Standardizing global gene expression analysis between laboratories and across platforms

To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12 microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories increased markedly when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Reproducibility was highest when analysis was based on biological themes defined by enriched Gene Ontology (GO) categories. These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used.     

Inter Subject Variability and Reproducibility of Diffusion Tensor Imaging within and between Different Imaging Sessions

The aim of these studies was to provide reference data on intersubject variability and reproducibility of diffusion tensor imaging. Healthy volunteers underwent imaging on two occasions using the same 3T Siemens Verio magnetic resonance scanner. At each session two identical diffusion tensor sequences were obtained along with standard structural imaging. Fractional anisotropy, apparent diffusion coefficient, axial and radial diffusivity maps were created and regions of interest applied in normalised space. The baseline data from all 26 volunteers were used to calculate the intersubject variability, while within session and between session reproducibility were calculated from all the available data. The reproducibility of measurements were used to calculate the overall and within session 95% prediction interval for zero change. The within and between session reproducibility data were lower than the values for intersubject variability, and were different across the brain. The regional mean (range) coefficient of variation figures for within session reproducibility were 2.1 (0.9–5.5%), 1.2 (0.4–3.9%), 1.2 (0.4–3.8%) and 1.8 (0.4–4.3%) for fractional anisotropy, apparent diffusion coefficient, axial and radial diffusivity, and were lower than between session reproducibility measurements (2.4 (1.1–5.9%), 1.9 (0.7–5.7%), 1.7 (0.7–4.7%) and 2.4 (0.9–5.8%); p<0.001). The calculated overall and within session 95% prediction intervals for zero change were similar. This study provides additional reference data concerning intersubject variability and reproducibility of diffusion tensor imaging conducted within the same imaging session and different imaging sessions. These data can be utilised in interventional studies to quantify change within a single imaging session, or to assess the significance of change in longitudinal studies of brain injury and disease.     

Comparison of Inter Subject Variability and Reproducibility of Whole Brain Proton Spectroscopy

The aim of these studies was to provide reference data on intersubject variability and reproducibility of metabolite ratios for Choline/Creatine (Cho/Cr), N-acetyl aspartate/Choline (NAA/Cho) and N-acetyl aspartate/Creatine (NAA/Cr), and individual signal-intensity normalised metabolite concentrations of NAA, Cho and Cr. Healthy volunteers underwent imaging on two occasions using the same 3T Siemens Verio magnetic resonance scanner. At each session two identical Metabolic Imaging and Data Acquisition Software (MIDAS) sequences were obtained along with standard structural imaging. Metabolite maps were created and regions of interest applied in normalised space. The baseline data from all 32 volunteers were used to calculate the intersubject variability, while within session and between session reproducibility were calculated from all the available data. The reproducibility of measurements were used to calculate the overall and within session 95% prediction interval for zero change. The within and between session reproducibility data were lower than the values for intersubject variability, and were variable across the different brain regions. The within and between session reproducibility measurements were similar for Cho/Cr, NAA/Choline, Cho and Cr (11.8%, 11.4%, 14.3 and 10.6% vs. 11.9%, 11.4%, 13.5% and 10.5% respectively), but for NAA/Creatine and NAA between session reproducibility was lower (9.3% and 9.1% vs. 10.1% and 9.9%; p <0.05). This study provides additional reference data that can be utilised in interventional studies to quantify change within a single imaging session, or to assess the significance of change in longitudinal studies of brain injury and disease.     

