Loss Of Assay Sensitivity Research Articles

Feasibility of Xpert Ebola Assay in Médecins Sans Frontières Ebola Program, Guinea.

Rapid diagnostic methods are essential in control of Ebola outbreaks and lead to timely isolation of cases and improved epidemiologic surveillance. Diagnosis during Ebola outbreaks in West Africa has relied on PCR performed in laboratories outside this region. Because time between sampling and PCR results can be considerable, we assessed the feasibility and added value of using the Xpert Ebola Assay in an Ebola control program in Guinea. A total of 218 samples were collected during diagnosis, treatment, and convalescence of patients. Median time for obtaining results was reduced from 334 min to 165 min. Twenty-six samples were positive for Ebola virus. Xpert cycle thresholds were consistently lower, and 8 (31%) samples were negative by routine PCR. Several logistic and safety issues were identified. We suggest that implementation of the Xpert Ebola Assay under programmatic conditions is feasible and represents a major advance in diagnosis of Ebola virus disease without apparent loss of assay sensitivity.

A reusable electrochemical proximity assay for highly selective, real-time protein quantitation in biological matrices.

Rapid and specific quantitation of a variety of proteins over a wide concentration range is highly desirable for biosensing at the point-of-care, in clinical laboratories, and in research settings. Our recently developed electrochemical proximity assay (ECPA) is a target-flexible, DNA-directed, direct-readout protein quantitation method with detection limits in the low femtomolar range, making it particularly amenable to point-of-care detection. However, consistent quantitation in more complex matrices is required at the point-of-care, and improvements in measurement speed are needed for clinical and research settings. Here, we address these concerns with a reusable ECPA, where a gentle regeneration of the surface DNA monolayer (used to capture the proximity complex) is achieved enzymatically through a novel combination of molecular biology and electrochemistry. Strategically placed uracils in the DNA sequence trigger selective cleavage of the backbone, releasing the assembled proximity complex. This allows repeated protein quantitation by square-wave voltammetry (SWV)—as quickly as 3 min between runs. The process can be repeated up to 19 times on a single electrode without loss of assay sensitivity, and currents are shown to be highly repeatable with similar calibrations using seven different electrodes. The utility of reusable ECPA is demonstrated through two important applications in complex matrices: (1) direct, quantitative monitoring of hormone secretion in real time from as few as five murine pancreatic islets and (2) standard addition experiments in unspiked serum for direct quantitation of insulin at clinically relevant levels. Results from both applications distinguish ECPA as an exceptional tool in protein quantitation.

D‐dimer concentration increases with age reducing the clinical value of the D‐dimer assay in the elderly

The D-dimer assay is used as an exclusion test in the assessment of suspected venous thromboembolic disease; patients with a negative result have a low probability of thrombosis. We reviewed the D-dimer results from a hospital and community laboratory using the vidas D-dimer test to assess the influence of age on the D-dimer assay. D-dimer results from 6631 unselected patients aged more than 16 years were analysed in four age groups and it was shown that the median D-dimer concentration increased with age (16-40 years, 294 ng/mL; 40-60 years, 387 ng/mL; 60-80 years; 854 ng/mL; >80 years, 1397 ng/mL). To test the effect of age on the assay specificity, a cohort of 1897 patients with suspected venous thromboembolic disease was analysed separately. Patients with a negative D-dimer were discharged without further investigation. Patients with a positive result and a clinical suspicion of thrombosis underwent further investigation. One hundred and sixty-five deep vein thrombosis or pulmonary embolus cases were identified. The assay specificity decreased with age from 70% in patients less than 40 years to below 5% in patients more than 80 years. Receiver operator curves were prepared for each age group and the effect of altering the threshold value was analysed. In patients 60-80 years old a threshold value of 1000 ng/mL increased assay specificity to 55% without loss of assay sensitivity. The vidas D-dimer assay with a threshold value of 500 ng/mL has little clinical value as an exclusion test in patients more than 80 years old. The assay specificity is poor (26%) in patients aged 60-80 years but could be improved by increasing the threshold value to 1000 ng/mL. We believe that this should be tested in a prospective trial.

