Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates. The multidimensional MA (multi-MA) and MA-loess both consider all samples of a microtiter plate per suspension bead array assay and thus do not require any external reference samples. We demonstrate the performance of the two MA normalization methods with data obtained from the analysis of 384 samples including both serum and plasma. Samples were randomized across 96-well sample plates, processed, and analyzed in assay plates, respectively. Using principal component analysis (PCA), we could show that plate-wise clusters found in the first two components were eliminated by multi-MA normalization as compared with other normalization methods. Furthermore, we studied the correlation profiles between random pairs of antibodies and found that both MA normalization methods substantially reduced the inflated correlation introduced by plate effects. Normalization approaches using multi-MA and MA-loess minimized batch effects arising from the analysis of several assay plates with antibody suspension bead arrays. In a simulated biomarker study, multi-MA restored associations lost due to plate effects. Our normalization approaches, which are available as R package MDimNormn, could also be useful in studies using other types of high-throughput assay data.

Configurational Statistics of Magnetic Bead Detection with Magnetoresistive Sensors.

Magnetic biosensors detect magnetic beads that, mediated by a target, have bound to a functionalized area. This area is often larger than the area of the sensor. Both the sign and magnitude of the average magnetic field experienced by the sensor from a magnetic bead depends on the location of the bead relative to the sensor. Consequently, the signal from multiple beads also depends on their locations. Thus, a given coverage of the functionalized area with magnetic beads does not result in a given detector response, except on the average, over many realizations of the same coverage. We present a systematic theoretical analysis of how this location-dependence affects the sensor response. The analysis is done for beads magnetized by a homogeneous in-plane magnetic field. We determine the expected value and standard deviation of the sensor response for a given coverage, as well as the accuracy and precision with which the coverage can be determined from a single sensor measurement. We show that statistical fluctuations between samples may reduce the sensitivity and dynamic range of a sensor significantly when the functionalized area is larger than the sensor area. Hence, the statistics of sampling is essential to sensor design. For illustration, we analyze three important published cases for which statistical fluctuations are dominant, significant, and insignificant, respectively.

Measurement of aberrant glycosylation of prostate specific antigen can improve specificity in early detection of prostate cancer.

INTRODUCTION: We previously identified prostate cancer (PCa)-associated aberrant glycosylation of PSA, where α2,3-linked sialylation is an additional terminal N-glycan on free PSA (S2,3PSA). We then developed a new assay system measuring S2,3PSA using a magnetic microbead-based immunoassay. We compared the diagnostic accuracy of conventional PSA and percent-free PSA (%fPSA) tests. METHODS: We used MagPlex beads to measure serum S2,3PSA levels using anti-human fPSA monoclonal antibody (8A6) for capture and anti-α2,3-linked sialic acid monoclonal antibody (HYB4) for detection. We determined the cutoff values in a training test and measured serum S2,3PSA levels in 314 patients who underwent biopsy, including 138 PCa and 176 non-PCa patients with PSA of <10.0 ng/ml. Serum S2,3PSA levels were presented as mean fluorescence intensity (MFI). Receiver operating characteristic curves were used to evaluate the diagnostic accuracy of total PSA, %fPSA, and S2,3PSA. RESULTS: We determined an MFI cutoff value of 1130 with a sensitivity of 95.0% and specificity of 72.0% for the diagnosis of PCa in the training test. In the validation study, the area under the curve for the detection of PCa with S2,3PSA was 0.84, which was significantly higher than that with PSA or %fPSA. CONCLUSIONS: Although the present study is small and preliminary, these results suggest that the measurement of serum S2,3PSA using a magnetic microbead-based immunoassay may improve the accuracy of early detection of PCa and reduce unnecessary prostate biopsy.

The C(RgdyK)-conjugated Fe3O4 nanoparticles with high drug load for dual-targeting integrin alpha(v)beta3-expressing cancer cells.

A novel drug delivery system c(RGDyK)-modified Fe3O4 nanoparticles with high DOX load (R-DMP), which combines magnetic targeting, integrin alpha(v)beta3 targeting and high drug loading properties, was developed by chemical coupling both doxorubicin and peptide c(RGDyK) on the synthetic dual function magnetic nanoparticles (DMP) using a multi-hand cross-linker poly-L-glutamic acid. R-DMP has high drug loading ratio and trapping efficiency for magnetic targeting, and the drug loading ratio can be controlled by adjusting the reactant ratio. Moreover, R-DMP presents narrow size distribution and is sensitive to pH for drug releasing. Compare with those of doxorubicin coupled DMP without peptide c(RGDyK) modification, D-DMP shows enhanced uptake by integrin alpha(v)beta3 targeting expressing tumor cells and displays stronger cancer cell cytotoxicity. This investigate provides a new approach for the dual-targeted delivery of therapeutic agents to tumors with controlled low carrier toxicity and high efficiency.

Rapid and sensitive detection of cancer cells by coupling with quantum dots and immunomagnetic separation at low concentrations.