The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses*

Questions concerning longitudinal data quality and reproducibility of proteomic laboratories spurred the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility of proteomic laboratories over an extended period of time. Developed as an open study, initially 64 participants were recruited from the broader mass spectrometry community to analyze provided aliquots of a six bovine protein tryptic digest mixture every month for a period of nine months. Data were uploaded to a central repository, and the operators answered an accompanying survey. Ultimately, 45 laboratories submitted a minimum of eight LC-MSMS raw data files collected in data-dependent acquisition (DDA) mode. No standard operating procedures were enforced; rather the participants were encouraged to analyze the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration, but rather to assess the temporal intralaboratory reproducibility. The outcome of the study was reassuring with 80% of the participating laboratories performing analyses at a medium to high level of reproducibility and quality over the 9-month period. For the groups that had one or more outlying experiments, the major contributing factor that correlated to the survey data was the performance of preventative maintenance prior to the LC-MSMS analyses. Thus, the Protein Research Group of the Association of Biomolecular Resource Facilities recommends that laboratories closely scrutinize the quality control data following such events. Additionally, improved quality control recording is imperative. This longitudinal study provides evidence that mass spectrometry-based proteomics is reproducible. When quality control measures are strictly adhered to, such reproducibility is comparable among many disparate groups. Data from the study are available via ProteomeXchange under the accession code PXD002114.The broad-reaching use and application of mass spectrometry-based proteomics in the international research community continues to exponentially grow and expand. As the technology has developed and practitioners have become skilled in performing complex workflows, the community has not only gained interest in assessing data across laboratories but also in maintaining consistent quality control within a laboratory. Koecher et al. raised the issue of quality control measures and how this aspect of mass spectrometry-based proteomics is generally neglected in scientific publications (1). Fortunately, studies characterizing the stability of liquid chromatography-tandem MS (LC-MSMS)¹ quality control performance among numerous laboratories are emerging. The relationship between sample preparation schemes, data acquisition and reduction strategies, and bioinformatic analyses have been comprehensively reviewed by Tabb (2).Several studies exist where intra- and interlaboratory reproducibility between multiple sites has been assessed under different settings. Perhaps the most systematic and detailed of these investigations are from the Human Proteome Organization (HuPO) test sample working group (3); the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (NCI CPTAC) (4); and the ProteoRed Consortium (5, 6). The HuPO group utilized an equimolar mixture of 20 highly purified recombinant human proteins (5 pmol per protein) distributed to 27 different laboratories and analyzed without constraint according to optimized LCMS and database search protocols from each of the laboratories (3). The study was not an assessment of instrument performance for highly sensitive detection of proteins, as all participating laboratories had acquired raw data of sufficient quality to identify all 20 proteins (and a specific subset of tryptic peptides). The study revealed, however, that discrepancies in peptide identification and protein assignment were the result of differences in data analysis strategies rather than data collection.The NCI CPTAC group used a standardized Saccharomyces cerevisiae proteome digest that was analyzed on ion-trap-based LCMS platforms in five independent laboratories according to both an established standard operating procedure (SOP) and with no SOP constraint (4). All data analysis was centralized, and thus, any observed variations were entirely because of the LCMS platform. By applying the performance metrics developed by Rudnick et al. (7), several key points emerged: (1) as expected, intralaboratory variation was less than interlaboratory variation; and (2) overall, the interlaboratory variation in peptide identifications and some of the other performance metrics were comparable between instruments, although there were large differences in the average values for some metrics (e.g. MS1 signal intensity, dynamic sampling).The ProteoRed Consortium initiated the ProteoRed Multicenter Experiment for Quality Control (PMEQC) (5, 6). This longitudinal QC multicenter study involved 12 institutes, and was designed to assess: (1) intralaboratory repeatability of LC-MSMS proteomic data; (2) interlaboratory reproducibility; and (3) reproducibility across multiple instrument platforms. Participants received samples of undigested or tryptically digested yeast proteins and were requested to follow strict analytical guidelines. Data analysis was centralized and performed under standard procedures using a common workflow. The study revealed that the overall performance with respect to metrics such as reproducibility, sensitivity, dynamic range etc. was directly related to the degree of operator expertise, and less dependent on instrumentation.Several studies not specifically focused on quality control have also yielded insight into proteomic reproducibility. The HuPO plasma proteome project (HuPO PPP) distributed 20 human samples (five serum plus 3 × 5 plasma samples treated with three different anticoagulants) to 35 laboratories spanning 13 countries (8). The purpose of this large-scale study was not to assess reproducibility per se, but rather to generate the largest and most comprehensive data set on the protein composition of human plasma/serum. On a smaller scale, the ISB standard 18 protein mixture (purified proteins from cow, horse, rabbit, chicken, E. coli, and B. licheniformus) was also assessed between laboratories on eight different LCMS platforms (9). These data reside in a comprehensive, multiplatform database as a resource for the proteomic community. Additional interlaboratory assessments have consisted of multiple reaction monitoring-based measurements of peptides/proteins in plasma (10, 11) and protein–protein interactions at both the biochemical and proteomic level (12).For team leaders/directors of proteomic laboratories and any researcher collaborating with such groups, major questions that may arise concerning data consistency are: how well are quality controls being implemented in the daily operations? Do the quality control measures effectively support data reproducibility? To address this, the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) designed a study whereby LC-MSMS data obtained from the analysis of a commercially available bovine protein mixture predigested with trypsin were collected at routine intervals over a period of 9 months. Raw MS data files from a total of 64 participating laboratories were accumulated, and HPLC and MS performance were evaluated through QC metrics (13). The main impetus of the study was to recognize key sources of variability in HPLC and MS analyses under extended and routine operating conditions for each laboratory and to catalog the state of quality control in a diverse set of proteomic laboratories.No standard operating protocol was imposed on the participants; instead, contributors were encouraged to employ the methods that were typically applied in individual laboratories. Optimization of instrument methods on the provided sample was discouraged. A survey was conducted with each sample submission to catalog individual laboratory practices, instrument configurations, acquisition settings, including routine and nonroutine maintenance procedures. Unlike previous investigations where emphasis was placed on the preparation, distribution, and evaluation of protein standards to appraise and/or standardize LCMS platforms between laboratories, the key interest in this study was purely to determine the intralaboratory performance, reproducibility, and consistency of participating laboratories over an extended period of time.The rapidly expanding number of proteomic laboratories have incorporated divergent HPLC systems, mass spectrometers, solvent systems, columns etc. As a result, analyzing data from a large number of laboratories necessitates tools that can accommodate data from a broad range of platforms. For example, to expect a small laboratory with a decade-old three-dimensional ion trap mass spectrometer to achieve the same sensitivity as a laboratory with a high-resolution hybrid instrument would be unfair. Correspondingly, the data analysis needs to include axes beyond simple peptide-level sensitivity. Nevertheless, the laboratory with the older instrumentation may be consistently better at maximizing performance from the chosen instrument platform compared with a laboratory with the latest high-end equipment.The focus of this study was to estimate the degree of variability in intralaboratory performance over a 9-month period. This goal was achieved using quality metrics that are applicable to most LC-MSMS workflows. The inclusion of data from many laboratories will enable the proteomic community to determine the current state of quality control within a typical laboratory. The survey data enabled the mapping of some alterations in instrument performance to documented laboratory events, e.g. mass spectrometer calibration. The study was designed neither to compare one laboratory with another, nor to discriminate between classes of instrumentation.Questions of data quality and performance in the proteomic community are appropriately aligned with the heightened awareness of a perceived lack of reproducibility of scientific findings in general (1). This community has endeavored to provide tools to assess proteomic data quality, and this study provides additional insight into the application of such tools and the quality of data within respective laboratories.     

