Statistical issues in assay development and use.
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Biological Assay↗
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Toward an international standard for PCR-based detection of Escherichia coli O157. Part 1. Assay development and multi-center validation.
As part of a major European research project, a diagnostic PCR assay, including an internal amplification control, was developed and validated in a collaborative trial for the detection of Escherichia coli O157. The assay is based on amplification of sequences of the rfbE O157 gene. The collaborative trial, including 12 international laboratories, was carried out in two phases: phase (a) was performed with identical PCR reagents, including the internal control, provided by the sending laboratory; phase (b) was performed on the same samples and internal control but using in-house PCR reagents of own choice. Phase (a) showed an inclusivity (detection of target strains) of 96.8% and the exclusivity (negative response from nontarget strains) was 100%. The overall performance resulted of phase (a) in an accordance of 98.8, concordance of 98.6, and a concordance odds ratio of 1.11. Phase (b) results showed an accuracy of 100% with all partners and by using different polymerase types and thermocycler models. This indicates that the assay, under consideration as an international standard, was just as reproducible between laboratories, as repeatable within a laboratory. The assay is taken further for validation on carcass-rinse samples.
Animals↗
Therapeutic drug monitoring assay development to improve efficacy and safety.
The development of therapeutic drug management (TDM) utilizing diagnostic assays as biomarker tests is described. TDM can be useful in establishing an individual patient's optimal blood concentration range, and benchmarking blood concentrations at which seizures are controlled, as well as those associated with AED-specific adverse effects. TDM requires the application of pharmacokinetic, pharmacodynamic, pharmacogenomic, pathophysiological and clinical principles to the management of patients in order to achieve safe and effective therapy. Optimal therapy requires rational application of all these principles to personalize patient care.
Anticonvulsants↗
High-throughput gene sequencing assay development for hereditary nonpolyposis colon cancer.
Hereditary nonpolyposis colorectal cancer (HNPCC) is the most common hereditary colon cancer syndrome and is responsible for as many as 10% of all colorectal cancers. Hereditary nonpolyposis colorectal cancer is autosomally dominant with a prevalence of 1 in 200-2000 and exhibits incomplete penetrance. Affected individuals have an approximately 70% lifetime risk of colon cancer with a mean age of onset of 44 years and an approximately 40% lifetime risk of endometrial cancer. At least 5 mismatch repair genes (MLH1, MSH2, MSH6, PMS1, PMS2) have been implicated in HNPCC; however, no predominant mutations were found in these genes. Mutation detection by direct sequencing has proven to be the most sensitive method. We have developed high-throughput full-length sequencing assays of the MLH1, MSH2, and MSH6 genes. These 3 genes account for approximately 90% of all germline mutations found in HNPCC. In our assays, 19 exons of MLH1, 16 exons of MSH2, 10 exons of MSH6, and the adjacent splice sites were amplified using polymerase chain reaction and loaded onto a capillary sequencing machine. Results were analyzed using sequence analysis software and stored in a relational database. Our assay method was validated using 15 affected patients and normal controls. It is anticipated that our high-throughput assay technique will provide accurate diagnoses for patients at risk for HNPCC and thereby facilitate early curative intervention.
Base Pair Mismatch↗
Assay development and screening of a serine/threonine kinase in an on-chip mode using caliper nanofluidics technology.
Kinases are key targets for drug discovery. In the field of screening in general and especially in the kinase area, because of considerations of efficiency and cost, radioactivity-based assays tend to be replaced by alternative, mostly fluorescence-based, assays. Today, the limiting factor is rarely the number of data points that can be obtained but rather the quality of the data, enzyme availability, and cost. In this article, the authors describe the development of an assay for a kinase screen based on the electrophoretic separation of fluorescent product and substrate using a Caliper-based nanofluidics environment in on-chip incubation mode. The authors present the results of screening a focused set of 32,000 compounds together with confirmation data obtained in a filtration assay. In addition, they have made a small-scale comparison between the on-chip and off-chip nanofluidics screening modes. In their hands, the screen in on-chip mode is characterized by high precision most likely due to the absence of liquid pipetting; an excellent confirmation rate (62%) in an independent assay format, namely, filtration; and good sensitivity. This study led to the identification of 4 novel chemical series of inhibitors.
