20-30% of CIN2/3 lesions and 11% of normal cervical biopsies by RT-PCR. Bi-allelic loss of the fragile histidine triad gene and the loss of fragile histidine triad protein expression detectable by immunochemical staining with a polyclonal fragile histidine triad specific antibody was rare. The genomic changes showed no association with the presence of human papillomavirus types which carry high risk for cervical cancer (high risk human papillomavirus) as assessed by a type-specific multiplex PCR. The presence of abnormal fragile histidine triad transcripts in a subset of CIN2/3 lesions with no high risk human papillomavirus suggests that this could be an independent risk factor associated with an alternative carcinogenic pathway.

Acid Anhydride Hydrolases↗

PubMedDate not supplied

Multiplexed systems of microsatellite markers for genetic analysis of mahogany, Swietenia macrophylla King (Meliaceae), a threatened neotropical timber species.

Mahogany (Swietenia macrophylla King [Meliaceae]) is the most valuable hardwood species in the neotropics. Its conservation status has been the subject of increasing concern due to overexploitation and habitat destruction. In this work we report the development and characterization of 10 highly variable microsatellite loci for S. macrophylla. Twenty-nine percent of the 126 sequenced mahogany clones yielded useful microsatellite loci. Three high-throughput genotyping systems were developed based on polymerase chain reaction (PCR) multiplexing of these mahogany loci. We identified a total of 158 alleles in 121 adult individuals of S. macrophylla, with an average of 15.8 alleles (range 11-25) per locus. All loci showed Mendelian inheritance in open-pollinated half-sib families. The mean expected heterozygosity was 0.84 and the mean observed heterozygosity was 0.73. The combined probability of identity-the probability that two individuals selected at random from a population would have identical genotypes--was 7.0 x 10(-15), and combined probability of paternity exclusion was 0.999998 overall loci. These microsatellite loci permit precise estimates of parameters such as gene flow, mating system, and paternity, thus providing important insights into the population genetics and conservation of S. macrophylla.

DNA↗

PubMed2005

PCR analysis of egyptian respiratory adenovirus isolates, including identification of species, serotypes, and coinfections.

Eighty-eight adenovirus (Ad) isolates and associated clinical data were collected from walk-in patients with influenza-like illness in Egypt during routine influenza surveillance from 1999 through 2002. Respiratory Ad distributions are geographically variable, and serotype prevalence has not been previously characterized in this region. Serotype identity is clinically relevant because it predicts vaccine efficacy and correlates strongly with both clinical presentation and epidemiological pattern. Species and serotype identities were determined using several well-validated multiplex PCR protocols culled from the literature and supplemented with a few novel primer sets designed to identify rare types. The isolates included common species B1 serotypes (Ad3 and Ad7), common species C serotypes (Ad1, Ad2, and Ad5), the less common species B2 serotype Ad11, and three isolates of the rare species B1 serotype Ad16. Two isolates that appear to be variant Ad16 were also identified. Fifteen coinfections of multiple adenoviral types, primarily AdB/AdC and Ad3/Ad7 dual infections, were detected. The majority of these were verified using redundant PCR tests targeted at multiple genes. PCR is able to resolve coinfections, in contrast to traditional serum neutralization tests. PCR is also comparatively rapid and requires very little equipment. Application of the method allowed an inclusive determination of the serotypes found in the Egyptian respiratory sample set and demonstrated that coinfections are common and may play a previously unrecognized role in adenovirus pathogenesis, evolution, and epidemiology. In particular, coinfections may influence adenoviral evolution, as interserotypic recombination has been identified as a source of emerging strains.

Adenovirus Infections, Human↗

PubMed2004

Use of cell culture-PCR assay based on combination of A549 and BGMK cell lines and molecular identification as a tool to monitor infectious adenoviruses and enteroviruses in river water.

Viral contamination in environmental samples can be underestimated because a single cell line might reproduce only some enteric viruses and some enteric viruses do not exhibit apparent cytopathic effects in cell culture. To overcome this problem, we evaluated a cell culture-PCR assay based on a combination of A549 and Buffalo green monkey kidney (BGMK) cell lines as a tool to monitor infectious adenoviruses and enteroviruses in river water. Water samples were collected 10 times at each of four rivers located in Gyeonggi Province, South Korea, and then cultured on group 1 cells (BGMK cells alone) and group 2 cells (BGMK and A549 cells). Reverse transcription and multiplex PCR were performed, followed by phylogenetic analysis of the amplicons. Thirty (75.0%) of the 40 samples were positive for viruses based on cell culture, and the frequency of positive samples grown on group 2 cells (65.0%) was higher than the frequency of positive samples grown on group 1 cells (50.0%). The number of samples positive for adenoviruses was higher with A549 cells (13 samples) than with BGMK cells (one sample); the numbers of samples positive for enteroviruses were similar with both types of cells. By using phylogenetic analysis, adenoviral amplicons were grouped into subgenera A, C, D, and F, and enteroviral amplicons were grouped into coxsackieviruses B3 and B4 and echoviruses 6, 7, and 30, indicating that A549 and BGMK cells were suitable for recovering a wide range of adenoviral and enteroviral types. The cell culture-PCR assay with a combination of A549 and BGMK cells and molecular identification could be a useful tool for monitoring infectious adenoviruses and enteroviruses in aquatic environments.

