Methods and compositions for producing labeled probe nucleic acids for use in array based comparative genomic hybridization applications

A method for comparing the relative copy number of nucleic acid sequences in two or more collections of nucleic acid molecules, the method comprising:

• (a) preparing at least a first collection of labeled nucleic acid probe molecules labeled with a first label and a second collection of labeled nucleic acid probe molecules labeled with a second label distinguishable from said first label, wherein each constituent member of said first and second collections of labeled nucleic acid probe molecules is prepared from a genomic nucleic acid template using a set of primers that includes at least one primer comprising a sequence of a conserved coding consensus region;
• (b) contacting said first and second collections of labeled probe molecules with a plurality of target elements bound to a solid surface, each is target element comprising a target nucleic acid;
• (c) evaluating the relative binding of the first and second collections of labeled nucleic acid probe molecules to the same target nucleic acid to compare the relative copy number of nucleic acid sequences in said first and second collections of labeled nucleic acid probe molecules.