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Results for “Multiplex PCR”

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PubMed2005

Effect of promoter methylation of the p16 gene on phosphorylation of retinoblastoma gene product and growth of hepatocellular carcinoma cells.

The biological significance of hypermethylation of p16 gene promoter in human hepatocellular carcinoma (HCC) cells remains to resolved. In order to clarify the significance of methylation of p16 gene promoter, we examined the methylation status of p16 gene in association with phosphorylation of retinoblastoma gene product (pRb) and cell growth in human HCC cell lines. The presence of methylation was examined by methylation-specific PCR. Expression and phosphorylation of p16 and pRb were examined by Western blot analysis. Genetic changes were analyzed by multiplex PCR and DNA sequencing. The effect of demethylation of p16 was assessed by cell growth. p16 gene promoter was methylated in HuH7 and HLF cells. The demethylating agent, 5-aza-2-deoxycytidine (5-Aza-CdR), upregulated p16 mRNA in HuH6 and HuH7 cells. 5-Aza-CdR increased p16 protein expression in HuH6, HuH7, and HLF cells, and it clearly decreased the phosphorylation level of pRb in HuH6, HuH7 and PLC/PRF/5 cells. Treatment with 5-Aza-CdR inhibited the growth of HuH7 cells. Homozygous deletion and significant mutations were absent. Methylation in the p16 promoter region is biologically significant, being associated with phosphorylation of pRb and cell growth in human HCC cells.

Amino Acid Sequence↗

PubMed1996

VJ rearrangements of the TCR gamma locus in peripheral T-cell lymphomas: analysis by polymerase chain reaction and denaturing gradient gel electrophoresis.

Using Southern blotting for the diagnosis of clonality in peripheral T-cell lymphomas (PTCLs), analysis of the T-cell receptor (TCR) gamma gene rearrangement was shown to be more informative than that of the TCR beta gene rearrangement. In order to amplify every VJ gamma rearrangement, a polymerase chain reaction (PCR) procedure using newly designed GC-clamp primers has been developed. All primers can be mixed in a single multiplex PCR. PCR products are analysed by denaturing gradient gel electrophoresis (DGGE), providing tumour-specific imprints inasmuch as the procedure characterizes N sequence polymorphism at the VJ junctions. In a series of 30 PTCL cases, the PCR procedure demonstrated 27 cases to be clonally rearranged and failed in three cases. PCR was more accurate than Southern blotting, showing 47 rearranged gamma alleles, four of which were undetectable on the Southern blot. When lymphomas were studied at different sites and at relapse, the DGGE pattern remained unchanged. In PTCL, the proposed PCR is helpful for the diagnosis and staging of the disease and should improve the follow-up monitoring. The undetectability of clonal rearrangements in a few cases is discussed in the light of concepts of lymphomagenesis and T-cell differentiation.

Base Sequence↗

PubMed1999

Differentiation of closely related but biologically distinct cherry isolates of Prunus necrotic ringspot virus by polymerase chain reaction.

Prunus necrotic ringspot ilarvirus (PNRSV) exists as a number of biologically distinct variants which differ in host specificity, serology, and pathology. Previous nucleotide sequence alignment and phylogenetic analysis of cloned reverse transcription-polymerase chain reaction (RT-PCR) products of several biologically distinct sweet cherry isolates revealed correlations between symptom type and the nucleotide and amino acid sequences of the 3a (putative movement protein) and 3b (coat protein) open reading frames. Based upon this analysis, RT-PCR assays have been developed that can identify isolates displaying different symptoms and serotypes. The incorporation of primers in a multiplex PCR protocol permits rapid detection and discrimination among the strains. The results of PCR amplification using type-specific primers that amplify a portion of the coat protein gene demonstrate that the primer-selection procedure developed for PNRSV constitutes a reliable method of viral strain discrimination in cherry for disease control and will also be useful for examining biological diversity within the PNRSV virus group.

DNA Restriction Enzymes↗

PubMed2001

PCR as a diagnostic and quantitative technique in veterinary parasitology.

