We propose to expand a pilot project to develop a high density gene copy number micro-array based on low complexity genomic representations. Such a tool will lead to improved classification of cancers, which will likely impact all areas of cancer diagnosis and treatment, and be an enormous boon to the discovery of cancer causing genes. We are poised to scale up from arrays of a thousand probes to sets of probes in excess of 30,000 that can be rapidly mapped to very high resolution in array format. Our method will be able to resolve changes in the genome with a resolution of every 50 to 100 kilobases. Moreover, we believe that we can significantly enhance the closure of human genome sequencing project by providing independently derived BAC contigs and probes for gaps in the existing BAC maps.
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