Drug Evaluation, Preclinical↗
A microlarval development assay for the detection of anthelmintic resistance in sheep nematodes.
A microlarval development test for the detection of anthelmintic resistance in nematodes is described. Haemonchus contortus, Teladorsagia circumcincta and Trichostrongylus colubriformis eggs were cultured to third stage larvae in the presence of Earle's balanced salt solution, yeast extract and bacteria in a total volume of 150 microliters. Good dose-response data were obtained with thiabendazole, levamisole, pyrantel tartrate and ivermectin allowing the determination of the 50 per cent lethal concentration and of resistance factors when resistant strains were available. The test was found to be accurate, sensitive, easy to carry out and applicable to the routine detection of resistance.
Animals↗
Monoclonal antibodies for dioxin: antibody characterization and assay development.
A set of 5 anti-dioxin monoclonal antibodies (mAbs), named DD-1, DD-3, DD-4, DD-5 and DD-6, have been isolated. In order to evaluate the ability of these mAbs to recognize various kinds of polychlorinated dibenzodioxins and dibenzofurans, a competition enzyme-linked immunosorbtion assay (ELISA) was developed. All 5 antibodies recognize tetrachloro- and pentachloro-dibenzodioxins and -dibenzofurans. They fail to bind either non-chlorinated, mono-, hexa-, or octa-chlorinated dibenzodioxins, nor do they recognize non-chlorinated, octachloro- or 1,2,3,4,8,9-hexachloro-dibenzofurans. Chlorine substitution on both rings appears necessary for antibody recognition. In the course of our experiments, 3 of the mAbs did not recognize any of the polychlorinated biphenyls (PCBs) tested, while 2 mAbs (DD-1 and DD-6) weakly recognized the 3,3',4,4'-tetrachloro congener. DD-4 and DD-5 are the most specific of the antibodies for the dibenzodioxin and dibenzofuran structure. They do not recognize any of a panel of chlorinated phenols, benzenes, or pesticides. Significantly, these antibodies do not react with PCBs, pentachlorophenol, 2,4-dichlorophenoxyacetic acid, trichlorophenol, or 2,4,5-trichlorophenoxyacetic acid (the latter is weakly recognized by DD-6), any or all of which might be present in large quantities in some dioxin-contaminated samples. Finally, the competition ELISA is able to easily detect 0.5 ng of the most toxic dioxin congener, 2,3,7,8-tetrachlorodibenzo-p-dioxin. It should thus prove useful as an environmental screen for contamination.
Animals↗
EMIT cyclosporine assay: development of an application protocol for Technicon AXON System.
Monitoring parent drug cyclosporine (CsA) concentrations in whole blood has been facilitated by the introduction of automated nonisotopic immunoassays [fluorescence polarization monoclonal whole blood assay (FPIA), EMIT Cyclosporine Assay]. The latter assay currently has a defined application only for Cobas Mira Chemistry Systems. The purpose of our work was to develop an application for this assay on the Technicon AXON. Instrument settings were optimized to arrive at the following assay performance characteristics. Limit of sensitivity was 50 micrograms/L. Interassay coefficients of variation (CV) were 11.2% (n = 16; mean = 81 micrograms/L) and 9.4% (n = 16; mean = 418 micrograms/L). Recoveries of 102, 112, and 117% were obtained by spiking aliquots of 10 whole blood patient pools of known CsA concentrations with 50, 100, and 200 micrograms/L CsA, respectively. Serial dilutions of two patient specimens demonstrated a linear relationship between expected and actual CsA concentrations (r = 0.996, 0.998; regression lines; y = 0.989x + 11.7; y = 0.979x + 9.5). Carryover and interference (lipemia) were not evident. Instrument calibration stability is at least 1 month. Comparison with CsA concentrations analyzed in renal transplant patients by the FPIA assay produced a linear regression equation of EMIT = 1.113x - 44.5, r = 0.968, Sy/x = 20.8, n = 32. Comparison with high-performance liquid chromatography (HPLC)-derived values in the same patient population produced a linear regression equation of EMIT = 1.114x - 16.4, r = 0.970, Sy/x = 20.2. FPIA-derived CsA concentrations averaged 14.2% more than those obtained with the EMIT method with the latter averaging 1.3% more than HPLC values.(ABSTRACT TRUNCATED AT 250 WORDS)
Antibodies, Monoclonal↗
Newly developed assay measuring cytokeratins 8, 18 and 19 in serum is correlated to survival and tumor volume in patients with esophageal carcinoma.
