Single-tube Polymerase Chain Reaction Research Articles

Screening for the human neutrophil antigen‐2 deficiency by a multiplex one‐tube polymerase chain reaction assay

ObjectivesThe aim of this study was to develop a rapid method for human neutrophil antigen‐2 (HNA‐2) genotyping and use it for fast screening for the HNA‐2 deficiency phenotype in the Chinese population.BackgroundHNA‐2 is encoded by the CD177 gene, and a single nucleotide polymorphism (SNP) at cDNA position 787 (CD177*787 A > T) creates a stop codon, which is responsible for the HNA‐2 deficiency phenotype. Recently, the SNP c.787A > T has been demonstrated to be the primary genetic mechanism for HNA‐2 deficiency.MethodsThis study focused on determination of CD177 SNP c.787A > T. We designed a set of allele‐ and sequence‐specific primers (SSP), which were used to develop a one‐tube polymerase chain reaction (PCR) assay for HNA‐2 genotyping. The HNA‐2 genotype of a total of 2185 Chinese blood donors was determined.ResultsThe validation of this HNA‐2 genotyping assay was confirmed by sequencing analysis. The HNA‐2 two alleles, CD177*787A and 787T, can be simultaneously determined in a single tube PCR. Thirteen individuals with the CD177*787AT genotype were detected in this study. The CD177*787TT homozygous genotype was absent, suggesting that HNA‐2 deficiency is rare in the Chinese population.ConclusionsThe validated assay described in this study is a rapid and reliable method for HNA‐2 genotyping, which may be used for fast screening for HNA‐2 deficiency.

Biochip-Based Genotyping Assay for Detection of Polymorphisms in Pigmentation Genes Associated with Cutaneous Melanoma.

The purpose of the study was to develop a new assay for genotyping nine single nucleotide polymorphisms (SNPs) that are known to be associated with melanoma. Two-stage single tube polymerase chain reaction (PCR) followed by hybridization on a biochip was developed and applied in the study. A total of nine SNPs were selected from five genes: MC1R (rs1805006, rs1805007, rs1805009, rs11547464), HERC2 (rs12913832), OCA2 (rs1800407), SLC45A2 (rs16891982), TYR (rs1393350), and a SNP from the intergenic locus rs12896399 were used for the synthesis of ssDNAs via a single-stage PCR process. The assays were performed on a biochip-based platform that is capable of SNP genotyping via a single reaction-tube PCR, followed by on chip hybridization. We tested 69 DNAs obtained from healthy persons and demonstrated the assays' ability to discriminate all three genotypes for almost all of the SNPs. The developed approach proved robust, suggesting that it might be useful for the personalized genotyping of large cohorts of patients.

Identification of microsatellite markers

To develop a single-tube polymerase chain reaction (PCR) panel of highly polymorphic markers for preimplantation genetic diagnosis (PGD) of fragile X syndrome (FXS). An in silico search was performed to identify all markers within 1 Mb flanking the FMR1 gene. Selected markers were optimized into a single-tube PCR panel and their polymorphism indices were determined from 272 female samples from three populations. The single-tube assay was also validated on 30 single cells to evaluate its applicability to FXS PGD. Thirteen markers with potentially high polymorphism information content (PIC) and heterozygosity values were selected and optimized into a single-tube PCR panel together with AMELX/Y for gender determination. Analysis of 272 female samples confirmed the high polymorphism (PIC > 0.5) of most markers, with expected and observed heterozygosities ranging from 0.31 to 0.87. More than 99% of individuals were heterozygous for at least three markers, with 95.8% of individuals heterozygous for at least two markers on either side of the FMR1 CGG repeat. The tetradecaplex marker assay can be performed directly on single cells or after whole-genome amplification, thus supporting its use in FXS PGD either as a standalone linkage-based assay or as a complement to FMR1 mutation detection.Genet Med 18 9, 869-875.