Visualization of anomalous origin and course of coronary arteries in 748 consecutive symptomatic patients by 64-slice computed tomography angiography

Background

While the order for a clinical transthoracic examination is fairly standardized, there is considerable variability between laboratories and even among physicians in the same laboratory with regard to the order for transesophageal echocardiograms (TEE). A systematic approach is desirable for more efficient use of physician and patient time, avoidance of inadvertent omission of important views, and to facilitate study review.

Methods

We propose a standardized approach to TEE data acquisition in which cardiac structures are systematically identified and characterized at sequential positions and imaging planes to facilitate organized, efficient and comprehensive assessment.

Results

Our approach to TEE study begins in the mid-esophagus with the imaging plane at 0°. Based on the specific indication for the TEE, a cardiac structure (e.g., mitral valve, left atrial appendage, or interatrial septum) is chosen as the primary focal point for a comprehensive, multiplane analysis. This structure is assessed in 20° – 30° increments as the imaging plane is advanced from 0° to 165°. Using the aortic valve as a reference point, pertinent cardiac structures are then assessed as the imaging plane is reduced to 135°, to 90°, to 40 – 60° and then back to 0°. The probe is then advanced into the stomach to obtain transgastric images at 0°, 90°, and 120°. Finally, the thoracic aorta and pulmonary artery are assessed as the probe is withdrawn from the body. Using this method, an organized and comprehensive TEE can be performed in 10 – 15 minutes.

Conclusion

A standardized and systematic TEE approach is described for efficient and comprehensive TEE study.     