Adenoviruses, Human↗

PubMed2004

Rearranged T-cell receptor beta genes represent powerful targets for quantification of minimal residual disease in childhood and adult T-cell acute lymphoblastic leukemia.

Current MRD studies in T-cell acute lymphoblastic leukemia (T-ALL) mainly use T-cell receptor gamma, delta and SIL-TAL1 gene rearrangements as MRD-PCR targets. However, low frequency or limited diversity of these markers restricts the number of evaluable patients, particularly because two markers are recommended for MRD monitoring. Hence, we developed a new strategy implementing the TCR beta (TCRB) locus for MRD quantification. The frequency and characteristics of complete and incomplete TCRB rearrangements were investigated in 53 childhood and 100 adult T-ALL patients using the BIOMED-2 multiplex PCR assay. Clonal rearrangements were identified in 92% both childhood and adult T-ALL (Vbeta-Dbeta-Jbeta rearrangements in 80%, Dbeta-Jbeta rearrangements in 53%). Comparative sequence analysis of 203 TCRB recombinations revealed preferential usage of the 'end-stage' segment Jbeta2.7 in childhood T-ALL (27%), whereas Jbeta2.3 was most frequently involved in adult T-ALL (24%). In complete rearrangements, three downstream Vbeta segments (19-1/20-1/21-1) were preferentially used. Subsequently, a TCRB real-time quantitative PCR assay to quantify MRD with 13 germline Jbeta primer/probe combinations and allele-specific oligonucleotides was developed and applied to 60 clonal TCRB rearrangements. The assay allowed the detection of one leukemic cell within at least 10(4) polyclonal cells in 93% of cases and will be of high value for future MRD studies.

Adult↗

PubMed2002

Direct detection of insertion/deletion polymorphisms in an autosomal region by analyzing high-density markers in individual spermatozoa.

Direct polymerase chain reaction (PCR) detection of insertion/deletion (indel) polymorphisms requires sample homozygosity. For the indel polymorphisms that have the deletion allele with a relatively low frequency in the autosomal regions, direct PCR detection becomes difficult or impossible. The present study is, to our knowledge, the first designed to directly detect indel polymorphisms in a human autosomal region (i.e., the immunoglobulin V(H) region), through use of single haploid sperm cells as subjects. Unique marker sequences (n=32), spaced at approximately 5-kb intervals, were selected near the 3' end of the V(H) region. A two-round multiplex PCR protocol was used to amplify these sequences from single sperm samples from nine unrelated healthy donors. The parental haplotypes of the donors were determined by examining the presence or absence of these markers. Seven clustered markers in 6 of the 18 haplotypes were missing and likely represented a 35-40-kb indel polymorphism. The genotypes of the donors, with respect to this polymorphism, perfectly matched the expectation under Hardy-Weinberg equilibrium. Three V(H) gene segments, of which two are functional, are affected by this polymorphism. According to these results, >10% of individuals in the human population may not have these gene segments in their genome, and approximately 44% may have only one copy of these gene segments. The biological impact of this polymorphism would be very interesting to study. The approach used in the present study could be applied to understand the physical structure and diversity of all other autosomal regions.

Genes, Immunoglobulin↗

PubMed2006

Impact of microbial diversity on rapid detection of enterohemorrhagic Escherichia coli in surface waters.

Enterohemorrhagic Escherichia coli (EHEC) are a physiologically, immunologically and genetically diverse collection of strains that pose a serious water-borne threat to human health. Consequently, immunological and PCR assays have been developed for the rapid, sensitive detection of presumptive EHEC. However, the ability of these assays to consistently detect presumptive EHEC while excluding closely related non-EHEC strains has not been documented. We conducted a 30-month monitoring study of a major metropolitan watershed. Surface water samples were analyzed using an immunological assay for E. coli O157 (the predominant strain worldwide) and a multiplex PCR assay for the virulence genes stx(1), stx(2) and eae. The mean frequency of water samples positive for the presence of E. coli O157, stx(1) or stx(2) genes, or the eae gene was 50%, 26% and 96%, respectively. Quantitative analysis of selected enriched water samples indicated that even in samples positive for E. coli O157 cells, stx(1)/stx(2) genes, and the eae gene, the concentrations were rarely comparable. Seventeen E. coli O157 strains were isolated, however, none were EHEC. These data indicate the presence of multiple strains similar to EHEC but less pathogenic. These findings have important ramifications for the rapid detection of presumptive EHEC; namely, that current immunological or PCR assays cannot reliably identify water-borne EHEC strains.