A Single-Tube Real-Time PCR Assay for Mycoplasma Detection as a Routine Quality Control of Cell Therapeutics

Background: Contamination of cell culture and biological material by mollicute species is an important safety issue and requires testing. We have developed a singletube real-time polymerase chain reaction (PCR) assay for rapid detection of Mollicutes species stipulated by the European Pharmacopeia. Methods: Primers and TaqMan probes (FAM-labeled) were deduced from 16S rDNA sequence alignment of 18 mollicutes species. A synthetic internal control (IC) DNA and an IC-specific TaqMan probe (VIC-labeled) were included. The analytical sensitivity of the assay was determined on DNA dilutions from 12 mollicute strains. Specificity was proven by the use of DNA from other bacteria. Results: Analytical sensitivities of the PCR assay were in the range of 405-2,431 genomes/ml for 11 of the 12 tested mollicute DNA samples. The lowest sensitivity was found for Ureaplasma urealyticum (19,239 genomes/ml). Negative results for DNA samples from 3 different ubiquitous bacteria demonstrated the specificity of the PCR assay for Mollicutes. Direct testing of cell culture supernatants spiked with Mycoplasma orale revealed similar sensitivity compared to isolated DNA. Conclusions: Our single-tube real-time PCR assay with internal reaction control enables rapid and specific detection of mollicute contaminants. The test protocol is suitable for routine quality control of cell therapeutics.

Detection of Bartonella quintana DNA in the presence of human and feline whole blood by single-tube PCR without DNA extraction

Introduction Nucleic acid amplification via polymerase chain reaction (PCR) is a well-established and highly sensitive tool for the molecular detection of pathogenic organisms from blood, tissues, and other clinical samples in humans and animals. Typically, highly purified template DNA is required for adequate gene amplification. However, a wide range of proteins,

One single-tube PCR assay to detect both CD17 (A>T) and IVS-II nt-654 (C>T) homozygous mutations of β-thalassemia

Several methods can be used to detect gene mutations associated with b-thalassemia, but it is difficult to achieve reliable and reproducible results. In this study, we introduce a new method, a single-tube multiplex polymerase chain reaction (PCR) assay, to detect both CD17 (A>T) and IVS-II nt-654 (C>T) homozygous mutations. Materials and methods: This new method designs specific primers to diagnose homozygous mutations and normal controls. Results: After PCR amplification, homozygous mutations produce different fragments from normal controls. Conclusion: This study represents an important step towards the development of a novel protocol to diagnose b-thalassemia and other diseases that target numerous mutations.

SYBR Green real-time quantitative PCR for the specific detection and quantification of ‘Candidatus Liberibacter solanacearum’ in field samples from New Zealand

Diseases of solanaceous crops caused by the phloem-limited bacterium ‘Candidatus Liberibacter solanacearum’ (Lso), vectored by the tomato potato psyllid Bactericera cockerelli, pose a major economic threat to crop production. Lso is yet to be cultured and, therefore, effective control strategies depend heavily on the early detection of the pathogen via polymerase chain reaction (PCR) assays. In this study, two new assays for the detection of Lso in New Zealand field samples were developed, and compared with previously available assays. Firstly, a single-tube semi-nested gel-based PCR assay was developed for the genus-specific detection of liberibacter species, and shown to provide increased sensitivity over standard and nested PCR. Secondly, a single-tube semi-nested SYBR Green real-time PCR (qPCR) assay was developed for the specific detection of Lso in field samples from New Zealand, with a limit of detection of five copies of the target gene per reaction. Semi-nested qPCR showed similar sensitivity compared with TaqMan qPCR with the primer-probe combination LsoF-HLBpr and was 10- to 50-fold more sensitive than the conventional PCR assays tested. Quantification of titre in Lso-affected tubers by SYBR Green qPCR revealed a positive relationship between pathogen titre and the discolouration of fried tuber slices, a symptom indicative of Lso infection. Quantification of Lso in field samples of potato and tomato also revealed many samples with titres below the limit of detection of conventional PCR. The observation of low-titre samples demonstrated the utility of SYBR Green qPCR for detection of Lso, as in addition to increased sensitivity melt-curve analysis enables confirmation of qPCR data by identifying false positive results.

Modified competing polymerase chain reaction primer for single tube quantitative PCR

We developed a modified polymerase chain reaction (PCR) primer with 3′ phosphate instead of hydroxyl group for single-tube accurate transcript quantification. 18S ribosomal RNA (rRNA) reference gene-specific modified primer was used for precise single-tube quantification of two target transcripts, namely chymotrypsin and jhamt (juvenile hormone acid methyl transferase) of Helicoverpa armigera. A comparative study of 3′ phosphorylated primers, 3′ mismatched primers, and commercial Competimers revealed that 3′ phosphorylation was more efficient than the 3′ mismatch and was on par with Competimers in blocking the primer extension. Thus, the modified primers can be used in single-tube, economical, and accurate PCR quantification of the target gene using any assay-specific reference gene.