Over the past 15 years, there has been a dramatic evolution in molecular approaches to study parasites and parasitic diseases. Many of these advancements have been brought about through the development of new applications of the polymerase chain reaction (PCR). Enhancements in sensitivity that can be achieved using PCR now permit scientists to investigate changes at the level of a single cell, far below what is often needed for parasite-derived applications. PCR has had a substantial impact on advances made in the areas of parasite systematics and epidemiology, immunology and host-parasite interactions, recombinant DNA vaccine development and most recently, the analysis of whole genomes either through directly sequencing the DNA, the analysis of expressed sequence tags (ESTs) or through the rapidly growing field of functional genomics. This paper, however, focuses on the application of PCR methodology to parasite detection and differentiation, and the diagnosis of disease. Specific attention is given to advances provided by multiplex PCR, fluorescence-based "real-time" PCR, and the utilization of PCR as a quantitative technique.

Animals↗

PubMed2002

X-linked recessive Menkes disease: identification of partial gene deletions in affected males.

Menkes disease is an X-linked recessive lethal disorder of copper metabolism, caused by defects in the ATP7A gene. Partial gene deletions comprise about 15% of the mutations causing Menkes disease. We have previously demonstrated identification of partial ATP7A deletions in patients by Southern blot analysis. In the present study, we report the use of three fast and reliable polymerase chain reaction (PCR)-based methods for the identification of partial ATP7A deletions in Menkes disease patients. First we demonstrate the use of multiplex PCR, a fast method for identification and rough localization of partial gene deletions, in which two exons of ATP7A are coamplified. Second, we present PCR amplification of genomic DNA across the deletion junctions, a method enabling identification of the deletion breakpoints and hence the exact size of the deletion. Finally, application of reverse transcription PCR (RT-PCR) for identification and localization of gene deletions at the cDNA level is demonstrated. By studying the mutation at the cDNA level the predicted effect of the mutation on the amino acid sequence and consequently the protein structure and function can be inferred. We demonstrate characterization of partial gene deletions in five patients, and in three of these we were able to determine the breakpoint sequences.

Adenosine Triphosphatases↗

PubMed2001

Single intragenic microsatellite preimplantation genetic diagnosis for cystic fibrosis provides positive allele identification of all CFTR genotypes for informative couples.

This study is part of a strategy aimed at using fluorescent polymerase chain reaction (PCR) on informative genetic microsatellite markers as a diagnostic tool in preimplantation genetic diagnosis (PGD) of severe monogenic disease. Two couples, both of whom had previously had children who were compound heterozygote for severe cystic fibrosis mutations, were offered PGD using fluorescent PCR of the highly polymorphic cystic fibrosis transmembrane conductance regulator (CFTR) intragenic microsatellite marker IVS17bTA. Cleavage-stage embryo biopsy followed by PCR resulted in transfer of one unaffected carrier embryo for each couple. This approach eliminates the need for single cell multiplex PCR strategies to detect CF compound heterozygotes. It also provides a control of chromosome 7 ploidy in the blastomeres and a selection against allele dropout by positive detection of each CFTR copy of all genotypes in preimplantation embryos from genetically informative families.

Alleles↗

PubMedDate not supplied

Characterization of hemoglobin Hotel Dieu in a Puerto Rican adolescent.

PURPOSE: Hemoglobin Hotel Dieu (HbHD) is a high-oxygen affinity variant of HbA never before reported in a Hispanic patient. This Hb variant was first reported in 1981 by Blouquit et al. in a white person with erythrocytosis with a substitution in the beta 99 aspartic acid residue by glycine. METHODS: A 13-year-old Puerto Rican boy had pain in his chest, headaches, easy fatigability, and high Hb (as high as 19.1 g/dl). Protein analysis was performed by cellulose acetate, citrate agar, and isoelectric focusing electrophoresis and high-pressure liquid chromatography (HPLC), polymerase chain reaction (PCR) amplification, and DNA sequencing of the second exon of the beta gene in samples obtained from the mother, father, and the patient, and DNA fingerprinting to determine paternity. RESULTS: The variant found in the patient migrated on cellulose acetate electrophoresis to a cathodic position relative to HbF, and a band cathodal to HbA and close to HbF on isoelectric focusing electrophoresis. The patient showed an abnormal well-resolved peak on HPLC with a retention time slightly shorter than that for HbS. DNA analysis by direct sequencing of the PCR product demonstrated heterozygosity for codon 99 (GAT-->GGT) in the patient but not in either parent. DNA fingerprinting by multiplex PCR amplification of three simple tandem repeat loci showed that the patient shared alleles in all three loci with both parents, ruling out nonpaternity. CONCLUSIONS: The protein and DNA analysis indicate that the erythrocytosis is caused by the presence of HbHD in this Hispanic adolescent.