Autolysin-targeted LightCycler assay including internal process control for detection of Streptococcus pneumoniae DNA in clinical samples.

The development and clinical evaluation of a LightCycler PCR assay, including an internal process control (IPC), to detect the Streptococcus pneumoniae autolysin gene in clinical samples is reported. The assay was developed to provide a second target for use in conjunction with existing pneumolysin PCR assays to increase the reliability of non-culture PCR diagnosis of pneumococcal infection. Primers amplify a 173 bp fragment of the autolysin gene (lytA), which is detected by fluorescence-labelled hybridization probes. An IPC was designed to check for the presence of PCR inhibitors and loss of assay sensitivity. The IPC product was amplified by the lytA primers and detected by a second set of hybridization probes. The analytical specificity of the autolysin PCR assay was 100% against 39 other bacterial species tested; these included related streptococci and other organisms. The assay, which could reliably detect 50 fg purified pneumococcal DNA per reaction, was capable of distinguishing between S. pneumoniae and atypical Streptococcus mitis and Streptococcus oralis strains known to contain the lytA gene. Using DNA extracts from a panel of EDTA bloods from patients with blood-culture-confirmed pneumococcal infection, the autolysin PCR had a sensitivity of 42.9%, which was similar to a previously reported TaqMan pneumolysin PCR (43.8%) run in parallel. Total agreement was shown between the autolysin assay and the pneumolysin TaqMan assay when used to test 23 culture-negative clinical samples, of which eight were positive by PCR, adding valuable clinical information. A specific autolysin-based LightCycler assay has been developed to complement pneumolysin PCR for the detection of S. pneumoniae in clinical samples. This should be a particularly useful tool for the rapid and sensitive diagnosis of pneumococcal meningitis, even after an antibiotic has been administered. However, poor sensitivity on blood samples limits its usefulness in other bacteraemic infections.

Novel multi-probe RNase protection assay (RPA) sets for the detection of murine chemokine gene expression

Chemokines play an essential role in immune and inflammatory reactions via the recruitment of leukocytes. Studying the role of chemokines in vivo is complicated by the redundancy of their action and by their promiscuous receptor usage. The simultaneous analysis of several chemokines is, therefore, advantageous in order to obtain a comprehensive view of chemokine participation in inflammatory and infectious processes. At present, no multi-probe detection systems are available for the analysis of recently described chemokines. In this study, new multi-probe RNase protection assay (RPA) template sets were developed for the analysis of murine chemokines. Chemokine cDNA fragments were generated by RT-PCR and individually subcloned into the plasmid pGEM-T providing a T7 promotor. In this way, two multi-probe template sets were constructed each containing six chemokine sequences (CXCL12/SDF-1, XCL1/lymphotactin, CCL20/exodus-1, CCL25/TECK, CX3CL1/fractalkine, CXCL1/KC, and CCL20/MDC, CXCL9/MIG, CCL9/10/MIP-1γ, CXCL13/BLC, CCL12/MCP-5, CCL19/ELC, respectively) and templates for the two house-keeping genes L32 and GAPDH. The evaluation of these RPA template sets in various murine models demonstrated their suitability for the analysis of the above chemokines both under constitutive and infection-induced conditions. To reduce the personal radiation hazard, we found that 32P could be replaced by 33P without any loss of assay-sensitivity. These new RPA multi-probe sets provide valuable tools for the simultaneous quantitative determination of gene expression of multiple murine chemokines of both constitutive and inducible type.