Enumeration of CD4(+) T-cells in the peripheral blood of HIV-infected patients: an interlaboratory study of the FACSCount system.

The aim of the present study was to assess the interlaboratory reproducibility of the FACSCount system for the enumeration of peripheral blood (PB) CD4(+) T-cells. In each of the seven participating centers, both previously stained and unstained PB samples (n = 49) were received and either analyzed or stained and then analyzed. Interlaboratory reproducibility was checked in two different groups of centers (n = 3 and n = 4) where the study was performed in parallel. In addition, both the intralaboratory precision and accuracy of this system were analyzed in comparison with results obtained with conventional flow cytometry. Accordingly, upon comparing both methods, a high degree of correlation was observed in the total number of CD3(+) T-cells (coefficient of correlation of 0.9750 +/- 0.0184, slope of the best linear fit: 0. 9214 +/- 0.0311, y-intercept of 12 +/- 47) as well as in the number of CD3(+)/CD4(+) (coefficient of correlation of 0.9794 +/- 0.1457, slope of the best linear fit: 0.9463 +/- 0.0753, y-intercept of -11 +/- 36) and CD3(+)/CD8(+) (coefficient of correlation of 0.9728 +/- 0.0192, slope of the best linear fit: 0.9682 +/- 0.0735, y-intercept of 7 +/- 95) major subsets. In addition, low coefficients of variation (CV) were obtained for replicates, indicating the method's high degree of accuracy. The present study shows that with respect to the interlaboratory reproducibility reported for most techniques used for the enumeration of PB CD4(+) T-cells, the FACSCount system results in data with much lower coefficients of variance (CVs) (mean CV of less than 10%). Upon measuring the impact on results of different variables associated with either sample preparation or data acquisition and analysis, our study clearly shows that data acquisition and analysis does not influence the results by increasing variability since the coefficients of variation obtained for samples prepared in the same laboratory under the same conditions and read in different laboratories with different instruments were identical to those obtained for the replicates of the same samples read in each individual center. In contrast, interlaboratory variability, although low, significantly increased when sample preparation was carried out in different laboratories, suggesting that pipetting still represents the major source of variability in the FACSCount system.     

Development and Validation of an Internationally-Standardized,High-Resolution Capillary Gel-Based Electrophoresis PCR-Ribotyping Protocol for Clostridium difficile

PCR-ribotyping has been adopted in many laboratories as the method of choice for C. difficile typing and surveillance. However, issues with the conventional agarose gel-based technique, including inter-laboratory variation and interpretation of banding patterns have impeded progress. The method has recently been adapted to incorporate high-resolution capillary gel-based electrophoresis (CE-ribotyping), so improving discrimination, accuracy and reproducibility. However, reports to date have all represented single-centre studies and inter-laboratory variability has not been formally measured or assessed. Here, we achieved in a multi-centre setting a high level of reproducibility, accuracy and portability associated with a consensus CE-ribotyping protocol. Local databases were built at four participating laboratories using a distributed set of 70 known PCR-ribotypes. A panel of 50 isolates and 60 electronic profiles (blinded and randomized) were distributed to each testing centre for PCR-ribotype identification based on local databases generated using the standard set of 70 PCR-ribotypes, and the performance of the consensus protocol assessed. A maximum standard deviation of only ±3.8bp was recorded in individual fragment sizes, and PCR-ribotypes from 98.2% of anonymised strains were successfully discriminated across four ribotyping centres spanning Europe and North America (98.8% after analysing discrepancies). Consensus CE-ribotyping increases comparability of typing data between centres and thereby facilitates the rapid and accurate transfer of standardized typing data to support future national and international C. difficile surveillance programs.     