Esophageal carcinoma is the seventh most common cause of cancer-related death in the Western world. In Sweden, approximately 400 new esophageal carcinomas are diagnosed yearly. Cytokeratins (CK) are specific for epithelial cells and the expression profile usually remains unchanged even when the epithelium undergoes malignant transformation. In the present study, MonoTotal, a newly developed RIA-assay detecting circulating CK 8, 18 and 19 fragments, was investigated in sera from patients with esophageal carcinoma. Serum samples from 40 patients with esophageal carcinoma were collected. The median value of circulating CK 8, 18 and 19 measured with MonoTotal was 378 U/L (range 53-6843) and with regard to the defined cut-off (< 75 U/L), 39/40 (98%) patients were shown to have elevated levels of circulating CK 8, 18 and 19. Patients with localized disease had a median value of circulating CK 8, 18 and 19 of 305 U/L (mean: 500 U/L), whereas the corresponding value for metastatic disease was 771 U/L (mean: 1506 U/L). This difference was statistically significant (P = 0.016). Circulating CK 8, 18 and 19, according to cut-off, were not associated with survival in univariate analysis (P = 0.34). However, continuous values of circulating levels of CK 8, 18 and 19 were associated with survival (P = 0.000083) in univariate as well as in the multivariate analysis (P = 0.03). In conclusion, circulating CK 8, 18 and 19 correlates with increased tumor burden and might, in conjunction with other clinical parameters, aid the clinician in estimating the prognosis of the individual patient.
Esophageal Neoplasms↗
SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes.
The SNP500Cancer Database provides sequence and genotype assay information for candidate single nucleotide polymorphisms (SNPs) useful in mapping complex diseases, such as cancer. The database is an integral component of the NCI's Cancer Genome Anatomy Project. SNP500Cancer provides bi-directional sequencing information on a set of control DNA samples derived from anonymized subjects (102 Coriell samples representing four self-described ethnic groups: African/African-American, Caucasian, Hispanic and Pacific Rim). All SNPs are chosen from public databases and reports, and the choice of genes includes a bias towards non-synonymous and promoter SNPs in genes that have been implicated in one or more cancers. The web site is searchable by gene, chromosome, gene ontology pathway and by known dbSNP ID. As of July 2003, the database contains over 3400 SNPs, 2490 of which have been sequenced in the SNP500Cancer population. For each analyzed SNP, gene location and over 200 bp of surrounding annotated sequence (including nearby SNPs) are provided, with frequency information in total and per subpopulation, and calculation of Hardy-Weinberg Equilibrium (HWE) for each subpopulation. Sequence validated SNPs with minor allele frequency > 5% are entered into a high-throughput pipeline for genotyping analysis to determine concordance for the same 102 samples. The website provides the conditions for validated genotyping assays. SNP500Cancer provides an invaluable resource for investigators to select SNPs for analysis, design genotyping assays using validated sequence data, choose selected assays already validated on one or more genotyping platforms, and select reference standards for genotyping assays. The SNP500Cancer Database is freely accessible via the web page at http://snp500cancer.nci.nih.gov/.
