Cytogenetic diagnostic approaches provide information on the single-chromosome level but suffer from low resolution and throughput. In contrast, next generation sequencing (NGS) based diagnostics provides single base resolution and high throughput but suffer from short reads that prevent analysis of large genomic aberrations as well as being prone to PCR-amplification bias and erasure of epigenetic information.
The BeyondSeq project aims to bridge the gap between these domains by analyzing long individual DNA molecules without PCR-amplification via utilization of emerging optical DNA mapping technologies.
In BeyondSeq we will develop a robust toolbox for integrated genetic and epigenetic profiling of single DNA molecules that will include automated sample preparation of native unamplified DNA as well as the hardware and software platforms and analysis tools for readout, extraction and quantification of medically relevant genomic information. This technology will be used to develop a set of specific, proof of principle diagnostic assays based on optical barcoding of individual DNA molecules.
These assays will address: Bacterial infections and antibiotic resistance; Diagnosis/prognosis tools for hematological malignancies; Spinal Muscular Atrophy; and Early diagnosis of colorectal and lung cancer.
Ultimately BeyondSeq will provide reagents, prototype DNA barcoding devices and data analysis software ready for a range of applications for large scale validation and early stage commercialization
Read more here.
Why are some people predisposed to Alzheimer's? A consortium of researchers has recently identified some unexpected and promising leads in the quest to understand the relationship between our intestinal bacteria and Alzheimer’s. They are analyzing the body’s microbiome – the microorganisms in our digestive tract – and how it is regulated. Determining the composition and functioning of the microbiome will help them identify risk factors, develop a new diagnostic tool and maybe even come up with a way to delay the onset of this neurodegenerative disorder.
The consortium is looking at what happens when probiotics are used to regulate the microbiome and how they may affect the progression of the disease. This approach will also be applied to developing a new diagnostic tool for Alzheimer’s.
The project, called AD-gut, will be coordinated by EPFL. The team lead by EPFL: Professors Aleksandra Radenovic, Dimitri Van de Ville and Theo Lasser will also work on developing various imaging techniques in order to decipher the microbiome along with theranostic methods aimed at revealing the beneficial effects of probiotics. The following European researchers are bringing their team’s skills to the project: Johan Hofkens (University of Leuven, Belgium), Tanja Weil (Max Planck Institute, Germany), Andrew Macpherson (University of Bern, Switzerland), Frida Fåk (Lund University, Sweden) and Jeroen Raes (VIB, Belgium).
Read more here.