Adhesins, Bacterial↗

PubMed2000

Extraction-free, filter-based template preparation for rapid and sensitive PCR detection of pathogenic parasitic protozoa.

Within the last several years, the protozoan parasites Cyclospora cayetanensis, Cryptosporidium parvum, and microsporidia have become recognized as important, rapidly emerging human pathogens in immunocompromised and immunocompetent individuals. Since the early 1990s, many of the reported outbreaks of enteric illness caused by these microorganisms have been attributed to food- and water-borne contamination. Many inherent obstacles affect the success of current surveillance and detection methods used to monitor and control levels of contamination by these pathogens. Unlike methods that incorporate preenrichment for easier and unambiguous identification of bacterial pathogens, similar methods for the detection of parasitic protozoa either are not currently available or cannot be performed in a timely manner. We have developed an extraction-free, filter-based protocol to prepare DNA templates for use in PCR to identify C. cayetanensis and C. parvum oocysts and microsporidia spores. This method requires only minimal preparation to partially purify and concentrate isolates prior to filter application. DNA template preparation is rapid, efficient, and reproducible. As few as 3 to 10 parasites could be detected by PCR from direct application to the filters. In studies, as few 10 to 50 Encephalitozoon intestinalis spores could be detected when seeded in a 100-microliter stool sample and 10 to 30 C. cayetanensis oocysts could be detected per 100 g of fresh raspberries. This protocol can easily be adapted to detect parasites from a wide variety of food, clinical, and environmental samples and can be used in multiplex PCR applications.

Animals↗

PubMed2001

PCR for specific detection of H7 flagellar variant of fliC among extraintestinal pathogenic Escherichia coli.

A newly developed PCR-based assay for the H7 variant of the Escherichia coli flagellin gene, fliC, was 100% sensitive and specific in comparison with serology and probe hybridization. It revealed broad conservation of the H7 fliC variant among phylogenetically diverse lineages of extraintestinal pathogenic E. coli (ExPEC) and superseded serotyping for certain isolates with ambiguous or non-H7 serotyping results. The H7 primers functioned well when incorporated into a multiplex PCR assay for diverse virulence-associated genes of ExPEC.

Bacterial Typing Techniques↗

PubMed2003

Development of a multiplex RT-PCR to detect transcription of varicella-zoster virus encoded genes.

The reverse transcription polymerase chain reaction (RT-PCR) is used commonly to analyse transcription of genes. In the field of virology it is an extremely helpful method to analyse the transcriptional activity of both, DNA and RNA viruses. The standard RT-PCR allows an investigation of the activity of only one gene. Here, we describe the development of a sensitive multiplex RT-PCR assay for single tube amplification to analyse a set of different genes encoded by the varicella-zoster virus (VZV), a member of the human-pathogenous herpesviruses. This multiplex RT-PCR amplifies the genes ORF 4, ORF 21 and ORF 68; each of these three genes belongs to a distinct class of genes, which is expressed one after the other within the infectious cycle. This method provides the possibility for rapid but extensive examination of VZV transcriptional activity and could be used in both fields, fundamental research as well as clinical diagnostic work.

Biopsy↗

PubMed2005

Rapid determination of common mutations in glutathione S-transferase gene by PCR-based methods in healthy Chinese.

BACKGROUND: The glutathione S-transferase (GST) superfamily comprises multiple isozymes with compelling evidence of functional polymorphisms in various ethnic groups. All these mutations, in particular those in class mu, pi and theta GST, are likely to contribute to interindividual differences in responses to xenobiotics including response to chemotherapy and associated with altered disease. The frequency of common GST mutations in Uygur Chinese is unknown. We investigated the common mutations of GSTM1, GSTT1, and GSTP1 in Uygur (N=154) Chinese and compare with Han Chinese (N=196). METHOD: GSTM1 and GSTT1 polymorphisms were analyzed by multiplexed PCR, and GSTP1 polymorphism was detected by PCR-based restriction fragment length polymorphism (RFLP) analysis. RESULTS: GSTM1 null genotype was found in 53.2% Uygur Chinese, which was close to that in Han Chinese (56.1%) (P=0.592). A significantly lower frequency (P<0.05) of GSTT1 null genotype in Uygur Chinese (26.6%) was observed compared with Han Chinese (50.0%). Uygur Chinese exhibited a GSTP1 genotype distribution of 51.3% I/I, 40.2% I/V and 8.4% V/V, which was different from that in Han Chinese (60.7% I/I, 35.2% I/V and 4.1% V/V). CONCLUSIONS: There is marked ethnic difference in the frequency of common GSTT1 and GSTP1 mutation, but not GSTM1 mutation, between Uygur and Han Chinese.

