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PubMed2000

Multisite comparison of CD4 and CD8 T-lymphocyte counting by single- versus multiple-platform methodologies: evaluation of Beckman Coulter flow-count fluorospheres and the tetraONE system. The NIAID DAIDS New Technologies Evaluation Group.

New analytic methods that permit absolute CD4 and CD8 T-cell determinations to be performed entirely on the flow cytometer have the potential for improving assay precision and accuracy. In a multisite trial, we compared two different single-platform assay methods with a predicate two-color assay in which the absolute lymphocyte count was derived by conventional hematology. A two-color method employing lymphocyte light scatter gating and Beckman Coulter Flow-Count fluorospheres for absolute counting produced within-laboratory precision equivalent to that of the two-color predicate method, as measured by coefficient of variation of replicate measurements. The fully automated Beckman Coulter tetraONE System four-color assay employing CD45 lymphocyte gating, automated analysis, and absolute counting by fluorospheres resulted in a small but significant improvement in the within-laboratory precision of CD4 and CD8 cell counts and percentages suggesting that the CD45 lymphocyte gating and automated analysis might have contributed to the improved performance. Both the two-color method employing Flow-Count fluorospheres and the four-color tetraONE System provided significant and substantial improvements in between-laboratory precision of absolute counts. In some laboratories, absolute counts obtained by the single-platform methods showed small but consistent differences relative to the predicate method. Comparison of each laboratory's absolute counts with the five-laboratory median value suggested that these differences resulted from a bias in the absolute lymphocyte count obtained from the hematology instrument in some laboratories. These results demonstrate the potential for single-platform assay methods to improve within-laboratory and between-laboratory precision of CD4 and CD8 T-cell determinations compared with conventional assay methods.

CD4-CD8 Ratio↗

PubMed1995

Cross-platform hypermedia examinations on the Web.

The authors developed a multiple-choice medical testing system delivered using the World Wide Web. It evolved from an older, single-platform, locally-developed computer-based examination. The old system offered a number of advantages over traditional paper-based examinations, such as digital graphics and quicker, easier scoring. The new system builds on these advantages with its true cross-platform design and the addition of hypertext learning responses. The benefits of this system will increase as more medical educational resources migrate to the Web. Faculty and student feedback has been positive. The authors encourage other institutions to experiment with Web-based teaching materials, including examinations.

Clinical Clerkship↗

PubMed2003

High-grade loss of leukocytes and hematopoietic progenitor cells caused by erythrocyte-lysing procedures for flow cytometric analyses.

All current-flow cytometric techniques use erythrocyte-lysing procedures before leukocyte analysis. We investigated the impact of four lysing procedures with different flow cytometric techniques on the loss of leukocytes and hematopoietic progenitor cells in blood samples. A total of 280 determinations out of 10 samples were measured by two flow cytometers (FCMs), using a FACS-Calibur (Becton Dickinson) and a particle-analyzing system (PAS) with a "true volumetric unit" (Partec). All samples were prepared with four different commercially available erythrocyte-lysing reagents (n = 10, respectively). CD34(+) cells were determined in relation to counted leukocytes with both FCMs (dual platform determinations, 2-PF). In addition, further immunologic and nuclear staining determinations of cells with and without erythrocyte-lysing procedures were performed in the "true volumetric unit" (single platform mode 1-PF) using the PAS system (n = 10, respectively). In the 2-PF mode, both systems showed identical results for CD34(+) cells (r = 0.997). The comparison of 1-PF and 2-PF modes with immunologic stainings revealed a mean decrease of 34.5% for absolute amounts of CD45(+) cells [in detail: Becton-Dickinson (BD) lysis 40%; Ortho Diagnostics (OD) lysis 31%; Uti lyse (UL) 38%; Cylyse (CL) 29%] and of 41.3% for absolute concentration of CD34(+) cells [in detail: BD lysis 45%; OD lysis 40%; UL lysis 45%; CL lysis 34%] by the lysing procedures. In contrast, the nuclear stainings revealed a mean leukocyte loss of only 5% for the nonlysed samples and of 12% for lysed samples. All investigated lysing procedures induced a large loss of leukocytes and progenitor cells, obviously due to cell membrane destruction as demonstrated for identical samples in the 1-PF and 2-PF modes by immunologic and nuclear staining methods.

