Rapid screening for HLA-B27 by a TaqMan-PCR assay using sequence-specific primers and a minor groove binder probe, a novel type of TaqMan trade mark probe

Basic Investigations in Pediatric Rheumatology

The spectrum of pediatric rheumatological disorders is diverse and they are important differential diagnoses in a variety of clinical scenarios. Basic investigations not only provide supporting evidence for the diagnosis of a rheumatological illness but also help in exclusion of other diseases as well as for monitoring the activity of disease. Among these, complete blood count, biochemical assays including tests for inflammatory response, urine analysis, and various autoantibodies are often used. In addition, depending on the clinical features, imaging and tissue biopsies are used to confirm the diagnosis.

What Does Human Leukocyte Antigen B27 Have to Do with Spondyloarthritis?

Human leukocyte antigen (HLA) B27 is the key laboratory parameter for axial spondyloarthritis (axSpA). Its prevalence is variable across different geographic zones and ethnicities, and often mirrors the prevalence of axSpA. HLA-B27 plays a role in axSpA physiopathology. It is correlated with spondyloarthritis phenotype with a consistent positive association with family history, early disease onset, shorter diagnostic delay, hip involvement, and acute anterior uveitis. HLA-B27 has a pivotal role in many referral strategies. However, these strategies were developed in European populations and need to be evaluated in populations with lower HLA-B27 background prevalence, and where additional parameters might be needed.

Real-time PCR based HLA-B*27 screening directly in whole blood

The linkage between the occurrence of human leucocyte antigen B*27 (HLA-B*27) and ankylosing spondylitis or other related spondyloarthritides is well documented. PCR based methods are widely used for HLA-B*27 screening. To refine HLA-B*27 testing we aimed at establishing a real-time PCR protocol to detect the HLA-B*27 allele directly in blood samples, without DNA extraction. HLA-B*27 analysis was performed by two real-time PCRs using TaqMan primer-probe assays for B*27 specific amplification of exon 2 or exon 3 of the HLA-B gene together with a mutant of Taq polymerase for direct blood PCR. Conditions for direct blood PCR were optimized and the reliability of the direct blood PCR protocol was evaluated by re-genotyping over 200 blood samples from patients who previously underwent routine DNA-based HLA-B*27 testing. Heating blood samples at 95°C for 10 minutes significantly improved PCR performance. Results from real-time PCR based HLA-B*27 testing directly in blood of over 200 patients were in 100% concordance with results obtained by routine DNA-based HLA-B*27 genotyping. In summary, we present a reliable real-time PCR protocol for HLA-B*27 screening directly in whole blood supporting fast clarification of the presence of ankylosing spondylitis or other spondyloarthritides in suspected cases.

HLA testing in the molecular diagnostic laboratory

The human leukocyte antigen (HLA) system is a highly polymorphic family of genes involved in immunity and responsible for identifying self versus non-self. HLA typing is essential for solid organ and bone marrow transplantation as well as in non-transplant settings such as disease association and pharmacogenomics. Typing of HLA genes differs from most molecular testing as, rather than evaluating differences from an accepted "wild-type" gene, it must distinguish between thousands of similar, but distinct alleles. This article will describe the HLA system and nomenclature. We will then discuss clinical uses of HLA typing including solid organ transplantation, hematopoietic stem cell transplantation, evaluation of platelet refractory patients, disease association, and pharmacogenetics. Finally, we describe common molecular methods of HLA typing.