Computational Biology↗
In vitro potency assays for nonreplicating veterinary vaccines: comparison to in vivo assays and considerations in assay development.
Each finished batch or serial of veterinary vaccine must be potency tested to assure the quality of marketed product. The potency assay must be correlated to efficacy in the target species. Potency assays of nonreplicating vaccines have traditionally measured the immune response to the vaccine in host or laboratory animals by serology or protection from challenge. Such tests are expensive, time-consuming, and raise animal welfare concerns. As disease agent protective antigens are described, in vitro techniques for quantitating them can be applied to vaccine potency measurement. However, in many cases the immunological adjuvants critical to the efficacy of the biological interfere with in vitro antigen quantitation techniques. The development of techniques that remove or compensate for the effect of adjuvants on the assays, sham vaccines containing no antigen, reference preparations containing a proven protective immunogen dose, characterization of the immunological reactants, and appropriate design and data analysis have contributed to the development of rapid, reproducible, humane, and relatively inexpensive in vitro potency assays to be used in the evaluation of veterinary biologicals.
Animal Testing Alternatives↗
Pyrokinin/PBAN radio-receptor assay: development and application for the characterization of a putative receptor from the pheromone gland of Heliothis peltigera.
A radio-receptor assay (RRA) for the insect pyrokinin/PBAN family has been developed. The development involved examination of the ligand (3H-tyrosyl-PBAN28-33NH2)-receptor interaction under various incubation conditions and variations on sex pheromone gland membrane preparation. Application of the RRA for a partial characterization of the putative pyrokinin/PBAN receptor in the pheromone gland of H. peltigera revealed age-dependence of its expression. Pharmacological characterization revealed a high correlation between the binding-affinity to the receptor of various PBAN-derived peptides and their in vivo pheromonotropic bioactivity, and shed light on the interaction of backbone cyclic and linear ([Arg27,D-Phe30]PBAN28-33NH2) PBAN antagonists with the receptor.
Animals↗
Serotonin (5-hydroxytryptamine) glucuronidation in vitro: assay development, human liver microsome activities and species differences.
1. The main purpose was to develop a high-performance liquid chromatography (HPLC)-based method to assay serotonin glucuronidation activity using liver microsomal fractions. Application of this method was then demonstrated by determining serotonin UDP-glucuronosyltransferase (UGT) enzyme kinetics using human liver microsomes and recombinant human UGT1A6. Interspecies differences were also evaluated using liver microsomes from 10 different mammalian species. 2. Incubation of liver microsomes with serotonin, UDP-glucuronic acid and magnesium resulted in the formation of a single product peak using HPLC with fluorescence and ultraviolet absorbance detection. This peak was confirmed as serotonin glucuronide based on sensitivity to beta-glucuronidase and by obtaining the expected mass of 352 with positive-ion mass spectrometry. 3. Following a preparative HPLC isolation, the structure of this metabolite was established as serotonin-5-O-glucuronide by (1)H-NMR spectroscopy. 4. Enzyme kinetic studies showed apparent K(m) and V(max) of 8.8 +/- 0.3 mM and 43.4 +/- 0.4 nmoles min(-1) mg(-1) protein, respectively, for human liver microsomes, and 5.9 +/- 0.2 mM and 15.8 +/- 0.2 nmoles min(-1) mg(-1), respectively, for recombinant UGT1A6. 5. The order of serotonin-UGT activities in animal liver microsomes was rat > mouse > human > cow > pig > horse > dog > rabbit > monkey > ferret. Cat livers showed no serotonin-UGT activity. Heterozygous and homozygous mutant Gunn rat livers had 40 and 13%, respectively, of the activity of the normal Wistar rat, indicating a significant contribution by a rat UGT1A isoform to serotonin glucuronidation. 6. This assay provides a novel sensitive and specific technique for the measurement of serotonin-UGT activity in vitro.
