Mapping and De Novo Assembly of Long Barcoded Molecules of DNA from a Cancer Genome

We present a rapid genome-wide analysis method based on new NanoChannel Array technology (IrysTM System) that confines and linearizes individual molecules of DNA to nearly 85% of their respective contour length. Once confined, extremely long DNA molecules (100 to 1,000 kilobases) are imaged with a custom three-color epifluorescence microscope. Genomic DNA is stained with YOYO and can be labeled specifically at the ‘GCTCTTC’ or ‘CCTCAGC’ sequence with different colored fluorescent probes allowing for each molecule to have a unique pattern and mapped to its corresponding location in a reference. By imaging hundreds of gigabases per run, a high-resolution genome map was assembled de novo from the extremely long single molecules, which retain the original context and architecture of the genome. This allows for the cataloging of complex repetitive regions and large-scale rearrangements. The advantages of genome mapping for rearrangement analysis are demonstrated here by several examples in which we identify hallmark fusions as well as rearrangements from cancer cells.