Adolescent↗

PubMed2005

Molecular strategies for identifying human papillomavirus infection in routinely processed samples: focus on paraffin sections.

OBJECTIVE: To optimize the protocols of human papillomavirus (HPV) detection in clinical samples, we used polymerase chain reaction (PCR)-based techniques in paraffin-embedded tissue sections and compared the results with those obtained with PCR and Hybrid Capture II (HC2) performed in liquid-based cytology (LBC) preservation medium. MATERIALS AND METHODS: Forty-five consecutive cervical biopsy specimens were taken from women participating in the ongoing Latin American Screening Study at Leonor Mendes de Barros Hospital, São Paulo, Brazil, during 2003 and 2004. The biopsy specimens were analyzed for HPV by a modified GP5+/GP6+ PCR protocol, and the results were compared with those obtained by PGMY PCR and HC2 in samples collected in LBC preservation medium. RESULTS: beta-Globin was detected in 100% of the multiplex PCR system from LBC samples and 66.7% with PCO4+/PCO3+ PCR in biopsy specimens. Of the three methods, PGMY PCR system and HC2 were equally effective in detecting HPV; both detected 13 cases in 45 samples (28.9%). The GP5+/GP6+ PCR applied in biopsy specimens showed a 20% HPV detection rate (9/45). CONCLUSIONS: Our PCR protocols worked reasonably well and allowed us to compare the three molecular methods with histological and cytological findings. The reproducibility of the results makes the technique applicable in archival materials.

Adolescent↗

PubMed2000

PCR-Based assay for discrimination between invasive and contaminating Staphylococcus epidermidis strains.

The discrimination between Staphylococcus epidermidis strains that contaminate and infect blood cultures is a daily challenge for clinical laboratories. The results of PCR detection of putative virulence genes were compared for contaminating strains, sepsis-related strains, catheter strains, and saprophytic strains. Multiplex PCR was used to explore the atlE gene, which is involved in initial adherence, the intercellular adhesion gene cluster (ica), which mediates the formation of the biofilm, and the agrA, sarA, and mecA genes, which might contribute to the pathogenicity of S. epidermidis. Whereas the atlE, agrA, and sarA genes were almost ubiquitously amplified, the ica and mecA genes were detected significantly more in infecting strains than in contaminating strains (P </= 0.02) and thus appeared to be related to the potential virulence of S. epidermidis.

Bacterial Adhesion↗

PubMed2000

Impact of genetic polymorphisms in cytochrome P450 2E1 and glutathione S-transferases M1, T1, and P1 on susceptibility to esophageal cancer among high-risk individuals in China.

Esophageal cancer, which is prevalent in China, is believed to be induced by environmental carcinogens such as nitrosamines and other agents. The disproportionate geographical distribution of this cancer among individuals suggests a role for gene-environment interactions in developing the disease. We have shown in our preliminary study that a genetic polymorphism in cytochrome P450 2E1 (CYP2E1) that is known to activate nitrosamines may be a susceptibility factor involved in the early events leading to the development of esophageal cancer (Lin et al., Cancer Epidemiol. Biomark. Prev., 7: 1013-1018, 1998). This relatively larger study was conducted to compare the results with our previous findings. One hundred and fifty cases with esophageal cancer, 146 cases with esophageal dysplasia, and 150 normal controls were residents of Linxian, China, a high-risk area. Genomic DNA samples were assayed for restriction fragment length polymorphisms in the CYP2E1 and GSTP1 loci by PCR amplification followed by digestion with RsaI and Alw26I, respectively. Deletion of the GSTM1 and GSTT1 genes was detected by multiplex PCR. The distribution of CYP2E1 c1/c1 allele frequency was found to be significantly different between controls (44.0%) and cases with cancer (71.3%) or cases with dysplasia (70.6%; P < 0.0001). Individuals having the c1/c1 genotype were at a 3.1-fold [95% confidence interval (CI), 2.4-3.9] increased risk of developing dysplasia and a 3.2-fold (95% CI, 2.5-4.1) increased risk of developing squamous cell carcinoma of the esophagus. Although polymorphisms in the GSTT1 and GSTP1 were not significantly different between cases with cancer or cases with dysplasia and controls, the frequency of the GSTM1 non-null (+/+ and +/0) genotypes appeared to be overrepresented in cases with cancer compared with controls (odds ratio, 2.3; 95% CI, 1.8-3.0). Furthermore, a joint effect of the CYP2E1 c1/c1 genotype and GSTM1 non-null genotype on the cancer risk was observed, showing an odds ratio of 8.5 (95% CI, 3.7-19.9). These results demonstrate that CYP2E1 and perhaps GSTM1 are genetic determinants in the development of squamous cell carcinoma of the esophagus.