Adult↗
Comparison of the Ames test and a newly developed assay for detection of mutagenic pollution of marine environments.
A new assay for detection of mutagenic pollution of marine environments, based on the use of a series of genetically modified Vibrio harveyi strains, was developed recently. Here, we compared this assay with a commonly used Ames test, employing mutants of Salmonella enterica serovar Typhimurium. We found that survival of S. enterica serovar Typhimurium in artificial marine water and in different samples of marine water is dramatically reduced relative to that of V. harveyi strains. This indicates that V. harveyi strains are significantly more useful in testing samples of marine water. Moreover, sensitivity of both assays was compared. We found that using the V. harveyi assay it is possible to detect significantly (from a few to several times) lower concentrations of typical chemical mutagens than employing the Ames test. Although the higher sensitivity of the V. harveyi test relative to the Ames assay may be of minor importance when testing mutagenicity of certain chemicals in their pure form under laboratory conditions, this feature is very important in testing samples of marine water. Therefore, we assume that the V. harveyi assay may be an adequate test for detection of mutagenic pollution of marine environments.
Environmental Monitoring↗
SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes.
The SNP500Cancer database provides sequence and genotype assay information for candidate SNPs useful in mapping complex diseases, such as cancer. The database is an integral component of the NCI Cancer Genome Anatomy Project (http://cgap.nci.nih.gov). SNP500Cancer reports sequence analysis of anonymized control DNA samples (n = 102 Coriell samples representing four self-described ethnic groups: African/African-American, Caucasian, Hispanic and Pacific Rim). The website is searchable by gene, chromosome, gene ontology pathway, dbSNP ID and SNP500Cancer SNP ID. As of October 2005, the database contains >13 400 SNPs, 9124 of which have been sequenced in the SNP500Cancer population. For each analysed SNP, gene location and >200 bp of surrounding annotated sequence (including nearby SNPs) are provided, with frequency information in total and per subpopulation as well as calculation of Hardy-Weinberg equilibrium for each subpopulation. The website provides the conditions for validated sequencing and genotyping assays, as well as genotype results for the 102 samples, in both viewable and downloadable formats. A subset of sequence validated SNPs with minor allele frequency >5% are entered into a high-throughput pipeline for genotyping analysis to determine concordance for the same 102 samples. In addition, the results of genotype analysis for select validated SNP assays (defined as 100% concordance between sequence analysis and genotype results) are posted for an additional 280 samples drawn from the Human Diversity Panel (HDP). SNP500Cancer provides an invaluable resource for investigators to select SNPs for analysis, design genotyping assays using validated sequence data, choose selected assays already validated on one or more genotyping platforms, and select reference standards for genotyping assays. The SNP500Cancer database is freely accessible via the web page at http://snp500cancer.nci.nih.gov.
Databases, Genetic↗
Insulin-like growth factor-I in the plasma of two reptiles: assay development and validations.
Radioimmunoassays (RIAs) of insulin-like growth factor-I (IGF-I) in nonmammals are complicated by two problems: decreased specificity due to heterologous assays and assay interference from IGF binding proteins. We have developed and validated an RIA for the detection of IGF-I in reptilian plasma that circumvents these problems. Biochemical validations show parallelism between standard curves, plasma dilutions, and internal standards. Further, biological validations indicate that (1) plasma IGF-I levels are significantly reduced in nonreproductive, female American alligators (Alligator mississippiensis) with high plasma estradiol-17 beta concentrations compared to individuals with low plasma estradiol-17 beta concentrations and (2) plasma IGF-I concentrations are elevated in juvenile Trachemys scripta elegans turtles fed higher quality diets (defined by protein and energy content). These results provide impetus for future studies of IGF-I in reptiles.
Alligators and Crocodiles↗
Simultaneous determination of rosuvastatin and fenofibric acid in human plasma by LC-MS/MS with electrospray ionization: assay development, validation and application to a clinical study.