This work presents a rapid and sensitive method for detecting cancer cells at low concentration. In this method, two biomarkers of T-help cancer cells are detected simultaneously. One biomarker is conjugated with magnetic beads to separate T-help cell from the mixed cells and the other biomarker, associated with quantum dots, is used to detect fluorescence. The specific T-help cells can be quantified using the relationship between the QD fluorescence intensity and the cell frequency following magnetic separation. The intensity of fluorescence increases linearly with the frequency of T-help cells from 10(-7) to 10(-3), and neither B cells nor red blood cells interfere with the detection of T-help cells. Moreover, the total detection time is under 15 min, even though the frequency of specific T-help cells is as low as 5×10(-7). The numerous advantages of detecting specific cells at low concentration using the presented method include ease of preparation, low cost, fast detection, and high sensitivity.

Circulating tumor cells in HER-2 positive metastatic breast cancer patients treated with trastuzumab and chemotherapy.

The detection of circulating tumor cells (CTCs) in peripheral blood may have important prognostic and predictive implications in breast cancer treatment. A limitation in this field has been the lack of a validated method of accurately measuring CTCs. While sensitivity has improved using RT-PCR, specificity remains a major challenge. The goal of this paper is to present a sensitive and specific methodology of detecting CTCs in women with HER-2 positive metastatic breast cancer, and to examine its role as a marker that tracks disease response during treatment with trastuzumab-containing regimens. The study included patients with HER-2-positive metastatic breast cancer enrolled on two different clinical protocols using a trastuzumab-containing regimen. Serial CTCs were measured at planned time points and clinical correlations were made. Immunomagnetic selection of circulating epithelial cells was used to address the specificity of tumor cell detection using cytokeratin 19 (CK19). In addition, the extracellular domain of the HER-2 protein (HER-2/ECD) was measured to determine if CTCs detected by CK19 accurately reflect tumor burden. The presence of CTCs at first restaging was associated with disease progression. We observed an association between CK19 and HER-2/ECD. The association of HER-2/ECD with clinical response followed a similar pattern to that seen with CK19. Finally, the absence of HER-2/ECD at best overall response and a change of HER-2/ECD from positive at baseline to negative at best overall response was associated with favorable treatment response. Our study supports the prognostic and predictive role of the detection of CTCs in treatment of HER-2-positive metastatic breast cancer patients. The association between CK19 and markers of disease burden is in line with the concept that CTCs may be a reliable measure of tumor cells in the peripheral blood of patients with metastatic breast cancer. The association of CTCs at first restaging with treatment failure indicates that CTCs may have a role as surrogate markers to monitor treatment response.

Sensitivity of Escherichia coli O157 detection in bovine feces assessed by broth enrichment followed by immunomagnetic separation and direct plating methodologies.

In order to more precisely predict food safety risks, the fecal presence of food-borne pathogens among animals at slaughter must be correctly determined. Quantification of Escherichia coli O157 is also desirable. In two separate experiments, detection and enumeration of a nalidixic acid-resistant strain of E. coli O157 in bovine feces was assessed by culture on MacConkey agar supplemented with nalidixic acid (MACnal) and compared to overnight broth enrichment followed by immunomagnetic separation (IMS) and to direct plating of dilutions of bovine feces onto sorbitol MacConkey agar containing cefixime and tellurite (SMACct). The sensitivity of detection of E. coli O157 by both direct plating and IMS was highly dependent upon the initial concentration of the target organism in the sample. Sensitivity of detection by IMS was poor below 100 CFU/g but was better, and not affected by initial E. coli O157 numbers, above this concentration. Sensitivity of detection of E. coli O157 in bovine feces at low initial concentrations is very poor for both direct plating and IMS. Direct plating of dilutions of bovine feces on SMACct can be used to determine the magnitude of fecal E. coli excretion among cattle excreting greater than 100 CFU/g. Among positive samples identified by direct plating on SMACct, the direct counts of E. coli O157:H7 were highly correlated with the estimates obtained with the MACnal plates (r = 0.88, P < 0.001). Because the majority of cattle excrete less than 10(2) CFU E. coli O157/g feces, most studies, including those using IMS methods, probably grossly underestimate the prevalence of E. coli O157 in cattle.

Distribution of Escherichia coli O157 in bovine fecal pats and its impact on estimates of the prevalence of fecal shedding.

The distribution of Escherichia coli O157 in bovine feces was examined by testing multiple samples from fecal pats and determining the density of E. coli O157 in immunomagnetic separation (IMS)-positive fecal samples. The density of E. coli O157 in bovine feces was highly variable, differing by as much as 76,800 CFU g(-1) between samples from the same fecal pat. The density in most positive samples was <100 CFU g(-1), the limit of reliable detection by IMS. Testing only one 1-g sample of feces per pat with IMS may result in a sensitivity of detection as low as 20 to 50%. It is therefore probable that most surveys have greatly underestimated the prevalence of E. coli O157 shedding in cattle and the proportion of farms with shedding cattle. The sensitivity of the detection of E. coli O157 in bovine feces can be as much as doubled by testing two 1-g samples per pat rather than one 1-g sample.