Alterations of Immune Parameters on Trichoplusia ni (Lepidoptera: Noctuidae) Larvae Exposed to Extremely Low-Frequency Electromagnetic Fields

Worldwide mobile telephone and microwave use have resulted in an increasing presence of extremely low-frequency electromagnetic field radiations (ELF-EMFs) in ecosystems. ELF-EMFs have been associated with altered physiological processes that can adversely affect exposed organisms. In this study, Trichoplusia ni Hübner larvae were exposed for 24, 48, or 72 h to ELF-EMFs (60 Hz and 2.0 mT) to assess effects on immune response parameters and fertility. Trichoplusia ni life cycle and fertility were not affected by 24-h exposure. However, the number of apoptotic-like cells and cellular immune response significantly increased (P < 0.01) after 72-h exposure (2- and 1.1-fold, respectively), whereas hemolymph total protein and hemocyte cells were reduced (P < 0.01; 16 and 50%, respectively) after 48-h exposure. Hemocyte cell type analysis resulted in significantly (P < 0.01) higher granulocytes number in the unexposed (2-fold increase) and oenocytoids in the 72-h-exposed larvae (28.6-fold increase). Quantitative retrotranscription (RT-qPCR) showed that after 72-h ELF-EMF exposure, the antimicrobial peptides cecropin, lysozyme, gallerimycin, and pgrp were downregulated by 24,866.0, 2.69-, 119.1-, and 1.45-fold, respectively, whereas attacin and defensin were upregulated by 1.59- and 1.85-fold, respectively. The effect of ELF-EMFs on the T. ni larvae immune response and their potential impact on its physiology and susceptibility to pathogens are discussed. This information may provide new insight of ELF-EMFs on other pest species, as well as for the preservation of ecologically important species.

Postnatal and non-invasive prenatal detection of β-thalassemia mutations based on Taqman genotyping assays

The β-thalassemias are genetic disorder caused by more than 200 mutations in the β-globin gene, resulting in a total (β⁰) or partial (β⁺) deficit of the globin chain synthesis. The most frequent Mediterranean mutations for β-thalassemia are: β⁰39, β⁺IVSI-110, β⁺IVSI-6 and β⁰IVSI-1. Several molecular techniques for the detection of point mutations have been developed based on the amplification of the DNA target by polymerase chain reaction (PCR), but they could be labor-intensive and technically demanding. On the contrary, TaqMan^® genotyping assays are a simple, sensitive and versatile method suitable for the single nucleotide polymorphism (SNP) genotyping affecting the human β-globin gene. Four TaqMan^® genotyping assays for the most common β-thalassemia mutations present in the Mediterranean area were designed and validated for the genotype characterization of genomic DNA extracted from 94 subjects comprising 25 healthy donors, 33 healthy carriers and 36 β-thalassemia patients. In addition, 15 specimens at late gestation (21–39 gestational weeks) and 11 at early gestation (5–18 gestational weeks) were collected from pregnant women, and circulating cell-free fetal DNAs were extracted and analyzed with these four genotyping assays. We developed four simple, inexpensive and versatile genotyping assays for the postnatal and prenatal identification of the thalassemia mutations β⁰39, β⁺IVSI-110, β⁺IVSI-6, β⁰IVSI-1. These genotyping assays are able to detect paternally inherited point mutations in the fetus and could be efficiently employed for non-invasive prenatal diagnosis of β-globin gene mutations, starting from the 9^th gestational week.

Developing a Risk-scoring Model for Ankylosing Spondylitis Based on a Combination of HLA-B27, Single-nucleotide Polymorphism, and Copy Number Variant Markers

OBJECTIVE

To develop a genotype-based ankylosing spondylitis (AS) risk prediction model that is more sensitive and specific than HLA-B27 typing.

METHODS

To develop the AS genetic risk scoring (AS-GRS) model, 648 individuals (285 cases and 363 controls) were examined for 5 copy number variants (CNV), 7 single-nucleotide polymorphisms (SNP), and an HLA-B27 marker by TaqMan assays. The AS-GRS model was developed using logistic regression and validated with a larger independent set (576 cases and 680 controls).