Carcinoma, Squamous Cell↗

PubMed2002

Blood group genotyping facilitates transfusion of beta-thalassemia patients.

We evaluated the usefulness of blood group genotyping as a supplement to hemagglutination to determine the red blood cell (RBC) antigen profile of polytransfused patients with beta-thalassemia. We selected 10 alloimmunized patients who were receiving antigen-matched RBCs based on phenotype, and had clinical evidence of delayed hemolytic transfusion reaction. DNA was prepared from blood samples and RH E/e, K1/K2, FY A/FY B, and JK A/JK B alleles were determined by PCR-RFLP. RH D/non-D was determined according to the PCR product size associated with the RHD gene sequence in intron 4 and exon 10/3'UTR. RH C/c was tested by multiplex PCR. The phenotypes and genotypes of nine of the 10 samples were discrepant. Five of the discrepancies occurred in the Rh system. One sample was phenotyped as Rhcc and genotyped as RH C/C, and two samples were phenotyped as RhCc and genotyped as RH C/C. Two other samples were phenotyped as RhEe and genotyped as RH e/e. Three samples had discrepancies in the Kidd system with phenotype Jk(a+b+) and were genotyped as homozygous for JK B. One sample had a discrepancy in the Duffy system: it was phenotyped as Fy(a+b-) and homozygous for FY B. Genotyping was very important in determining the true blood groups of many polytransfused patients with beta-thalassemia, and it assisted in the identification of suspected alloantibodies and the selection of antigen-negative RBCs for transfusion.

Agglutination Tests↗

PubMed2005

Forensic evaluation and haplotypes of 19 Y-chromosomal STR loci in Koreans.

In this study, 19 Y-specific STR loci (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, DYS446, DYS449, and DYS464) were analyzed in 301 unrelated Korean males by three multiplex PCR systems. The haplotype diversity using the classical set of Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and DYS385; multiplex I) was 0.9963. For the same individuals, the haplotype diversity value using the new set of highly informative Y-STRs (DYS385, DYS446, DYS449, and DYS464; multiplex III) was 0.9989, while that using the combined set of Y-STRs by adding DYS388 to the previously studied DYS434, DYS435, DYS436, DYS437, DYS438, and DYS439 (multiplex II) was 0.9509. A total of 297 different haplotypes were identified using the 19 Y-STR markers, of which 293 were unique and 4 were found twice. The overall haplotype diversity was 0.9999. The evaluation of the information of selected markers by combination of each marker with the minimal haplotype showed that DYS434, DYS435, DYS436, DYS437, and DYS438 do not significantly contribute to increment of haplotype diversity. However, respective conjunction of DYS464, DYS449, and DYS446 with the minimal haplotype considerably increased the haplotype diversity. Especially, DYS464 is expected to be the most useful marker that can be included in the expanded minimal haplotype. These results including the haplotype data at 19 Y-STR loci in the present study would provide useful information in forensic practice in a Korean population.

Asian People↗

PubMed2003

Simultaneous analysis of interleukin-10 gene microsatellites and single-nucleotide polymorphisms in parallel with tumour necrosis factor and interferon-gamma short tandem repeats by fluorescence-based polymerase chain reaction.