Evaluation of an automated immunomagnetic separation method for the rapid detection of Salmonella species in poultry environmental samples.

Automated immunomagnetic separation (AIMS), using Dynabeads anti-Salmonella (Dynal, Oslo), was evaluated for its ability to detect Salmonella spp. in poultry environmental samples in comparison with standard, culture-based method (Health Canada, Health Protection Branch, MFHPB-20). AIMS was found to be more reliable in detecting Salmonella from artificially inoculated enrichment broths at low levels and exhibited a 15.5% higher sensitivity value than the culture method.

Magnetophoretic mobilities correlate to antibody binding capacities.

METHODS: A methodology and a mathematical theory have been developed, which allow quantitation of the expression levels of cellular surface antigens using immunomagnetic labels and cell tracking velocimetry (CTV) technology. RESULTS: Quantum Simply Cellular (QSC) microbeads were immunomagnetically labeled with anti-CD2 fluorescein isothiocyanate (FITC) antibodies and anti-FITC MACS paramagnetic nanoparticles. Magnetophoretic mobility has been defined as the magnetically induced velocity of the labeled cell or microbead divided by the magnetophoretic driving force, proportional to the magnetic energy density gradient. DISCUSSION: Using computer imaging and processing technology, the mobility measurements were accomplished by microscopically recording and calculating the velocity of immunomagnetically labeled QSC microbeads in a nearly constant magnetic energy gradient. A calibration curve correlating the measured magnetophoretic mobility of the immunomagnetically labeled microbeads to their antibody binding capacities (ABC) has been obtained. CONCLUSION: The results, in agreement with theory, indicate a linear relationship between magnetophoretic mobility and ABC for microbeads with less than 30,000 ABC. The mathematical relationships and QSC standardization curve obtained allow determination of the number of surface antigens on similarly immunomagnetically labeled cells.

Comparison of T cell depletion strategies from bone marrow, umbilical cord and peripheral blood using five separation systems.

The development of bone marrow transplantation in mismatched or matched unrelated donor situations, the recent use of peripheral blood stem cells for allogeneic transplants, the standardization and respect of good methodology practices highlight the need to evaluate new safe methods of T cell depletion (TCD). We have performed 79 in vitro TCD using five techniques: rabbit complement cytotoxicity, CD2-CD7 immunomagnetic depletion, CD5-CD8 panning system, CD34 positive purging and counterflow centrifugation elutriation (CCE). We analyzed these different approaches with regard to the degree of T and B depletion, recovery of progenitors and NK cells. In our hands, the 5 systems evaluated showed a TCD of between 1.3 and 3 log. The CCE, immunomagnetic, complement and panning methods all give similar a TCD of around 2 log. In contrast, we obtained a TCD of approximately 3 log with CD34 positive purging. The progenitor yield was around 50% regardless of the technique used. However, the degree of B and NK cell depletion was dependent on the method: specific TCD resulted in low BCD (under 0.5 log), whereas CCE or CD34 positive purging gave a BCD of greater than 1 log. Moreover, CD34 positive selection resulted in a virtually complete elimination of NK cells. CCE was the only technique allowing isolation of the small lymphocyte population which can be useful for adoptive therapy. To obtain TCD over three logarithms, double purging techniques are necessary. Because specific roles of T cells subsets in engraftment, graft versus host disease, Epstein Barr virus associated B cell lymphoproliferative disorders and disease relapse have not yet been completely elucidated, new techniques such as CD34 positive purging and double purging methods (positive and negative purging) need to be clinically evaluated, especially with respect to peripheral blood stem cells.

Analytical evaluation of the CK-MB mass assay on the Technicon Immuno 1 system.

OBJECTIVES: To evaluate the performance of the Technicon Immuno 1 CK-MB mass assay. DESIGN AND METHODS: The precision was measured using the BioRad Liquichek CK-MB controls and the Technicon Immuno 1 SETpoint CK-MB calibrators. The linearity was verified by diluting 9 patient serum samples containing high CK-MB concentrations, and the minimum detectable concentration determined by repetitive analysis of the zero calibrator. The assay was compared with the Johnson & Johnson Vitros CK-MB activity assay using 111 patient serum samples. The reference range was determined using serum samples from 100 healthy adult volunteers. RESULTS: The assay shows within-run CVs varying from 1.5 to 7.5% and between-day CVs from 1.5 to 4.8% for CK-MB concentrations ranging from 3.9 to 99.0 micrograms/L. The linearity study gave correlation coefficients greater than 0.9961. There was a very good correlation between mass and activity assays (r = 0.985). The reference values were estimated at 0.0-4.2 micrograms/L and the minimum detectable concentration at 0.5 micrograms/L. CONCLUSIONS: The evaluation shows that the Technicon Immuno 1 CK-MB mass assay has the analytical characteristics suitable for its inclusion in the modern clinical repertoire.