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Beads on String Genomics: Experimental Toolbox for Unmasking Genetic / Epigenetic Variation in Genomic DNA and Chromatin

Final Report Summary - BEADSONSTRING (Beads on String Genomics: Experimental Toolbox for Unmasking Genetic / Epigenetic Variation in Genomic DNA and Chromatin)

The Beads-on-string projects aimed to develop a toolbox for genomic analysis of individual DNA molecules and to visualize genetic and epigenetic patterns on such genomic fragments. This was done by attaching fluorescent markers to the DNA at specific locations followed by stretching the labeled DNA in nanochannel arrays for imaging. During the project the team has developed a method for fluorescent labelling of the epigenetic marks 5mC and 5hmC, and demonstrated for the first time a combined genetic and epigenetic profile of individual genomic DNA molecules. They also developed labeling schemes for DNA damage and chromatin accessibility, and combined all these techniques to generate comprehensive genetic and epigenetic maps. In addition, a novel method, CATCH, was developed to target specific genomic regions and excise them from the genome for further analysis. This method enabled deep and high coverage analysis at relatively low cost, by focusing on the region of interest and without the need to analyze the entire genome. The project has led to several advances in the field of human disease diagnostics, including detailed analysis of the breast cancer-related gene BRCA1, and establishment of a new and accurate diagnosis approach for facioscapulohumeral muscular dystrophy (FSHD).