RESULTS

Through logistic regression, we built the AS-GRS model consisting of 5 genetic components: HLA-B27, 3 CNV (1q32.2, 13q13.1, and 16p13.3), and 1 SNP (rs10865331). All significant associations of genetic factors in the model were replicated in the independent validation set. The discriminative ability of the AS-GRS model measured by the area under the curve was excellent: 0.976 (95% CI 0.96-0.99) in the model construction set and 0.951 (95% CI 0.94-0.96) in the validation set. The AS-GRS model showed higher specificity and accuracy than the HLA-B27-only model when the sensitivity was set to over 94%. When we categorized the individuals into quartiles based on the AS-GRS scores, OR of the 4 groups (low, intermediate-1, intermediate-2, and high risk) showed an increasing trend with the AS-GRS scores (r² = 0.950) and the highest risk group showed a 494× higher risk of AS than the lowest risk group (95% CI 237.3-1029.1).

CONCLUSION

Our AS-GRS could be used to identify individuals at high risk for AS before major symptoms appear, which may improve the prognosis for them through early treatment.

A multiplex allele-specific real-time polymerase chain reaction assay for HLA-B*13:01 genotyping in four Chinese populations

Human leukocyte antigen HLA-B*13:01 is identified currently as a marker of individual susceptibility to drug-induced hypersensitivity reaction, such as dapsone-induced hypersensitivity reactions (DIHRs) and trichloroethylene-induced dermatitis. Therefore, screening for the HLA-B*13:01 allele can assist clinics in identifying patients at risk of developing DIHRs. By combining the allele-specific primers with TaqMan probes, we established a single tube, triplex real-time PCR to detect HLA-B*13:01. The reliability of this assay was validated by the comparison of genotyping results with those by sequence-based typing (SBT). With this assay, the distribution of HLA-B*13:01 in a total of 350 blood samples from four ethnic groups: Han, Tibetan, Uighur, and Buyei were determined. A 100% concordance was observed between the results with the established real-time PCR and SBT in 100 samples. The detection limit of this assay was 0.016 ng genomic DNA. The prevalence of HLA-B*13:01 carriers were 11%, 8%, 1%, and 2% in the Buyei (n = 100), Northern Han (n = 100), Tibetan (n = 100), and Uighur (n = 50) populations, respectively. The multiplex real-time PCR assay provided a fast and reliable method for accurate detection of HLA-B*13:01 allele prior to dapsone administration in clinical practice and onset of the reaction after exposure to trichloroethylene.

Rapid and reliable genotyping of HLA-B*58:01 in four Chinese populations using a single-tube duplex real-time PCR assay

AIM

HLA-B*58:01 is strongly associated with allopurinol-induced severe cutaneous adverse reactions. This study aimed to develop a new and convenient method for HLA-B*58:01 genotyping and to investigate HLA-B*58:01 distribution in different Chinese populations.

MATERIALS & METHODS

Combining of sequence-specific primers and TaqMan probe, a single-tube duplex real-time PCR assay for HLA-B*58:01 typing was established.

RESULTS

The HLA-B*58:01 genotyping result in Buyei (n = 100) by real-time PCR showed 100% concordance with those by sequence-based typing. The prevalence of HLA-B*58:01 carrier in Buyei (17%, n = 100) was significantly higher than those in Northern Han (4%, n = 100), Tibetan (5.1%, n = 99) and Uighur (2%, n = 50) populations (p < 0.05).

CONCLUSION

The newly developed reliable assay was appropriate for HLA-B*58:01 detection prior to allopurinol administration in clinical settings.

Genetic determinants of cocaine-associated agranulocytosis

Background

Drug-induced agranulocytosis is a recognized adverse drug event associated with serious infectious complications. Levamisole is an antihelminthic and immunomodulator withdrawn from North American markets in 2005 after reports of agranulocytosis. Previous studies of levamisole, suggest that the human leukocyte antigen (HLA)-B27 confers a genetic predisposition to this adverse drug event. Since 2009, emergency room visits due to agranulocytosis in individuals consuming levamisole-adulterated crack-cocaine have increased.

Methods

We performed a case–control study using a genotyping assay and novel gene chip to test the association between cocaine-associated agranulocytosis (CAA) and HLA-B27 and to identify pharmacokinetic and pharmacodynamic gene variants associated with the phenotype.