Quality assessment of human mitochondrial DNA quantification: MITONAUTS, an international multicentre survey

Mitochondrial DNA quantification by qPCR is used in the context of many diseases and toxicity studies but comparison of results between laboratories is challenging. Through two multigroup distributions of DNA samples from human cell lines, the MITONAUTS group anonymously compared mtDNA/nDNA quantification across nine laboratories involved in HIV research worldwide. Eight of the nine sites showed significant correlation between them (mean raw data R(2)=0.664; log(10)-transformed data R(2)=0.844). Although mtDNA/nDNA values were well correlated between sites, the inter-site variability on the absolute measurements remained high with a mean (range) coefficient of variation of 71 (37-212) %. Some variability appeared cell line-specific, probably due to chromosomal alterations or pseudogenes affecting the quantification of certain genes, while within cell line variability was likely due to differences in calibration of the standard curves. The use of two mtDNA and two single copy nDNA genes with highly specific primers to quantify each genome would help address copy number variants. Our results indicate that sample shipment must be done frozen and that absolute mtDNA/nDNA ratio values cannot readily be compared between laboratories, especially if assessing cultured cell mtDNA content. However, within laboratory and relative mtDNA/nDNA comparisons between laboratories should be reliable.     

Harmonization guidelines for HLA-peptide multimer assays derived from results of a large scale international proficiency panel of the Cancer Vaccine Consortium

Purpose  The Cancer Vaccine Consortium of the Cancer Research Institute (CVC-CRI) conducted a multicenter HLA-peptide multimer proficiency panel (MPP) with a group of 27 laboratories to assess the performance of the assay. Experimental design  Participants used commercially available HLA-peptide multimers and a well characterized common source of peripheral blood mononuclear cells (PBMC). The frequency of CD8+ T cells specific for two HLA-A2-restricted model antigens was measured by flow cytometry. The panel design allowed for participants to use their preferred staining reagents and locally established protocols for both cell labeling, data acquisition and analysis. Results  We observed significant differences in both the performance characteristics of the assay and the reported frequencies of specific T cells across laboratories. These results emphasize the need to identify the critical variables important for the observed variability to allow for harmonization of the technique across institutions. Conclusions  Three key recommendations emerged that would likely reduce assay variability and thus move toward harmonizing of this assay. (1) Use of more than two colors for the staining (2) collect at least 100,000 CD8 T cells, and (3) use of a background control sample to appropriately set the analytical gates. We also provide more insight into the limitations of the assay and identified additional protocol steps that potentially impact the quality of data generated and therefore should serve as primary targets for systematic analysis in future panels. Finally, we propose initial guidelines for harmonizing assay performance which include the introduction of standard operating protocols to allow for adequate training of technical staff and auditing of test analysis procedures. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Overview, conclusions, and recommendations of the IPCS collaborative study on complex mixtures.

The International Programme on Chemical Safety (IPCS) sponsored an international collaborative study to examine the variability associated with the extraction and bioassay of standard reference materials (SRMs) that are complex environmental mixtures provided by the U.S. National Institute of Standards and Technology (NIST). The study was also intended to evaluate the feasibility of establishing bioassay reference values and ranges for the SRMs. Twenty laboratories from North America, Europe, and Japan participated in the study. As part of the mandatory core protocol, each laboratory extracted the organic material from two particulate samples and bioassayed these extracts. A coal tar polycyclic aromatic hydrocarbon (PAH) solution and two mutagenic control compounds were also subjected to bioassay without prior extraction by the participating laboratories. The bioassay used was the Salmonella/microsomal plate incorporation assay. For the optional portion of the study, a laboratory was free to use the SRMs for any type of exploratory research. The primary purpose of the required portion of the study was to estimate the intra- and inter-laboratory variability in mutagenic potencies of the test materials and to determine whether or not the NIST mixtures could be used as reference materials by others performing the Salmonella assay. Repeatability (intra-laboratory variance) of the bioassay results ranged from 16% to 88% depending on the SRM and the bioassay conditions (tester strain and metabolic activation), whereas reproducibility (inter-laboratory variance) ranged from 33% to 152%. Between-laboratory variability was the main source of variation accounting for approximately 55-95% of the total variation for the three environmental samples. Variation in the mutagenic potency of the control compounds was comparable, with the exception of 1-nitropyrene for which the reproducibility ranged from 127% to 132%. In summary, NIST SRMs provided useful materials for an international inter-laboratory study of complex mixtures. By establishing both intra- and inter-laboratory variance for the mutagenicity results for these materials, the usefulness of these SRMs as reference materials for the Salmonella bioassay was established, critical procedures within the bioassay protocol were identified, and recommendations for future efforts were delineated.     