Antigens, CD↗

PubMed2002

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

Animals↗

PubMed2005

Development of a microfluidic platform with an optical imaging microarray capable of attomolar target DNA detection.

In this paper, DNA hybridization in a microfluidic manifold is performed using fluorescence detection on a fiber-optic microarray. The microfluidic device integrates optics, sample transport, and fluidic interconnects on a single platform. A high-density optical imaging fiber array containing oligonucleotide-labeled microspheres was developed. DNA hybridization was observed at concentrations as low as 10 aM with response times of less than 15 min at a flow rate of 1 microL/min using 50 microL of target DNA samples. The fast response times coupled with the low sample volumes and the use of a high-density, fiber-optic microarray format make this method highly advantageous. This paper describes the initial development, optimization, and integration of the microfluidic platform with imaging fiber arrays.

Bacillus thuringiensis↗

PubMed2004

Cytometric bead array: a multiplexed assay platform with applications in various areas of biology.

The introduction of flow cytometric bead-based technology has added a new approach for investigators to simultaneously measure multiple analytes in biological and environmental samples. This new technology allows for (1) evaluation of multiple analytes in a single sample; (2) utilization of minimal sample volumes to glean data; (3) reproducibility and results comparative with previous experiments; (4) direct comparison with existing assays; and (5) a more rapid evaluation of multiple samples in a single platform. The cytometric bead array (CBA) system enables simultaneous measurement of multiple analytes in sample volumes too small for traditional immunoassays. Results have been presented for the analysis of a variety of human cytokines. In addition, the technology allows for the design and creation of assays to measure a variety of analytes including inflammatory mediators, chemokines, immunoglobulin isotypes, intracellular signaling molecules, apoptotic mediators, adhesion molecules, and antibodies. New initiatives put forward by the Human Genome Project and the FDA require the development and use of assays for the rapid simultaneous quantitation of multiple analytes. The CBA technology provides the ability to quantify multiple proteins within a given sample, with precision and consistency.

Anaphylatoxins↗

PubMed2006

Comparison of two alternative methods for CD4+ T-cell determination (Coulter manual CD4 count and CyFlow) against standard dual platform flow cytometry in Uganda.

BACKGROUND: In this study we evaluated alternative CD4(+) T-cell counting methods in clients of a PMTCT Programme in rural Uganda. METHODS: The Coulter Manual CD4 Count method for CD4(+) T-cell enumeration (Cyto-Spheres) and an automated method (volumetric, single-platform flow cytometry; CyFlow) were compared with a standard, dual-platform flow cytometry protocol (DPFC, FACScan). RESULTS: Correlation and precision of agreement were higher for the CyFlow method (r = 0.929 and eta = 0.08) when compared to DPFC than for the Cyto-Spheres method (r = 0.725 and eta = 0.3). Multiple linear regression analysis showed that CD4(+) cell counts by the CyFlow method were a stronger predictor for results of DPFC than those of the Cyto-Spheres method (r(2) = 0.864 and r(2) = 0.552, respectively). When compared to DPFC the CyFlow method generated higher CD4(+) cell counts than the Cyto-Spheres method, as expressed by a higher median and mean difference (+70 and +90 cells for CyFlow, +28 and -1.4 cells for Cyto-Spheres). CONCLUSION: Both, the manual Cyto-Spheres method and the CyFlow method can be used for the enumeration of CD4(+) cells in resource-limited settings. Under supervised conditions, the CyFlow method produced results more consistent with the reference method than the Cyto-Spheres method.

Algorithms↗

PubMed2000

Automated mass spectrometry: a revolutionary technology for clinical diagnostics.

For various diagnostic analyses and the studies of functional genomics, the use of an accurate and cost-effective analytic platform to analyze large numbers of samples is essential. An automated platform called MassArray (Sequenom, Inc, San Diego, CA), designed for high-throughput diagnostic analyses, has recently been validated. The platform combines miniaturized, two-dimensional chip arrays with proven high-fidelity enzymatic procedures and matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Nanoliter dispensing of samples in high-density formats of 384 or greater results in improved throughput and reduced costs. Automation prevails from the initial assay design through sample processing and data analysis, for the most part eliminating the labor component of assay development and implementation. The MassArray platform is being used in the following areas: (1) molecular diagnosis of genetic disease and infectious agents, (2) pharmacogenomics, (3) paternity and/or identity testing, and (4) agriculture (e.g., marker-assisted breeding). MALDI-TOF mass spectrometry can also be used for analyzing proteins; therefore, genotype/phenotype testing can be performed on a single platform.