Results

Fifty-one CAA cases were identified through a provincial physician reporting system between 2008 and 2011. We examined eight of these cases and 26 matched controls. Genotyping revealed a significant association between HLA-B27 and CAA (odds ratio [OR] 9.2, 95% confidence interval [CI], 1.54–54.6). We also observed a similar association with the HLA-B27 tag single nucleotide polymorphism rs4349859 (OR 9.2, 95% CI 1.5–54.6) and rs13202464 (OR 6.7, 95% CI 1.1–41). Further associations were identified with variants in the ARBCC12 (OR 10.0, 95% CI 2.7–36.8) and CYP11A1 (OR 7.4, 95% CI 2.1–26.6) genes, while a novel protective association was observed with variants in the ARDB1 gene (OR 0.06, 95% CI 0.007–0.46).

Conclusions

We confirmed the association of HLA-B27 with CAA and identified additional susceptibility variants. Health care providers should inform people who are identified as having CAA that it is genetically determined and can recur with continued cocaine use. The severity of infections and subsequent hospitalization, and the risk of recurrence may prompt health-promoting behaviour changes of the affected individuals. These genetic associations warrant the attention of public health and knowledge translation efforts to highlight the implications for susceptibility to this severe adverse drug event.

Novel Approaches and Technologies in Molecular HLA Typing

The invention of the Polymerase Chain Reaction (PCR) has revolutionized molecular biology enabling gene isolation and characterization in hours rather than days. Scientists working in transplant diagnostics have proven to be pioneers in adapting this molecular technique to the clinical needs of histocompatibility testing. This chapter describes a number of novel genotyping technologies which have been used to address the challenges posed by genetic diversity seen in the extensive polymorphism in HLA genes. These novel approaches include single-stranded and duplex conformational analyses, real-time PCR, microarray hybridization, RNA-based sequencing, and the present day Next Generation Sequencing. The chapter concludes with a brief look at a possible next, Next Generation Sequencing system.

Real-time PCR detection chemistry

Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.

Rapid and reliable genotyping of HLA-B*27 in the Chinese Han population using a duplex real-time TaqMan PCR assay

OBJECTIVES

To develop a duplex real-time TaqMan PCR assay for genotyping HLA-B*27 in the Chinese Han population.

DESIGN AND METHODS

A standard curve was constituted to deduce amplification efficiency, dynamic range and detection limit of the duplex real-time TaqMan PCR assay, whereas PCR-SBT (PCR with sequence-based typing) was used to evaluate the accuracy of the assay.

RESULTS

A linear standard curve for determining HLA-B*27 was obtained within the range of 10(1)-10(9) copies per reaction with the correlation coefficient of 0.99 and amplification efficiency of 98.30%. The detection limit was 3.09 copies per reaction. Complete concordance was found between the results obtained by the duplex real-time TaqMan PCR assay and PCR-SBT. Fifty-nine of the 178 genomic samples were HLA-B*27 positive and the other 119 were HLA-B*27 negative.

CONCLUSIONS

The duplex real-time TaqMan PCR approach appears to be a reliable, sensitive, rapid and high-throughput method to genotype HLA-B*27 in the Chinese Han population.

Rapid identification and quantification of Campylobacter coli and Campylobacter jejuni by real-time PCR in pure cultures and in complex samples

Background

Campylobacter spp., especially Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli), are recognized as the leading human foodborne pathogens in developed countries. Livestock animals carrying Campylobacter pose an important risk for human contamination. Pigs are known to be frequently colonized with Campylobacter, especially C. coli, and to excrete high numbers of this pathogen in their faeces. Molecular tools, notably real-time PCR, provide an effective, rapid, and sensitive alternative to culture-based methods for the detection of C. coli and C. jejuni in various substrates. In order to serve as a diagnostic tool supporting Campylobacter epidemiology, we developed a quantitative real-time PCR method for species-specific detection and quantification of C. coli and C. jejuni directly in faecal, feed, and environmental samples.