One-Step Fluorescent Probe Product-Enhanced Reverse Transcriptase Assay

Recently developed PCR-based reverse transcriptase (RT) assays are useful in the detection of retroviruses since they are approximately a millionfold more sensitive than conventional RT assays. However, these assays are both labor- and time-intensive. The previously described product-enhanced reverse transcriptase (PERT) assay involves a two-step RT-PCR followed by detection and quantitation of PCR products by either Southern blot or enzyme-linked immunosorbent assay (ELISA). We have modified the PERT assay to be a one-step, fluorescent probe, PCR-based RT assay that can be completed from sample dilution to final quantitative assay results in approximately 5 h without loss of assay sensitivity or specificity. The assay has a dynamic range of 6 logs, and therefore, extensive sample dilution is not necessary for quantitation. This newly enhanced fluorescent PERT assay can play an important role in the high-throughput detection of retroviral infection and characterization of RT activity.

Use of modified nucleotides and uracil-DNA glycosylase (UNG) for the control of contamination in the PCR-based amplification of RNA

The inadvertent carryover of amplified fragments of nucleic acids (amplicons) is a potential source of contamination in the polymerase chain reaction. Recently, a method has been developed to generate amplicons with deoxyuracil triphosphate (dUTP) and to specifically hydrolyze these amplicons with uracil-DNA glycosylase (UNG) following the completion of the assay. We evaluated this system for the specific amplification of RNA from coxsackievirus A3 and B3. We found that RNA from both viruses could be amplified with dUTP, although the use of this triphosphate in place of TTP resulted in some loss of assay sensitivity. We also found that the dUTP-containing amplicons could be efficiently hydrolyzed by UNG, resulting in a 10,000,000-fold reduction in amplicon concentration with little effect on the native nucleic acid. The dUTP-UNG method has a great deal of potential for reducing amplicon contamination during the routine performance of nucleic acid amplification reactions.

The measurement of testosterone and oestradiol-17β using iodinated tracers and incorporating an affinity chromatography extraction procedure

The development of sensitive radioimmunoassays (RIA) for testosterone and oestradiol-17β, utilising 125I-radioligands, is described. Use of an homologous bridge at the same site of attachment, for both the radioligand and the steroid-carrier protein conjugate employed in raising antibodies, normally results in a loss of assay sensitivity and precision. This was overcome in the oestradiol assay by utilising an heterologous configuration at the site of attachment (11α vs 11β). In contrast, for testosterone, even though an homologous bridge and site of attachment was used for the radioligand and the steroid-carrier protein conjugate, a very sensitive assay with extremely high antibody titres (dilution of 1:2 × 10 6) was achieved. This finding was repeated with a different antiserum suggesting that the “bridge binding” phenomenon may be related to the position of attachment to the steroid molecule. In addition, an antibody-Sepharose 4B affinity chromatography extraction procedure has been developed for both oestradiol and testosterone. This approach allows the measurement of very low concentrations of steroids from large volumes of a variety of biological fluids. As antibody-linked Sepharose 4B uses high concentrations of antibody, steroids of similar structure are extracted from biological fluids. However, the cross-reactivity of these related steroids are very low in the RIA's, ensuring good specificity.

2] Fluorescence excitation transfer immunoassay (FETI)

This chapter discusses the different aspects of fluorescence excitation transfer immunoassay (FETI). Immunoassays have become the single most important tool for the determination of analytes in human body fluids. FETI has somewhat more demanding requirements for antibody specificity than heterogeneous immunoassay methods. The fluorescence enhancement produced upon antibody binding to fluorescein-iodothyronine conjugates is caused, by the relief of internal heavy atom-induced, quenching in the conjugate. A significant factor, in applying FETIs, generally, is the need to obtain pure labeled antigen. In order to avoid a large unmodulatable fluorescence background and loss of assay sensitivity, the labeled antigen must generally have greater than about 50% purity. The purity problem is exacerbated, by the apparent loss of fluorescent dyes, from relatively impure conjugates on storage in the solution. Two basic procedures are employed in FETIs. In the endpoint protocol, maximum utilization of the total modulatable signal, and hence maximum sensitivity is obtained. It is found that good correlations have been obtained, using patient serum samples, when FETI data were compared, with heterogeneous fluorescence immunoassay and radioimmunoassay procedures.