Adolescent↗

PubMed2006

Metabolic biotinylation provides a unique platform for the purification and targeting of multiple AAV vector serotypes.

The development of rationally designed targeted gene delivery vectors is an important focus for gene therapy. While genetic modification of AAV can produce vectors with modified tropism, incorporation of targeting peptides into the structural context of the AAV virion often results in loss of function or loss of virion integrity. To address this issue, we have developed a targeting system using metabolically biotinylated AAV. We generated serotype 1, 2, 3, 4, and 5 AAV capsids with small peptide insertions that are metabolically biotinylated in packaging cells during vector production by coexpression of the Escherichia coli BirA, biotin ligase, gene. Biotin moieties are exposed on the surface of assembled AAV particles and can interact with avidin. Metabolically biotinylated AAV vectors produced in this manner maintained endogenous titer and tissue tropism, could be purified on monomeric avidin resin, and could be retargeted to cells engineered to express an artificial avidin-biotin receptor. This technology provides not only a single platform for the purification of multiple AAV vector serotypes, but also a means for the development of multiple targeted AAV vectors utilizing a single capsid modification via straightforward avidin-biotin ligand coupling.

Amino Acid Sequence↗

PubMed2003

Detection of single unit activity from the rat vagus using cluster analysis of principal components.

In vivo recordings from subdiaphragmatic vagal afferent nerves generally lack the resolution to distinguish single unit activity. Several methods for data acquisition and analysis were combined to produce a high degree of reliability in recording electrophysiological signals from gastrointestinal and hepatic afferent fibers in the rat. Recordings with low noise were achieved by paralysis of the respiratory muscles and by pinning the nerve to a recording platform. Single unit activity was isolated using principal component (PC) analysis and cluster cutting of data in multi-dimensional space (1-3 PCs). Cluster assignments were determined by a semi-automated approach using the k-means algorithm. The accuracy of single unit classification was assessed by checking inter-spike intervals (ISIs) to determine the length of the refractory period, and by cross-correlation analysis to assess whether single units were mistakenly split into more than one cluster. These analyses produced up to four isolated single units from each nerve filament (a bundle of nerve fibers), and typically it was possible to further increase yield by recording from several nerve filaments simultaneously using an array of electrodes.

Action Potentials↗

PubMed2004

Cross-site comparison of gene expression data reveals high similarity.

Consistency and coherence of gene expression data across multiple sites depends on several factors such as platform (oligo, cDNA, etc.), environmental conditions at each laboratory, and data quality. The Hepatotoxicity Working Group of the International Life Sciences Institute Health and Environmental Sciences Institute consortium on the application of genomics to mechanism-based risk assessment is investigating these factors by comparing high-density gene expression data sets generated on two sets of RNA from methapyrilene (MP) experiments conducted at Abbott Laboratories and Boehringer-Ingelheim Pharmaceuticals, Inc. using a single platform (Affymetrix Rat Genome U34A GeneChip) at seven different sites. This article focuses on the evaluation of data quality and statistical models that facilitate the comparison of such data sets at the probe level. We present methods for exploring and quantitatively assessing differences in the data, with the principal goal being the generation of lists of site-insensitive genes responsive to low and high doses of MP. A combination of numerical and graphical techniques reveals important patterns and partitions of variability in the data, including the magnitude of the site effects. Although the site effects are significantly large in the analysis results, they appear to be primarily additive and therefore can be adjusted in the statistical calculations in a way that does not bias conclusions regarding treatment differences.

Animals↗

PubMed2006

Snap: an integrated SNP annotation platform.

Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical research. Using a user-friendly web interface, genes can be searched by name, description, position, SNP ID or clone name. Several public databases are integrated, including gene information from Ensembl, protein features from Uniprot/SWISS-PROT, Pfam and DAS-CBS. Gene relationships are fetched from BIND, MINT, KEGG and are integrated with ortholog data from TreeFam to extend the current interaction networks. Integrated tools for primer-design and mis-splicing analysis have been developed to facilitate experimental analysis of individual genes with focus on their variation. Snap is available at http://snap.humgen.au.dk/ and at http://snap.genomics.org.cn/.

Databases, Nucleic Acid↗

PubMed2004

Multiple sample amplification and genotyping integrated on a single electronic microarray.