Results

With a sensitivity of 10 genome copies and a linear range of seven to eight orders of magnitude, the C. coli and C. jejuni real-time PCR assays allowed a precise quantification of purified DNA from C. coli and C. jejuni. The assays were highly specific and showed a 6-log-linear dynamic range of quantification with a quantitative detection limit of approximately 2.5 × 10² CFU/g of faeces, 1.3 × 10² CFU/g of feed, and 1.0 × 10³ CFU/m² for the environmental samples. Compared to the results obtained by culture, both C. coli and C. jejuni real-time PCR assays exhibited a specificity of 96.2% with a kappa of 0.94 and 0.89 respectively. For faecal samples of experimentally infected pigs, the coefficients of correlation between the C. coli or C. jejuni real-time PCR assay and culture enumeration were R² = 0.90 and R² = 0.93 respectively.

Conclusion

The C. coli and C. jejuni real-time quantitative PCR assays developed in this study provide a method capable of directly detecting and quantifying C. coli and C. jejuni in faeces, feed, and environmental samples. These assays represent a new diagnostic tool for studying the epidemiology of Campylobacter by, for instance, investigating the carriage and excretion of C. coli and C. jejuni by pigs from conventional herds.

Quantification of Campylobacter spp. in pig feces by direct real-time PCR with an internal control of extraction and amplification

The rapid and direct quantification of Campylobacter spp. in complex substrates like feces or environmental samples is crucial to facilitate epidemiological studies on Campylobacter in pig production systems. We developed a real-time PCR assay for detecting and quantifying Campylobacter spp. directly in pig feces with the use of an internal control. Campylobacter spp. and Yersinia ruckeri primers-probes sets were designed and checked for specificity with diverse Campylobacter, related organisms, and other bacterial pathogens before being used in field samples. The quantification of Campylobacter spp. by the real-time PCR then was realized on 531 fecal samples obtained from experimentally and naturally infected pigs; the numeration of Campylobacter on Karmali plate was done in parallel. Yersinia ruckeri, used as bacterial internal control, was added to the samples before DNA extraction to control DNA-extraction and PCR-amplification. The sensitivity of the PCR assay was 10 genome copies. The established Campylobacter real-time PCR assay showed a 7-log-wide linear dynamic range of quantification (R²=0.99) with a detection limit of 200 Colony Forming Units of Campylobacter per gram of feces. A high correlation was found between the results obtained by real-time PCR and those by culture at both qualitative and quantitative levels. Moreover, DNA extraction followed by real-time PCR reduced the time needed for analysis to a few hours (within a working day). In conclusion, the real-time PCR developed in this study provides new tools for further epidemiological surveys to investigate the carriage and excretion of Campylobacter by pigs.

Rapid HLA-B27 screening with real-time TaqMan PCR: a clinical validation in the Dutch population

Human leukocyte antigen B27 (HLA-B27) is strongly associated with ankylosing spondylitis. The B27 allele is present in 90% of patients with this disease, whereas it is present in only 9% of Caucasians. Molecular detection of HLA-B27 is traditionally based on allele specific amplification of exon 2 (Olerup method) or exon 3 (Dominguez method) by PCR, followed by gel analysis.

We developed a real-time TaqMan PCR based on the Dominguez method with a β-Globin PCR as internal control.

A total of 544 clinical samples were used to compare the real-time TaqMan PCR with the traditional Dominguez PCR, the traditional Olerup PCR and a commercial Olerup based HLA-B27 detection kit (

With a correct result for 543 out of 544 samples (99.8%), we consider our real-time HLA-B27 PCR is a reliable method to detect HLA-B27 in the Dutch population, with reduced hands-on time and contamination risk compared to traditional PCR methods.