A method for simple and accurate identification of the multiple sclerosis associated allele HLA-DRB1*1501 in neuroscience research laboratories

Research on multiple sclerosis (MS) frequently requires typing for allele HLA-DRB1*1501, which the complexities of the HLA system can restrict to specialised histocompatibility laboratories. To overcome this limitation, we have implemented a simple, robust and highly specific method for DRB1*1501 detection. One single-tube polymerase-chain reaction (PCR) per DNA sample allows for detecting DR2 individuals. The spare PCR products of these are then sequenced to identify allele DRB1*1501 by comparison with the official, publicly accessible HLA database. This approach, much simpler than previously available methods, should facilitate research on MS by making accurate identification of DRB1*1501 accessible to neuroscience laboratories.

MULTIPLEX PCR FOR DIRECT IDENTIFICATION OF THERMOPHILIC CAMPYLOBACTER, C. JEJUNI, C. COLI, C. LARI AND C. UPSALIENSIS AND SIMULTANEOUS DETECTION OF CDTB GENE

ABSTRACT A multiplex polymerase chain reaction (PCR) assay has been developed for the identification of the four thermophilic Campylobacter commonly associated with human gastroenteritis including C. jejuni, C. coli, C. lari and C. upsaliensis. The best combination of primers and the annealing temperature of multiplex PCR were examined. Detection limit was 2 × 105 cfu and 100 ng of DNA or whole‐cell suspension. The multiplex PCR was applied for the direct detection and differentiation of Campylobacter species in 33 human and 45 chicken caeca isolates. Of the 78 specimens evaluated by the multiplex PCR, 55 (70.5%) were identified as C. jejuni, 18 (23.0%) as C. coli and 5 (6.41%) as a mixed infection with both species. Comparison of hippurate test and multiplex PCR demonstrated five (6.41%) isolates with false‐positive hippurate enzymic activity and three (3.85%) with false‐negative activity. cdtB gene was detected in 100% and 38.9% of C. jejuni and C. coli, respectively. This multiplex PCR was found to be rapid, easy to perform and had a high sensitivity and specificity, even with mixed cultures. The system is useful for the detection of the presence of cdtB gene that is responsible for toxin activity in Campylobacter.PRACTICAL APPLICATIONSOur multiplex polymerase chain reaction (PCR) allows in a single tube PCR, the identification of the four clinically important Campylobacter species, with a simultaneous detection of the cdtB gene. The PCR works well in our hands with both purified genomic DNA and whole‐cell suspension. This should greatly speed up identification by replacing the current biochemical phenotypic schemes. In addition, the system can detect the presence of cdtB gene that encodes the cytolethal‐distending toxin activity.

Rapid Diagnosis of the α-Thalassemia-1 Southeast Asian Type Deletion Using a Single Tube Real-Time SYBR-Polymerase Chain Reaction Combined with Dissociation Curve Analysis

Dear Sir,A single tube polymerase chain reaction (PCR) with three primers and SYBR GREEN1 combined with dissociation curve analysis was set up that can clearly differentiate between Hb Bart's hydrops fetalis, normal subjects and − −SEA heterozygotes. This method seems to be simpler than that using a two-tube real-time SYBR-PCR with two different primer sets followed by analyses of ΔCT and CT ratio.

Development of a single-tube polymerase chain reaction assay for the simultaneous detection of Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus spp. directly in clinical samples

This study describes the development and evaluation of a multiplex single-tube polymerase chain reaction assay for the simultaneous detection of Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus spp. used as target species-specific or genus-specific genes. The assay enables the detection of 5 to 50 pg of bacterial DNA. The sensitivity of the assay was evaluated as 100% for P. aeruginosa, S. aureus, and Streptococcus spp., and 94.3% for H. influenzae; the specificity was 100% for all 4 microorganisms (positive predictive value, 100%; negative predictive value, 98.2%). The assay permits rapid and accurate detection of these 4 microorganisms in a wide range of clinical samples such as whole blood, cerebrospinal, ear, pleural and ophthalmic fluids, as well as bronchoalveolar lavage and bronchial secretions.

