A method for localizing epigenetic modifications of DNA is provided, including: providing a target DNA strand having a least one epigenetic modification, wherein the target DNA strand is annealed to a non-target DNA stand, wherein each of the target DNA strand and the non-target DNA strand is labeled with a first fluorophore; labeling the at least one epigenetic modification with a second fluorophore; annealing a first probe to the target DNA strand and annealing a second probe to the non-target DNA strand; immobilizing the target DNA strand on a support; and detecting the first and second fluorophores immobilized on the support. Also provided is a method of diagnosing a disease or condition, such as cancer, in a subject suspected of having the disease by localizing epigenetic modifications of DNA from a patient sample and comparing to a reference epigenetic profile associated with the disease or condition.
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