Quantum dots-based multifunctional dendritic superstructure for amplified electrochemiluminescence detection of ATP

A novel multifunctional dendrimeric CdSe-CdS-Quantum dots (QDs) hybrid superstructure with highly intense electrochemiluminescence (ECL), fluorescence and excellent magnetic property is prepared for the first time, and successfully applied to amplified ECL assays of ATP using DNA cycle amplification technique. The magnetic nanoparticles (MNPs) were firstly assembled with unique dendrimer nanoclusters (NCs), then large numbers of QDs were labeled onto the dendrimer NCs, the superstructure exhibits highly enhanced ECL and fluorescence than the pure QDs. Remarkable ECL quenching of the nanocomposites by gold nanoparticles (GNPs) was observed, based on which a novel strategy for highly sensitive ATP detection was developed by cycle amplification technique. Furthermore, the nanocomposites with excellent magnetic properties can be easily labeled, separated and immobilized onto a magnetic electrode. In particular, all the procedures such as linking GNPs, sensing target and DNA cycle amplification were directly accomplished on the nanocomposites, which is more rapid, convenient, complete and has better reproducibility than the conventional methods on electrode. To the best of our knowledge, this is the first report on the multifunctional QDs superstructure with highly intense ECL, fluorescence, excellent magnetism and its ECL biosensing, which opens a new pathway for developing QD-based nanocomposites for broad applications in ECL bioassays and optical imaging.     

Considerations of Noise and Measurement Reproducibility of Circular Dichroism Measurements Using Na[Co(III) (EDDS)

Although circular dichroism (CD) spectroscopy has become ubiquitous in biological, chemical, and pharmacological laboratories, several issues with instrument calibration and standardization, measurements quality, and reproducibility still remain. In the context of validating and developing a wide-wavelength-range stable standard for CD that is available in both enantiomeric forms, (R,R)- and (S,S)-Na[Co(III) (EDDS)] (where EDDS is ethylenediaminedisuccinato), we have become aware of sources of error in CD spectroscopy in addition to instrument calibration and user issues. This article summarizes those errors and suggests procedures for minimizing them by averaging over sufficient independent data accumulations with appropriate parameters. Chirality 24:699-705, 2012. ? 2012 Wiley Periodicals, Inc.     

Properties of isolated gastric enterochromaffin-like cells.

The gastric enterochromaffin-like cell (ECL) has been studied in gastric fundic glands by confocal microscopy and as a purified cell preparation by video imaging of calcium signaling and measurements of histamine release. Regulation of gastric acid secretion is largely due to alterations of histamine activation of the H2 receptor on the parietal cell and can be divided into central neural regulation, with direct actions of neuronally released mediators and into peripheral regulation by substances released from other endocrine cells. Gastric neuronal stimulation of acid secretion by alteration of ECL cell function is probably mediated by pituitary adenylate cyclase activating peptide (PACAP) receptors on the ECL cell, which activate calcium signaling and histamine release. Peripheral stimulation of acid secretion via the ECL cell is largely mediated by gastrin stimulation of calcium signaling and histamine release. Gastric neuronal inhibition of ECL cell function is probably mediated by galanin inhibition of calcium signaling, and histamine release and peripheral inhibition of ECL cell function is mainly due to somatostatin release from D cells.     

Interlaboratory reproducibility of the immunocytochemical assessment of oestrogen and progesterone receptors and proliferative activity in fine needle aspiration of breast cancer

The purpose of this study was to establish the interlaboratory reproducibility of immunocytochemical analysis of oestrogen (ER) and progesterone (PR) expression and Mib1 growth fraction on fine needle aspiration (FNA) smears. A set of 44 immunostained slides for ER, PR and Mib1 were randomly selected from the archives of the Center for the Study and Prevention of Cancer (CSPO) of Florence, Italy, and submitted for reading to 6 Italian laboratories. The generalized kappa statistic was used as an indicator of agreement among the six laboratories. A good correlation for ER and PR was evident. For Mib1 the results showed some discrepancies. In addition to adequate standardization of procedures, these data confirm that the reliability of the immunocytochemistry is strictly linked to accurate analysis of the results.     