We report a novel method that allows simultaneous in situ amplification and then genotyping of single nucleotide polymorphism (SNP) for multiple samples on a single electronic microarray. The locus coding for one of the common inherited thrombosis risk factors, Factor V Leiden (FVL), was chosen as a model system for SNP analysis. This method combines strand displacement amplification (SDA) with electrophoretic movement and concentration of DNA on electronic microarrays to provide a single platform for DNA amplification and analysis. The method includes: electronic anchoring of allele-specific SDA amplifiable primers (APs) and a nonamplifiable primer (NAP) to different electrodes, electronic hybridization of genomic DNA from different samples to those primers, in situ amplification of target DNA, and genotyping of FVL. Compared to previous anchored SDA methods, the addition of a NAP improves detection signals by at least 20-fold. The sensitivity of this method is dependent on the amplification time. Using this method, nine different genomic DNA samples with known FVL genotypes were amplified and correctly genotyped on a single electronic microarray without any contamination between samples. The present method could streamline development of nucleic acid-based assays in applications of molecular diagnostic, point-of-care testing, and forensic detection, which often require the capability to analyze multiple samples efficiently.

Base Sequence↗

PubMed2002

CD45-assisted PanLeucogating for accurate, cost-effective dual-platform CD4+ T-cell enumeration.

BACKGROUND: North American and European guidelines for dual-platform (DP) flow cytometry recommend absolute CD4 T-cell counts to be calculated from two parameters: the absolute lymphocyte counts obtained on a hematology analyzer and the percentages of CD4+ cells among lymphocytes (CD4%/lympho) obtained by flow cytometry. Nevertheless, the identification of lymphocytes is error-prone: a poor match between these common denominators in the two systems is the main source of inaccuracy. In contrast, total leucocyte counts (white cell counts [WCC]) and CD4% among the gated CD45+ leucocytes (CD4%/leuco) can be determined with greater accuracy. METHODS: We introduced "PanLeucogating," i.e., we used total leucocytes as the common denominator for improving the precision of DP absolute CD4 counting. Correlations and Bland-Altman tests were used for statistical analysis. RESULTS: First, 22 stabilized blood product samples were provided by U.K. National External Quality Assessment Scheme (NEQAS) and a higher accuracy and precision of CD4 counts were documented using PanLeucogating compared with lymphocyte gating. Next, 183 fresh and 112 fixed (TransFix) whole blood samples were used to compare DP methods and single-platform (SP) methodology, including both volumetric and bead-based techniques. A particularly high correlation and comparable precision of absolute CD4 counts were observed between the SP volumetric method and DP PanLeucogating (R(2) = 0.990; bias 6 +/- SD 17%). The SP volumetric method showed lower levels of agreement with the DP lymphocyte gating (R(2) = 0.758; bias 14 +/- SD 51%) and with the SP bead-based method (R(2) = 0.923; bias 4 +/-SD 31%). CONCLUSIONS: These observations show that DP leucocyte counts (WCC) should replace lymphocyte counts as the "common denominator" although CD4%/lympho values can, as an extra step, be also provided readily if requested. When coupled with quality control for WCC on hematology analyzers, the DP method with CD45 PanLeucogating represents a robust CD4 T-cell assay that is as accurate as the SP volumetric technique. This DP method uses only two, CD45 and CD4, antibody reagents and can be run on any pair of hematological analyzer plus flow cytometer.

CD4-Positive T-Lymphocytes↗

PubMed2026

'PePApipe': A complete bioinformatics analysis pipeline for African Swine Fever Virus genome.

African Swine Fever Virus (ASFV) is of high concern in porcine livestock across the world due to both the high mortality rates and the trade restrictions imposed on affected regions. The viral genome is large and complex, and genomic analysis is essential for tracing its origin and evolution. Although several bioinformatics tools exist for genome assembly and analysis, no single platform integrates all necessary steps in an accessible and systematic way. In this study the authors developed 'PePApipe', a custom-built, user-friendly pipeline that enables rapid, complete, and efficient ASFV genome analysis. It is specifically designed for laboratory professionals with limited bioinformatics experience, requiring only basic command-line knowledge. Starting from raw sequencing data, PePApipe integrates thirteen software tools into one automated workflow, covering quality control and pre-processing of raw reads, de novo genome assembly and variant calling. Programmed in Python, it can be executed locally through bash scripts, or using a Slurm protocol for batch processing of multiple samples. The main outputs are the ASFV consensus genome sequence and a file listing its putative variants compared to the selected reference genome. PePApipe classifies generated files into structured folders and produces intermediate files that can be used as inputs for further or parallel analyses; users can also enable or disable specific steps in each particular case. This pipeline is adaptable and complementary to downstream steps such as viral genome annotation or genome visualization. By consolidating all stages of viral genome analysis into a single automated workflow, PePApipe reduces the likelihood of user error, and enhances reproducibility and efficiency. This user-friendly pipeline facilitates the transition from sequencing to assembly and downstream analysis of viral genomes, ensuring a fast and reliable response to molecular analysis demands. Finally, the pipeline can be easily adapted to the study of other viral species, expanding its application in infectious diseases surveillance.

