CD4+ T lymphocytes enumeration by an easy-to-use single platform image cytometer for HIV monitoring in resource-constrained settings

Backround: HIV monitoring in resource-constrained settings demands affordable and reliable CD4+ T lymphocytes enumeration methods. We developed a simple single platform image cytometer (SP ICM), which is a dedicated volumetric CD4+ T lymphocytes enumeration system that uses immunomagnetic and immunofluorescent technologies. The instrument was designed to be a low-cost, yet reliable and robust one. In this article we test the instrument and the immunochemical procedures used on blood from HIV negative and HIV positive patients. - \ud Methods: After CD4 immunomagnetic labeling in whole blood, CD4+ T lymphocytes, CD4+dim monocytes and some nonspecifically labeled cells are magnetically attracted to an analysis surface. Combining with CD3-Phycoerythrin (PE) labeling, only CD3+CD4+ T lymphocytes are fluorescently labeled and visible in a fluorescent image of the analysis surface. The number of CD4+ T lymphocytes is obtained by image analysis. Alternatively, CD3 immunomagnetic selection in combination with CD4 immunofluorescent labeling can also be applied for CD4+ T lymphocytes enumeration. - \ud Results: The SP ICM system was compared with two single platform flow cytometer (SP FCM) methods: tetraCXP and TruCount methods. The SP ICM system has excellent precision, accuracy and linearity for CD4+ T lymphocytes enumeration. Good correlations were obtained between the SP ICM and the SP FCM methods for blood specimens of 44 HIV- patients, and of 63 HIV+ patients. Bland-Altman plots showed interchangeability between the SP ICM and the SP FCM methods. - \ud Conclusions: The immunolabeling methods and the instrumentation are simple and easy-to-handle for less-trained operators. The SP ICM system is a good candidate for CD4+ T lymphocytes enumeration in point-of-care settings of resource-constrained countries

ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation

Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance