Abstract: The present invention provides a high-throughput method for the parallel analysis of many potential sites of chemical modification (e.g., methylation) in DNA. It makes use of chemical treatment of the DNA to alter its sequence in a way that depends upon the modification of interest and subsequent analysis of the resulting sequence by hybridization to an array of probes. A device, comprising the array of probes, is provided by the invention, and principles and methods for its design and fabrication are also provided.

Abstract: An apparatus and method for comparative genomic mapping of a sample and a reference is disclosed that includes an array of oligonucleotides having a surface derived from a selected portion of a genome. A reader capable of producing a signal disposed to detect events that occur at the surface of the array of oligonucleotides and a computer attached to the reader, wherein the computer processes a signal from the reader to determine the relative intensity produced at the array surface and capable of comparing the intensity of the signal from the array to provide map with a resolution of about 20, 30, 50, 100, 200, 500, 1,000, 2,000, 5,000, 20,000, 50,000, 100,000, 200,000, 500,000, 1,000,000, 2,000,000 basepairs.