Different cytokine genotypes exist in the population, for example, as a result of selective pressure of infectious diseases. It may be that specific cytokine genotypes that are beneficial by creating a 'proinflammatory' phenotype predispose to severe inflammatory disease with worse clinical outcome. There is individual variation in the production of certain cytokines in relation to their genotypes. IL-10, IFN-gamma and TNF-alpha are key components in the regulation of immune responses and the balance of their expression levels is predictive in certain diseases. To describe cytokine genotypes, a one-tube PCR reaction was developed to analyse simultaneously DNA sequence variations of cytokine genes IL-10, IFN-gamma, and TNF. This multiplex PCR approach was used to provide genotypic data for two geographically independent donor groups from Germany and Gabon. Significant differences were obtained for the majority of sequence variations comparing both populations. However, the SNPs within the 5'-flanking region of the IL-10 gene at position -1087 and -6208 are comparable in their genic and genotypic behaviour. Comparing allelic and genotypic disequilibrium between pairs of loci revealed different association patterns for both populations according to the geographical polymorphism. This assay may improve immunogenetic studies in disease, characterized by disbalanced IL-10, IFN-gamma and TNF-alpha expression.

5' Flanking Region↗

PubMed2000

Detection and identification of mycobacteria by amplification of the internal transcribed spacer regions with genus- and species-specific PCR primers.

We evaluated the usefulness of PCR assays that target the internal transcribed spacer (ITS) region for identifying mycobacteria at the species level. The conservative and species-specific ITS sequences of 33 species of mycobacteria were analyzed in a multialignment analysis. One pair of panmycobacterial primers and seven pairs of mycobacterial species-specific primers were designed. All PCRs were performed under the same conditions. The specificities of the primers were tested with type strains of 20 mycobacterial species from the American Type Culture Collection; 205 clinical isolates of mycobacteria, including 118 Mycobacterium tuberculosis isolates and 87 isolates of nontuberculous mycobacteria from 10 species; and 76 clinical isolates of 28 nonmycobacterial pathogenic bacterial species. PCR with the panmycobacterial primers amplified fragments of approximately 270 to 400 bp in all mycobacteria. PCR with the M. tuberculosis complex-specific primers amplified an approximately 120-bp fragment only for the M. tuberculosis complex. Multiplex PCR with the panmycobacterial primers and the M. tuberculosis complex-specific primers amplified two fragments that were specific for all mycobacteria and the M. tuberculosis complex, respectively. PCR with M. avium complex-, M. fortuitum-, M. chelonae-, M. gordonae-, M. scrofulaceum-, and M. szulgai-specific primers amplified specific fragments only for the respective target organisms. These novel primers can be used to detect and identify mycobacteria simultaneously under the same PCR conditions. Furthermore, this protocol facilitates early and accurate diagnosis of mycobacteriosis.

Base Sequence↗

PubMedDate not supplied

New method for the extraction of DNA from white blood cells for the detection of common genetic variants associated with thrombophilia.

In the last few years, FV Leiden, prothrombin 20210 and thermolabile methylene tetrahydrofolate reductase (MTHFR) 677 variants have been identified as possible risk factors associated with thrombophilia, and many PCR-based methods have been described for detecting these variations. However, the genomic DNA extraction is still a rate-limiting and time-consuming step in the PCR process. In an attempt to accelerate this procedure and make it suitable for routine laboratory, we report a single preparative technique for DNA extraction from peripheral blood samples using an anion-binding resin (GeneFizz). This method enables white blood cell lysis, DNA extraction and PCR amplification directly in the thermocycling tube on the thermocycler. The use of this new DNA extraction system coupled to a multiplex PCR allows rapid genetic screening of large cohorts of patients for thrombophilic risk factors.

Anion Exchange Resins↗

PubMed2006

Screening petting zoo animals for the presence of potentially pathogenic Escherichia coli.

Several outbreaks of Escherichia coli O157 have been reported in petting zoos, resulting in hospitalization of many children. At present, no standard procedure has been adopted to monitor the presence of enterohemorrhagic E. coli (EHEC) or Shiga-toxin-producing E. coli (STEC) in petting zoo animals. Direct detection of these strains from rectal swabs of animals in petting zoos was developed and obviated the need to culture the organisms. DNA extracted from bacteria in the swabs was tested for the presence of wecA gene specific for E. coli by polymerase chain reaction (PCR). The wecA positive samples were further tested for Shiga-toxin genes stxl and stx2, and the intimin eae by multiplex PCR and for the presence of O157 and H7. Swabs (n=104) from 15 animal species in a petting zoo were tested; 7 goats and 3 cows were found to carry STEC. The method is rapid and convenient for monitoring potentially pathogenic E. coli in petting zoo animals.