A simple, sensitive and specific LC-MS/MS method for simultaneous determination of rosuvastatin (RST) and fenofibric acid (FFA) was developed and validated with 500 microL human plasma using carbamazepine as an internal standard (IS). The assay procedure involved a simple one-step liquid/liquid extraction of RST and FFA and IS from plasma into ethyl acetate. The organic layer was separated and evaporated under a gentle stream of nitrogen at 40 degrees C. The residue was reconstituted in the mobile phase and injected onto X-Terra MS C-18 column (4.6 mm x 50 mm, 5.0 microm). Separation of RST, FFA and IS was achieved with a mobile phase consisting of 0.05 M formic acid:acetonitrile (45:55, v/v) at a flow rate of 0.40 ml/min. The API-3000LC-MS/MS was operated under the multiple reaction-monitoring mode (MRM) using the electrospray ionization technique. Positive ion acquisition chromatographic run was used in the present method. Nominal retention times of RST, FFA and IS were 2.35, 4.70 and 2.32 min, respectively. Absolute recovery of RST, FFA and IS was 74, 61 and 69%, respectively. The lower limit of quantification (LLOQ) of RST and FFA was 1.00 ng/ml and 0.50 microg/ml, respectively. Response function was established for the range of concentrations 1.00-50.0 ng/ml and 0.50-20.0 microg/ml for RST and FFA, respectively, with a coefficient of determination (r2) of 0.999 for both the compounds. The inter- and intra-day precision in the measurement of RST quality control (QC) samples 5, 15, 400 and 800 ng/ml, were in the range 8.93-9.37% relative standard deviation (R.S.D.) and 1.74-16.1% R.S.D., respectively. Similarly, the inter- and intra-day precision in the measurement of FFA quality control (QC) samples 0.5, 1.5, 8.0 and 15.0 microg/ml, were in the range 9.78-11.6% relative standard deviation (R.S.D.) and 0.22-17.4% R.S.D., respectively. Accuracy in the measurement of QC samples for RST and FFA were in the range 88.1-108 and 87-115%, respectively, of the nominal values. RST and FFA were stable in the battery of stability studies, viz., bench-top, auto-sampler and freeze/thaw cycles. Stability of RST and FFA was established for 1 month at -80 degrees C. The application of the assay to a clinical study confirmed the utility of the assay.
Acetates↗
Enzyme-linked immunosorbent assay development for the beta-adrenergic agonist zilpaterol.
Zilpaterol is an beta-adrenergic agonist approved for use in cattle in South Africa and Mexico as a growth promoter. It is not currently approved for use in the EU, USA, or Asia. Here, we report the development of an ELISA for zilpaterol. Zilpaterol was reacted with ethyl 4-bromobutyrate followed by refluxing in 0.1 M potassium hydroxide. The resulting hapten was reacted with two carrier proteins, bovine serum albumin (BSA) or keyhole limpet hemocyanin (KLH), using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) as an activating agent. Immunization of goats with the zilpaterol-butyrate-KLH resulted in an antibody useful for an ELISA. We utilized zilpaterol-butyrate-BSA as a coating antigen for ELISA development. The average IC(50) derived from the developed zilpaterol immunoassay was 3.94 +/- 0.48 ng/mL (n = 25). The antibody did not cross react with N-alkyl [bamethane, clenbuterol, (-)-isoproterenol, (+)-isoproterenol, metaproterenol, or salbutamol] or N-arylalkyl (dobutamine, fenoterol, isoxsuprine, ractopamine, or salmeterol) beta-agonists. The assay was tolerant of up to 10% (v/v) of acetone, ethanol, or methanol, and 15% (v/v) of acetonitrile or DMSO. Salt concentrations ranging from 0.05 to 1.0 M minimally affected B(0) or IC(50) values. When buffer pH was <7 or >8.8, the IC(50) values increased in comparison to those measured at pH 7.4. In conclusion, a sensitive, specific zilpaterol ELISA has been developed that can serve as a rapid screening assay.
Adrenergic beta-Agonists↗