Multiple Laboratory Comparison of the Doubly Labeled Water Technique*

A double-blind study was conducted to determine between-laboratory variability in the doubly labeled water method for measurement of total energy expenditure in humans, and to compare the accuracy and precision of three widely-used procedures for calculating rates of carbon dioxide production from the original isotope data. Eighteen laboratories from five countries participated in the study. All laboratories were provided with five water standards containing varying amounts of ²H and ¹⁸O, and in addition 11 laboratories were provided with urine and dose specimens from one (six laboratories) or two (five laboratories) healthy elderly subjects of normal height and weight undergoing a calorimetric validation of the doubly labeled water method. The data from the five water standards were analyzed to predict between-laboratory variability in the doubly labeled water technique in all laboratories. In addition, data from the subjects were analyzed using the “slope-intercept”, “2-point” and “modified” methods of calculation. The results confirm that the doubly labeled water method can be an accurate technique for the measurement of energy expenditure in adult human subjects in some laboratories. However, there was substantial between-laboratory variability in the results and some laboratories returned physiologically impossible results. There was no significant effect of calculation procedure on the accuracy of the technique in this limited comparison, although the slope-intercept procedure appeared to be more susceptible to analytical error than the other procedures. The isotope standards analyzed by participants in this study will be made available to other investigators on request.     

Variability of Microcirculation Detected by Blood Pulsation Imaging

The non-invasive assessment of blood flow is invaluable for the diagnostic and monitoring treatment of numerous vascular and neurological diseases. We developed a non-invasive and non-contact method of blood pulsation imaging capable of visualizing and monitoring of the two-dimensional distribution of two key parameters of peripheral blood flow: the blood pulsation amplitude and blood pulsation phase. The method is based on the photoplethysmographic imaging in the reflection mode. In contrast with previous imaging systems we use new algorithm for data processing which allows two dimensional mapping of blood pulsations in large object''s areas after every cardiac cycle. In our study we carried out the occlusion test of the arm and found (i) the extensive variability of 2D-distribution of blood pulsation amplitude from one cardiac cycle to another, and (ii) existence of the adjacent spots to which the blood is asynchronously supplied. These observations show that the method can be used for studying of the multicomponent regulation of peripheral blood circulation. The proposed technique is technologically simple and cost-effective, which makes it applicable for monitoring the peripheral microcirculation in clinical settings for example, in diagnostics or testing the efficiency of new medicines.     

Nanoparticle-based electrochemiluminescence immunosensor with enhanced sensitivity for cardiac troponin I using N-(aminobutyl)-N-(ethylisoluminol)-functionalized gold nanoparticles as labels

A novel nanoparticle-based electrochemiluminescence (ECL) immunosensor was designed for highly sensitive and selective detection of human cardiac troponin I (cTnI), an important Acute Myocardial Infarction (AMI)-related biomarker, by using N-(aminobutyl)-N-(ethylisoluminol)-functionalized gold nanoparticles (ABEI-AuNPs) as labels. ABEI-AuNPs were successfully synthesized via a simple seed growth method. A great number of luminescence molecules ABEI as stabilizers were coated on the surface of the AuNPs, which exhibited better ECL activities than previously reported luminol functionalized gold nanoparticles. ABEI-AuNPs were used as new ECL labels to build bio-probes by conjugation with secondary antibodies, which showed good ECL activity, immunological activity, and stability. Another kind of AuNPs functionalized with streptavidin was modified on the electrode surface for biotinylated antibodies capture through the specific interaction of biotin/streptavidin and enhancing the electrical connectivity. By combining with the novel ECL labels and amplification of AuNPs and biotin-streptavidin system, a high sensitive sandwich-type electrochemiluminescence immunoassay was developed for detecting human cTnI with a low detection limit of 2 pg/mL. The immunosensor showed good precision, acceptable stability and reproducibility and could be used for the detection of cTnI in real samples, which was of great potential application in clinical analysis. Importantly, the sensitive detection would have far more diagnostic value than would absolute measurements during the early stage of AMI.     