Improved Real-Time Multiplex Polymerase Chain Reaction Detection of Methylenetetrahydrofolate Reductase ( MTHFR) 677C>T and 1298A>C Polymorphisms Using Nearest Neighbor Model-Based Probe Design

The disorders of folate metabolism caused by methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms may lead to several disease states including coronary heart disease, venous thrombosis, and several types of cancer. We have developed a real-time multiplex single-tube polymerase chain reaction procedure on the LightCycler for the detection of the two most commonly occurring variants, 677C>T and 1298A>C, in the MTHFR gene. An improved probe design, based on the nearest neighbor model for nucleic acid-probe duplex stability, resulted in a better separation (DeltaTm approximately 10 degrees C) of melting peaks of the wild-type and mutant alleles than that by the existing method (DeltaTm approximately 3 degrees C) for specimens heterozygous for the 1298A>C polymorphism. Of the 333 blood specimens analyzed by this procedure, we did not find any samples that gave ambiguous results. The specimens with homozygous mutation for one polymorphism were of the wild type for the other variant. The assay was validated by the comparison of the genotyping results of 50 blood specimens from the LightCycler polymerase chain reaction with the conventional restriction fragment length polymorphism procedures. There was 100% concordance of the test results obtained by the two techniques. This assay is reliable, economical, and can be performed by less trained technologists compared with the procedure performed by the conventional restriction fragment length polymorphism technique.

A Ribeiroia Spp. (Class: Trematoda)–-Specific PCR-Based Diagnostic

Increased reporting of amphibian malformations in North America has been noted with concern in light of reports that amphibian numbers and species are declining worldwide. Ribeiroia ondatrae has been shown to cause a variety of types of malformations in amphibians. However, little is known about the prevalence of R. ondatrae in North America. To aid in conducting field studies of Ribeiroia spp., we have developed a polymerase chain reaction (PCR)-based diagnostic. Herein, we describe the development of an accurate, rapid, simple, and cost-effective diagnostic for detection of Ribeiroia spp. infection in snails (Planorbella trivolvis). Candidate oligonucleotide primers for PCR were designed via DNA sequence analyses of multiple ribosomal internal transcribed spacer-2 regions from Ribeiroia spp. and Echinostoma spp. Comparison of consensus sequences determined from both genera identified areas of sequence potentially unique to Ribeiroia spp. The PCR reliably produced a diagnostic 290-base pair (bp) product in the presence of a wide concentration range of snail or frog DNA. Sensitivity was examined with DNA extracted from single R. ondatrae cercaria. The single-tube PCR could routinely detect less than 1 cercariae equivalent, because DNA isolated from a single cercaria could be diluted at least 1:50 and still yield a positive result via gel electrophoresis. An even more sensitive nested PCR also was developed that routinely detected 100 fg of the 290-bp fragment. The assay did not detect furcocercous cercariae of certain Schistosomatidae, Echinostoma sp., or Sphaeridiotrema globulus nor adults of Clinostomum sp. or Cyathocotyle bushiensis. Field testing of 137 P. trivolvis identified 3 positives with no overt environmental cross-reactivity, and results concurred with microscopic examinations in all cases.

Single step high-throughput determination of Toll-like receptor 4 polymorphisms

Background: Toll-like receptors are central components of host defence in humans, responsible for recognition of pathogen-associated molecular patterns and activation of innate immunity. Toll-like receptor 4 (TLR4) is activated by lipopolysaccharide (LPS) and other microbial components, thereby initiating the expression and release of pro-inflammatory cytokines. The common, frequently co-segregating allelic variants Asp299Gly and Thr399Ile have been related to susceptibility to gram-negative infections and sepsis and may be involved in the development of atherosclerosis. Identification of TLR4 Asp299Gly and Thr399Ile genotypes can be important for examination of genotype/phenotype relationships as well as for individual risk assessment of patients. Methods: TLR4 Asp299Gly and Thr399Ile genotypes were detected by a single tube polymerase chain reaction (PCR), based on exonuclease degradation of dual labelled allele-specific oligonucleotides. The assay results were compared with conventional restriction fragment length polymorphism (RFLP) analysis. Results: Genotypes of 345 individuals were determined simultaneously in a single PCR assay. Allele frequencies for our population were 6.8% for the TLR4 Asp299Gly polymorphism and 6.4% for the Thr399Ile polymorphism. Validation by RFLP analysis revealed a correct detection of all genotypes. Conclusions: We have developed a novel method for the detection of the TLR4 Asp299Gly and Thr399Ile mutations, permitting rapid genotyping which should be useful for large-scale population studies as well as applicable for routine clinical testing.

A multicenter international evaluation of single-tube amplification protocols for sequencing-based typing of HLA-DRB1 and HLA-DRB3,4,5.