Evaluation of two commercial HLA-B27 real-time PCR kits

BACKGROUND

The standard PCR with sequence-specific primers (SSP) is a widely used method of HLA-B27 typing in clinical practice. The aim of our study was to evaluate 2 Korean HLA-B27 kits with different real-time PCR chemistries.

METHODS

To validate the accuracy of real-time PCR kits, we selected 28 HLA-B27-positive samples and 33 HLA-B27-negative samples with a wide range of different HLA-B specificities typed by standard PCR-SSP. The 2 real-time PCR kits used were the AccuPower HLA-B27 real-time PCR kit (Bioneer, Korea) with TaqMan probes and the Real-Q HLA-B*27 detection kit (BioSewoom, Korea) with SYBR Green I dye for melting curve analysis.

RESULTS

All 61 samples typed by PCR-SSP demonstrated a perfect concordance with the 2 real-time PCR assays. It was possible to clearly discriminate between HLA-B27-positive and -negative samples in both real-time assays.

CONCLUSIONS

In summary, both real-time PCR assays for HLA-B27 were fast, reliable, well-adapted for routine laboratory testing, and attractive alternatives to the conventional PCR-SSP method.

A real-time polymerase chain reaction assay for the rapid identification of the autoimmune disease-associated allele HLA-DQB1*0602

Many autoimmune diseases share a genetic association with the presence or absence of human leukocyte antigen (HLA)-DQB1*0602, including type I diabetes, multiple sclerosis, and narcolepsy. High-resolution HLA typing to determine the presence of this allele is cumbersome and expensive by currently available techniques. We present a real-time polymerase chain reaction (PCR) assay for the identification of HLA-DQB1*0602, using sequence-specific primers and probes, that provides rapid and sensitive identification of this allele, involves minimal hands-on time, and provides major cost savings compared with existing methods. The assay allows the simultaneous determination of both the presence and the number of copies of this allele. Because there is no post-PCR handling, the risk of contamination is avoided. We have validated the assay using 44 blinded and 32 unblinded samples, previously typed by standard techniques, which were identified with 100% accuracy, sensitivity, and specificity. Furthermore, using a narcolepsy cohort of 722 subjects, we demonstrated the robustness of the assay to analyze DNA isolated from buccal swabs, demonstrating the applicability of this assay as a suitable approach for population-based studies.

Rapid HLA-DR fluorotyping based on melting curve analysis

Real-time polymerase chain reaction (PCR) has been used in the study of human leukocyte antigen (HLA) genotyping as a potential alternative for routinely used molecular methods such as PCR-sequence specific primers (PCR-SSP) and PCR-sequence specific oligonucleotide probes (PCR-SSO). Combined with fluorescent dye like SYBR GREEN I, it has more advantages such as low cost and consistent background. The aim of this study was to optimize the fluorescent dye-based method and introduce it into the fluorotyping for HLA-DR lotus. 24 pairs of allele-specific primers and 1 pair of internal control were optimized to discriminate HLA-DRB1, -DRB3/B4/B5 alleles. Additionally, conditions of real-time PCR amplifying and melting curve recording had been improved for convenient and clear readout. Forty-two clinical samples previously typed by conventional PCR-SSP or sequence based typing (SBT) were tested and all got identical results. With this technique, 15 DNA samples can be assayed in parallel within 2 hours on the Real-time PCR instrument. These data strongly suggest a rapid HLA-DR fluorotyping method based on melting curve analysis, which could be a more economic and automatic alternative for clinical HLA-DR typing.

Association of cell-free plasma DNA with hospital mortality and organ dysfunction in intensive care unit patients

OBJECTIVE

To investigate the concentration of cell-free plasma DNA and its association with organ dysfunction and hospital mortality in intensive care unit patients.

DESIGN AND SETTING

Prospective cohort study in a medical and two medical-surgical intensive care units in a university hospital.

PATIENTS

228 critically ill patients admitted to the ICUs between January 2004 and July 2005.