Adolescent↗

PubMed2002

Differential diagnosis of Taenia saginata and Taenia solium infections: from DNA probes to polymerase chain reaction.

The objective of this work was the rapid and easy differential diagnosis of Taenia saginata and T. solium. First, a T. saginata size-selected genomic deoxyribonucleic acid (gDNA) library was constructed in the vector lambda gt10 using the 2-4 kb fraction from the parasite DNA digested with EcoR1, under 'star' conditions. After differential screening of the library and hybridization analysis with DNA from T. saginata, T. solium, T. taeniaeformis, T. crassiceps, and Echinococcus granulosus (bovine, porcine, and human), 2 recombinant phages were selected. They were designated HDP1 and HDP2. HDP1 reacted specifically with T. saginata DNA, and HDP2 recognized DNA from both T. saginata and T. solium. The 2 DNA probes were then sequenced and further characterized. HDP1 was a repetitive sequence with a 53 bp monomeric unit repeated 24 times in direct tandem along the 1272 bp fragment, while the 3954 bp HDP2 was not a repetitive sequence. Using the sequencing data, oligonucleotides were designed and used in a polymerase chain reaction (PCR). The 2 selected oligonucleotides from probe HDP1 (PTs4F1 and PTs4R1) specifically amplified gDNA from T. saginata, but not T. solium or other related cestodes, with a sensitivity of < 10 pg of T. saginata gDNA, about the quantity of DNA in one taeniid egg. The 3 oligonucleotides selected from the HDP2 sequence (PTs7S35F1, PTs7S35F2, and PTs7S35R1) allowed the differential amplification of gDNA from T. saginata, T. solium and E. granulosus in a multiplex PCR, again with a sensitivity of < 10 pg. These diagnostic tools have immediate application in the differential diagnosis of T. solium and T. saginata in humans and in the diagnosis of dubious cysts in the slaughterhouse. We also hope to apply them to epidemiological surveys of, for example, soil and water in endemic areas.

Animals↗

PubMed2003

Development of PCR assays for detection of Streptococcus canis.

Streptococcus canis isolates, also including S. canis of artificially contaminated milk, could be identified by polymerase chain reaction (PCR) amplification using oligonucleotide primers designed according to species-specific parts of the 16S rRNA gene and, after sequencing, according to S. canis-specific parts of the 16S-23S rDNA intergenic spacer region and with oligonucleotide primers detecting an internal fragment of the group G streptococcal CAMP factor gene cfg. The 16S rRNA gene- and CAMP factor gene cfg-specific oligonucleotide primers could be used together in a multiplex PCR. No cross-reactivities could be observed with other group G streptococcal isolates or with any of the other control strains of various streptococcal species and serogroups. The PCR methods presented in this study allowed a rapid and reliable identification of S. canis and might help to improve the diagnosis of this bacterial species in animal and human infections.

Animals↗

PubMed2004

[Study of dual rearrangements of lymphocytic antigen receptor genes in non-Hodgkin lymphoma].

OBJECTIVE: To investigate the rate of dual rearrangements of lymphocytic antigen receptor genes in non-Hodgkin lymphomas (NHL) and its pathogenesis and pathologic significance. METHODS: PCR analysis of monoclonal, polyclonal and dual rearrangements of IgH and TCR gamma, TCR beta genes was carried out in 125 cases of NHL to evaluate the rate of dual rearrangements, immunohistochemistry was performed for a Ki67 protein expression in 117 cases and the proliferation index was calculated. The relationship between antigen receptor gene rearrangements and proliferation index was analyzed. RESULTS: Combination of the two pairs of IgH gene primers with the multiplex PCR for TCR gamma and TCR beta gene revealed dual rearrangements in 8% (8/96) of B-NHL, 17% (5/29) of T-NHL. In B cell NHL, IgH gene monoclonal, dural and polyclonal rearrangements were identified in 65, 8 and 15 cases respectively, while in T-cell NHL, they were in 15, 5 and 9 cases, respectively. There was no significant difference between proliferation index and monoclonal, dual, polyclonal rearrangements in both B-NHL and T-NHL by One-way test. CONCLUSION: Dual rearrangements in NHL are not rare and have no relationship with proliferation index.

Adolescent↗