The EU FP7 funded project CD-MEDICS has the goal to develop a technology platform for point-of-care diagnostics, capable of simultaneous genomic and proteomic detection, for the management monitoring and diagnosis of coeliac disease. Coeliac disease affects 1 in 100-300 genetically predisposed individuals who develop a small intestinal inflammation (enteropathy) on exposure to dietary gluten. Accurate and reliable diagnosis together with dietary monitoring are a must for the well-being of CD patients and their social environment. The chip system developed within CD-MEDICS will enable fast and accurate diagnosis by combining serology tests with HLA-typing.

With the EU FP6 funded project SmartHealth, we contribute to the development of the next generation of smart diagnostic systems fully integrated into healthcare systems in Europe. Driven by key applications in cancer diagnostics, SmartHealth will enable enhanced medical diagnosis leading to earlier and more precise results and thus contributing to an increased quality of life.

COMICS

A battery of reliable and validated in vitro assays is needed to test for genotoxic and cytotoxic effects of chemicals without resorting to animal experiments. Within the EU FP6 funded project COMICS the comet assay, a sensitive indicator of DNA damage, is combined with the Cell Array system, to establish and validate high capacity assays suitable for chemical testing. Up to 800 cell samples will be processed for comets on a single microscope slide. Arrays will use cells with different metabolic capabilities, and data on cytotoxicity will be obtained in parallel with DNA damage. A medium-throughput assay is also being developed.

MagRSA

The EU FP6 funded project MagRSA aims at the development of a new diagnostics platform that will provide a fast, simple and accurate identification of Methicillin-resistant Staphylococcus aureus (MRSA) from clinical samples. The diagnostic protocol relies on a new and clinically validated procedure that consists in a direct one-step enrichment of MRSA present in either nasal or inguinal swabs, followed by DNA extraction of immunocaptured bacteria and their identification by multiplex quantitative sequences amplification with quantitative PCR. This protocol will be integrated within a simple “hand-off” system based on: (1) novel strategies for the integration of unit operations required for the entire nucleic acid analysis chain in a microfluidic platform, and (2) advanced microfluidic magnetic nanoparticles manipulation technology allowing efficient capture and extraction of the target bacteria and nucleic acids. The separate steps of sample preparation, signal amplification by multiplex PCR, and simultaneous detection of multiple genes will be implemented as one step in a single fluidic chip, thereby providing a simple fully automated and miniaturized system for MRSA diagnostics.

Biomatcell

Is a Swedish center of excellence with focus on biomaterial sciences and cell therapy. Using real-time PCR and techniques we develop for single cell expression profiling we study the growth of cells at the surface of implants. We are developing methods to study the expression of genes in individual cells, and to correlate the expression to physiologic cell properties such as membrane potential as measured by patch clamp technique on the same cell.

Single-cell and sub cell qPCR

We also study heterogeneity on cellular level, and have found that expression of certain genes can differ several orders of magnitude between cells in the same seemingly homogeneous population (Genome Research 15, 1388-1392, 2005, Nature Reviews Genetics 6, 1, 2006). In particular, we discovered that expression of genes in individual cell varies according to the log normal distribution. We also developed technique to measure intracellular mRNA gradient by real-time PCR.

Expression profiling

In collaboration with MultiD Analyses we develop methods for multivariate real-time PCR expression profiling. These methods are particularly powerful for the classification of genes and samples with similar expression patterns, and they are useful for applications from the identification of expression pathways to classification of diseases based on expression profiles.

Immuno-qPCR

In many cases expression of proteins is more informative than gene expression profiles. We have combined the sensitivity and accuracy of QPCR with the specificity of immunoassays in immuno-Q-PCR (J. Immun. Meth. 304, 107-116, 2005). Binding the protein by two specific antibodies, one of which is tagged with an oligonucleotide, we can, after careful washing, determine the amount of target protein by amplifying the DNA. Immuno-Q-PCR can be performed in most conventional standard Q-PCR instrument.

New dyes for qPCR

We are developing and evaluating new dyes for real-time PCR applications. Our dyes are designed to bind in the DNA minor groove, which makes them more selective for double-stranded DNA than, for example, SYBRGreen. The dyes are designed with different colours and can be combined with probes for quality control (Biotechniques 40, 315-319, 2006). The dyes are also excellent for high resolution melt applications.