MEASUREMENTS AND RESULTS

Blood samples were collected as soon as possible after ICU admission, the following morning, and 48[Symbol: see text]h after the second sample. The cell-free plasma DNA was measured by real-time quantitative PCR assay for the beta-globin gene. Physiological and mortality data were collected to the clinical database. Hospital mortality rate and SOFA scores were primary outcome measures. The maximum plasma DNA concentrations were correlated significantly with APACHE II points and with maximum SOFA scores. Cell-free plasma DNA concentrations were higher in hospital non-survivors than in survivors (median 9,366 vs. 6,506 GE/ml). Using logistic regression analysis, the maximum plasma DNA was an independent predictor of hospital mortality.

CONCLUSIONS

The maximum plasma DNA concentration measured during the first 96[Symbol: see text]h of intensive care is associated with the degree of organ dysfunction and disease severity. Moreover, the maximum DNA concentration is independently associated with hospital mortality.

Development and evaluation of a Taqman duplex real-time PCR quantification method for reliable enumeration of Legionella pneumophila in water samples

This study describes the development and evaluation of a specific Legionella pneumophila Taqman duplex real-time PCR (qPCR) for fast and reliable quantification of this human pathogen in suspected man-made water systems. The qPCR assay was 100% specific for all L. pneumophila serogroups 1-15 with a sensitivity of 60 genome units/l and an amplification efficiency of 98%. Amplification inhibitors were detected via an exogenous internal positive control, which was amplified simultaneously with L. pneumophila DNA using its own primer and probe set. Mean recovery rates of the qPCR assay for tap water and cooling circuit water, spiked with a known number L. pneumophila bacteria, were 93.0% and 56.3%, respectively. Additionally, by using the Ultraclean Soil DNA isolation kit, we were able to remove amplification inhibitors ubiquitously present in cooling water. The practical value of our qPCR assay was evaluated through analysis of 30 water samples from showers, taps, eyewash stations, fire sprinklers and recirculation loops with qPCR and traditional culture. In conclusion, the described L. pneumophila Taqman duplex real-time assay proved to be specific, sensitive and reproducible. This makes it a promising method complementing the current time-consuming culture standard method.

A real-time PCR approach for rapid high resolution subtyping of HLA-DRB1*04

We present a real-time PCR approach for the identification and subtyping of HLA-DR4 alleles. The technique, which uses sequence-specific primers and probes in conjunction with real-time PCR for the detection and differentiation of target alleles, is rapid, involves minimal hands-on time, and is inexpensive compared to existing methods. Further, there is no post-PCR handling, so the risk of contamination is avoided. We have validated the assay using 44 blinded and 56 unblinded samples, which were identified with 100% accuracy, sensitivity, and specificity. We demonstrate the applicability of this assay as an alternative approach to traditional HLA typing methods.

Real-Time PCR Using Fluorescent Resonance Emission Transfer Probes for HLA-B Typing

HLA genotyping by polymerase chain reaction (PCR) has some inherent labor-intensive and effort-demanding limitations. To overcome them, we have developed a real-time PCR with hybridization probes approach able to obtain a medium-low resolution HLA-B genotyping with fewer tubes and probes and with a shorter time requirement. Our strategy used 18 simultaneous reactions amplifying HLA-B alleles and an internal control. Monitorization of both amplifications in each tube is performed by the simultaneous application of two fluorescent resonance emission transfer probes: the first probe, different for each tube, is specific for the HLA-B locus and the second probe detects the control gene. A medium-low resolution (300 HLA-B allelic groups) typing is obtained for each sample by analyzing the melting curve patterns. Because some alleles may be determined without using the complete set of reactions, we present an alternative strategy: a first round of seven reactions and, according to the result, a second (or third) round of PCRs to solve the ambiguities. This method was validated in pretyped clinical samples and the results were completely concordant. Moreover, fewer ambiguous results were obtained. In summary, we present a new, faster, and more accurate method than currently used PCR techniques to type HLA-B alleles.

Simultaneous genotyping of DRB1/3/4/5 loci by oligonucleotide microarray

Matching of the HLA antigens for donor-recipient in transplantation, disease predisposition or protection, population studies, and forensic testing requires accurate but simple typing methods. Here, we describe a DNA-based tissue-typing assay that determines the haplotype of the DRB1/3/4/5 loci in hy-bridization of oligonucleotide array after sample amplification. Using this multianalyte DNA hybridization system, we analyzed seven regions of exon 2 of DRB loci that have single-base discrimination. Thirty-six oligonucleotide probes complementary to the alleles of interest were immobilized on each microslide. The efficiency and specificity of identifying DRB genotypes using the oligonucleotide arrays was evaluated by blinded analysis of 147 samples from reference standards and subjects. The established method provides a rapid and inexpensive DRB "low-resolution" typing tool for prescreening a large number of samples.

HLA-B27 testing in Thai patients using the PCR-SSP technique

We develop the HLA-B27 test kit using the PCR-SSP technique. Five hundred forty blood samples were tested for HLA-B27 by microlymphocytotoxicity test (LCT) and PCR-SSP. It was found that 127 (23.5%) and 134 (24.8%) of these samples were positive for HLA-B27 by LCT and PCR-SSP, respectively. The sensitivity and specificity of the PCR-SSP were 94.8 and 100%, respectively, when using LCT as the standard method. The PCR-SSP positive predictive value was 100%, negative predictive value was 98.3%, and a concordance rate of 98.7%. This study shows that the PCR-SSP is simple, convenient, and a more cost-effective in-house test kit.

Rapid and/or high-throughput genotyping for human red blood cell, platelet and leukocyte antigens, and forensic applications

BACKGROUND

Traditionally, transfusion medicine, platelet and human leukocyte antigen (HLA) typing, and forensic medicine relied on serologic studies.

METHODS

In recent years, molecular testing on nucleic acids has been increasingly applied to these areas. Although conventional molecular diagnostic methods such as PCR-sequence-specific priming, PCR-restriction fragment-length polymorphism, PCR-single-strand conformation polymorphism, sequence-based typing, and DNA fingerprinting have been shown to perform well, their use is limited by long turnaround times, high cost, labor-intensiveness, the need for special technical skills, and/or the high risk of amplicon contamination. With advance of fast and/or high-throughput methods and platforms that often combine amplification and detection, a new era of molecular genotyping is emerging in these fields dominated by serology for a century. As new targets, short tandem repeats, mitochondrial DNA and Y-chromosome sequences were introduced for forensic applications. This article reviews the current status of the application of rapid and/or high-throughput genotyping methods to these areas.

RESULTS

The results are already promising with real-time PCR, pyrosequencing, microarrays, and mass spectrometry and show high concordance rates with classic serologic and earlier manual molecular diagnostic methods. Exploration of other emerging methodologies will likely further enhance the diagnostic utility of molecular testing in these areas.

The use of real-time PCR methods in DNA sequence variation analysis

BACKGROUND

Real-time (RT) PCR methods for discovering and genotyping single nucleotide polymorphisms (SNPs) are becoming increasingly important in various fields of biological sciences. SNP genotyping is widely used to perform genetic association studies aimed at characterising the genetic factors underlying inherited traits. The detection and quantification of somatic mutations is an important tool for investigating the genetic causes of tumorigenesis. In infectious disease diagnostics there is an increasing emphasis placed on genotyping variation within the genomes of pathogenic organisms in order to distinguish between strains.

METHODS

There are several platforms and methods available to the researcher wishing to undertake SNP analysis using real-time PCR methods. These use fluorescent technologies for discriminating between the alternate alleles of a polymorphism. There are several real-time PCR platforms currently on the market. Two of the key technical challenges are allele discrimination and allele quantification.

CONCLUSIONS

Applications of this technology include SNP genotyping, the sensitive detection of somatic mutations and infectious disease subtyping.