Animals↗

PubMed2005

Genotyping the hemophilia inversion hotspot by use of inverse PCR.

BACKGROUND: Factor VIII intron 22 inversions (Inv22) cause 40%-45% of severe cases of hemophilia A in all human populations. Currently, Inv22 can be analyzed either by Southern blotting or by rapid long-distance-PCR-based approaches. We describe an alternative method using inverse-PCR (I-PCR). METHODS: I-PCR involved 3 steps: (a) BclI restriction; (b) self-ligation of restriction fragments, providing BclI rings; and (c) standard multiplex-PCR analysis. PCR was achieved by use of a set of 3 primers that yielded a 487-bp amplicon for the nonrearranged intragenic allele and a 559-bp amplicon for the Inv22 allele. Specific primer sites were targeted by masking relevant regions for human repeats and low-complexity DNA. Inv22 I-PCR was applied to samples from 16 individuals (8 women and 8 men) representing 24 X chromosomes previously genotyped by Southern blotting. Additionally, we evaluated the sensitivity and the ability to assess eventual Inv22 carrier mosaicisms by experiments using artificial DNA mixtures (Inv22 + no-Inv22 male samples). RESULTS: Results for previously genotyped samples agreed with results of Southern blot analyses. As expected, cell composition of the artificial mosaic was linearly reflected by the relative intensities of Inv22 signals. I-PCR was estimated to detect Inv22-positive cells at concentrations as low as approximately 5%. CONCLUSION: The proposed technique provides a rapid tool for Inv22 genotyping.

Blotting, Southern↗

PubMed2005

A variant form of Oguchi disease mapped to 13q34 associated with partial deletion of GRK1 gene.

PURPOSE: The purpose of this paper is to map the locus for a variant form of Oguchi disease in a Pakistani family and to identify the causative mutation. METHODS: Family 61029 was ascertained in the Punjab province of Pakistan. It includes three 13- to 19-year-old patients with night blindness and 12 unaffected family members. A complete ophthalmological examination including fundus photography and electroretinography (ERG) was performed on each family member. A genome-wide scan was performed using microsatellite markers at about 10 cM intervals, and two-point lod scores were calculated. Polymerase chain reaction (PCR) cycle dideoxynucleotide sequencing was used to screen candidate genes inside the linked region for mutations and to delineate the deletion. Multiplex PCR and long template PCR were used to detect deletions and to define the size of deletions. Evaluation of fundus changes and ERG, lod score estimation, and identification of a mutation in the GRK1 gene were carried out. RESULTS: All patients had night blindness since early childhood. Irregular coarse pigmentation was observed in the peripheral retina of each patient. The fundus appearance before and after 4 h of dark adaptation was similar except that the peripheral retinal pigmentary changes were slightly less evident after extended dark adaptation. Minimal or no rod function with normal cone function on ERG recordings were detected in all three affected members. The rod showed slow recovery to nearly normal amplitude after 4 h in the dark ERG in one individual but not in two other patients. A genome-wide scan showed linkage only to D13S285. Fine mapping defined a region from D13S1315 to 13qter, with a lod score of 2.89 at theta=0 shown by D13S285 and 2.90 at theta=0 by the D13S261-D13S285-D13S1295-D13S293 haplotype. Analysis of the GRK1 gene, which is included in this interval, identified a c.827+623_883del mutation. This intragenic deletion cosegregates with the disease in the family and is only homozygous in affected individuals. This mutation was not detected in 96 controls. CONCLUSIONS: The retinal disease in the family reported here has several features differing from typical Oguchi disease, including an atypical Mizuo-Nakamura phenomenon and a non-recordable rod ERG even after 4 h of dark adaptation. Normal visual acuity, normal caliber of retinal blood vessels, and normal cone response on ERG recording suggest retinal dysfunction rather than degeneration (i.e., a variant form of Oguchi disease but unlikely to be retinitis pigmentosa). The disease in the Pakistani family localizes to 13q34 and is caused by a novel deletion including Exon 3 of the GRK1 gene.

Adolescent↗