Influence of Noise Correction on Intra- and Inter-Subject Variability of Quantitative Metrics in Diffusion Kurtosis Imaging

Diffusion kurtosis imaging (DKI) is a promising extension of diffusion tensor imaging, giving new insights into the white matter microstructure and providing new biomarkers. Given the rapidly increasing number of studies, DKI has a potential to establish itself as a valuable tool in brain diagnostics. However, to become a routine procedure, DKI still needs to be improved in terms of robustness, reliability, and reproducibility. As it requires acquisitions at higher diffusion weightings, results are more affected by noise than in diffusion tensor imaging. The lack of standard procedures for post-processing, especially for noise correction, might become a significant obstacle for the use of DKI in clinical routine limiting its application. We considered two noise correction schemes accounting for the noise properties of multichannel phased-array coils, in order to improve the data quality at signal-to-noise ratio (SNR) typical for DKI. The SNR dependence of estimated DKI metrics such as mean kurtosis (MK), mean diffusivity (MD) and fractional anisotropy (FA) is investigated for these noise correction approaches in Monte Carlo simulations and in in vivo human studies. The intra-subject reproducibility is investigated in a single subject study by varying the SNR level and SNR spatial distribution. Then the impact of the noise correction on inter-subject variability is evaluated in a homogeneous sample of 25 healthy volunteers. Results show a strong impact of noise correction on the MK estimate, while the estimation of FA and MD was affected to a lesser extent. Both intra- and inter-subject SNR-related variability of the MK estimate is considerably reduced after correction for the noise bias, providing more accurate and reproducible measures. In this work, we have proposed a straightforward method that improves accuracy of DKI metrics. This should contribute to standardization of DKI applications in clinical studies making valuable inferences in group analysis and longitudinal studies.     

Interlaboratory reproducibility of selective reaction monitoring assays using multiple upfront analyte enrichment strategies

Over the past few years, mass spectrometry has emerged as a technology to complement and potentially replace standard immunoassays in routine clinical core laboratories. Application of mass spectrometry to protein and peptide measurement can provide advantages including high sensitivity, the ability to multiplex analytes, and high specificity at the amino acid sequence level. In our previous study, we demonstrated excellent reproducibility of mass spectrometry-selective reaction monitoring (MS-SRM) assays when applying standardized standard operating procedures (SOPs) to measure synthetic peptides in a complex sample, as lack of reproducibility has been a frequent criticism leveled at the use of mass spectrometers in the clinical laboratory compared to immunoassays. Furthermore, an important caveat of SRM-based assays for proteins is that many low-abundance analytes require some type of enrichment before detection with MS. This adds a level of complexity to the procedure and the potential for irreproducibility increases, especially across different laboratories with different operators. The purpose of this study was to test the interlaboratory reproducibility of SRM assays with various upfront enrichment strategies and different types of clinical samples (representing real-world body fluids commonly encountered in routine clinical laboratories). Three different, previously published enrichment strategies for low-abundance analytes and a no-enrichment strategy for high-abundance analytes were tested across four different laboratories using different liquid chromatography-SRM (LC-SRM) platforms and previously developed SOPs. The results demonstrated that these assays were indeed reproducible with coefficients of variation of less than 30% for the measurement of important clinical proteins across all four laboratories in real world samples.     

Round robin investigation of methods for recovering human enteric viruses from sludge.

To select a tentative standard method for detection of viruses in sludge the American Society for Testing and Materials D19:24:04:04 Subcommittee Task Group initiated round robin comparative testing of two procedures that, after initial screening of several methodologies, were found to meet the basic criteria considered essential by the task group. Eight task group member laboratories agreed to perform round robin testing of the two candidate methods, namely, The Environmental Protection Agency or low pH-AlCl3 method and the Glass or sonication-extraction method. Five different types of sludge were tested. For each particular type of sludge, a single laboratory was designated to collect the sludge in a single sampling, make samples, and ship it to the participating laboratories. In most cases, participating laboratories completed all the tests within 48 h of sample arrival. To establish the reproducibility of the methods, each laboratory tested each sludge sample in triplicate for the two candidate virus methods. Each processed sludge sample was quantitatively assayed for viruses by the procedures of each individual round robin laboratory. To attain a more uniform standard of comparison, a sample of each processed sample from all laboratories was reassayed with one cell line and passage number by a single laboratory (Environmental Protection Agency Environmental Monitoring and Support Laboratory, Cincinnati, Ohio). When the data were statistically analyzed, the Environmental Protection Agency method was found to yield slightly higher virus recoveries for all sludge types, except the dewatered sludge. The precisions of both methods were not significantly different.(ABSTRACT TRUNCATED AT 250 WORDS)