African Swine Fever Virus↗

PubMed2001

Affordable CD4+ T cell counts by flow cytometry. II. The use of fixed whole blood in resource-poor settings.

We tested the feasibility and precision of affordable CD4+ T cell counting in resource-poor settings using a recently standardised fixative, TransFix in whole blood (WB) by flow cytometry (FCM). The precision of the assays was established under optimal conditions for single-platform FCM such as the volumetric CytoronAbsolute and the bead-based FACSCan. Fresh WB samples from HIV-seropositive and seronegative patients were tested in Tanzania and South Africa, fixed and sent to the UK for reanalysis 7 days later. Correlation, bias and limits of agreements were analysed by linear regression and the Bland-Altman test. Absolute CD4+ T cell counts remained stable for at least 10 days when TransFix was added to WB in 1:10 dilution at 20-25 degrees C, and for 7 days when added in 1:10 or 1:5 dilution to samples stored to mimic 'tropical' conditions at 37 degrees C. Higher temperatures such as 42 degrees C were tolerated for only short periods since the recovery had decreased to 63% by day 3. The reproducibility of lymphocyte subset analysis remained unchanged by TransFix with coefficient of variations <6% for all T cell subsets. Absolute CD4+ T cell counts and CD4+ T cell % values on fixed samples in the UK showed a high correlation with the results using fresh samples in Tanzania (r=0.993 and 0.969, respectively) and with the samples handled in Johannesburg (r=0.991 and 0.981) with minimal bias. Primary CD4 gating using only a single CD4 antibody also remained accurate in TransFixed samples (r=0.999). Thus, TransFix permits optimal fixation and transport of WB samples in the developing world for FCM to local regional laboratories and for quality assurance in international centres. When used together with inexpensive primary CD4 gating, TransFix will allow reliable and affordable CD4+ T cell counting by FCM in resource-poor settings.

Adult↗

PubMed2004

Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array.

Like most human cancers, oral squamous cell carcinoma (SCC) is characterized by genetic instabilities. In this study, a single platform (Affymetrix 10K SNP mapping array) was used to generate both loss of heterozygosity (LOH) and DNA copy number abnormality (CNA) read-outs for precise and high-resolution genetic alteration profiles. As a proof of principle, we performed this concordant analysis on a panel of deletion and trisomy cell lines with known chromosomal alterations and the precise LOH and CNA regions were detected as expected. Using a previously described oral SCC progression model system, we identified a set of genomic regions that may be associated with the malignancy progression, including chromosome regions 3pter-3p35.3, 3p14.1-3p13, 11p, 11q14.3-11q22.2, and 11q13.5-11q14.1. These data show that it is feasible to utilize high-density SNP arrays to generate concordant LOH and CNA profiles at high resolution.

Carcinoma, Squamous Cell↗

PubMed1999

Cell analysis for hematopoietic stem/progenitor cell transplantation.

Cytometric analysis has become an important aspect in the quality control of cells in all phases of hematopoietic cell transplantation. In the stage of donor conditioning the counting of stem and progenitor cells is important and several reliable single platform tests for CD34+ cells have become available recently. It has been shown, that the count of certain subsets of CD34 may predict best time for harvesting stem cells better than just CD34. In many cases manipulation of the cell sample after collection from the donor is necessary before the cells are adequate for transplantation. Characterization of the resulting cell preparations requires reliable quantitative analysis of a variety of cell types like the enumeration of T-cells at the level of one in ten thousand for some allogeneic transplantations. It is discussed how these clinical requirements will need a refinement of cytometric procedures to achieve adequate clinical decisions.

Genetic Therapy↗