We have described previously a novel single-tube polymerase chain reaction (PCR) amplification (STAmp) protocol for the efficient sequencing-based typing (SBT) of human leukocyte antigen (HLA)-DRB1. The PCR amplification mix includes primers to each of seven allele group-sequence motifs. We have applied this principle to the simultaneous SBT of HLA-DRB3, -DRB4, and -DRB5 using locus specific primers. We report here a multicenter international evaluation of the STAmp protocols performed as a component of the 13th International Histocompatibility Workshop. Identical amplification primer mixes, sequencing primers, and DNA were sent to participating laboratories. The primer mixes contained the amplification primers and the PCR buffer. Each laboratory was requested to amplify the DNA with the primer mixes and perform SBT on the resulting PCR protocols, using their own protocols, and return the typing results for analysis. The reported results indicated that the expected sequence could be obtained with a variety of PCR amplification and sequencing platforms and protocols. There were difficulties but these seemed unrelated to STAmp reagents and suggest that optimal SBT results can be obtained if bi-directional sequencing is performed and software is used for sequence verification and editing. This indicates that SBT by STAmp can be applied in many laboratories for high-throughput HLA-DRB1 and HLA-DRB3,4,5 SBT.

A rapid non-enzymatic method of DNA extraction for PCR detection of white spot syndrome virus in shrimp

The present study describes a simple method of extraction of white spot syndrome viral DNA (WSSV) from infected shrimp for the polymerase chain reaction (PCR) detection of WSSV. The DNA preparation using this method was found to be free from the host DNA, RNA and protein, and is suitable for different PCR protocols such as single-step PCR, nested PCR and single-tube semi-nested PCR. This method of extraction has worked successfully for extracting the WSSV-DNA from different organs (haemolymph, eyestalk, carapace, head muscle, heart, gills, appendages, heptopancreas, stomach, intestine, abdominal muscle and tail muscle) of WSSV-infected adult shrimp, and WSSV-infected larvae and postlarvae.

High-level multiplex DNA amplification.

We present data on efficient amplification of large number of DNA targets using a single-tube polymerase chain reaction (PCR). This is a further enhancement of our approach to multiplexed PCR based on PCR suppression, which allows multiple DNA amplification using only one sequence-specific primer per amplicon while the second primer is common for all targets (Broude, N.E., et al., Proc. Natl. Acad. Sci. USA 98, 206-211, 2001). The reaction conditions have been optimized for simultaneous synthesis of 30 DNA targets, mostly consisting of fragments containing single nucleotide polymorphisms (SNP). The size of the amplified fragments, derived from many different human chromosomes, varies from 100 to 600 bp. We conclude that this method has potential for highly multiplexed DNA amplification useful for SNP analyses, DNA diagnostics, and forensics.

Whey hydrolysate formula reduced crying time in infantile colic

OBJECTIVE: To examine the epidemiology of the tetM gene in Neisseria gonorrhoeae strains with high level resistance to tetracycline (TRNG) using a polymerase chain reaction (PCR) assay. METHODS: A single...

Single‐Tube Multiplex PCR for Rapid and Sensitive Diagnosis of Subgenus B and Other Subgenera Adenoviruses in Clinical Samples

We developed a new diagnostic method of subgenus (Sub) B adenovirus (Ad) in clinical samples using non-nested polymerase chain reaction (PCR). Sequences of the conserved hexon-coding region of representative strains of eight serotypes (3, 7, 11, 14, 16, 21, 34 and 35) of Sub B Ad were heterogeneous. In order to distinguish Ad serotype 3 (Ad 3) and Ad 7 from the other serotypes of Sub B Ad, and to differentiate Ad 3 and 7 from each other, 3 different downstream primers were designed based on the sequence heterogeneity. By a single-tube PCR method using a combination of 6 primers including the 3 new primers, Ads demonstrated to amplify 188, 206, 284, and 301 bp DNA fragments for Ad 3, Ad 7, other Sub B Ads, and non-Sub B Ads, respectively. A total of 114 clinical samples were selected to evaluate the direct applicability of our PCR. The results were compared with previous culture results. Sixty-seven out of 71 (94%) Sub B Ad culture-positive samples, and 15 out of 19 (79%) Sub C or E-positive samples amplified products of the expected size. Two of 20 (10%) culture-negative samples from pharyngoconjunctival fever patients were identified as Ad 3 by the PCR. Four samples, from which non-Ad viruses were isolated, were negative by the PCR. The present study might provide a rapid and sensitive diagnosis method for infections caused by Sub B Ads.