Comparative Genomic Hybridization Assays Using Immobilized Oligonucleotide Features and Compositions for Practicing the Same

A method for comparing the copy number of at least one nucleic acid sequence in at least two genomic sources, said method comprising:

• (a) preparing at least a first collection of nucleic acid molecules from a first genomic source and a second collection of nucleic acid molecules from a second genomic source, wherein said first and second genomic sources have a complexity of 1×109 base pairs or more and said first and second collections are of non-reduced complexity;
• (b) contacting said first and second collections of nucleic acid molecules with one or more pluralities of distinct oligonucleotide features bound to a surface of a solid support, wherein said one or more pluralities of distinct oligonucleotide features comprise oligonucleotides that range in size from 20 nt to 200 nt in length and said contacting occurs under stringent assay conditions;
• (c) measuring the binding of the first and second collections of nucleic acid molecules to said features to produce data;
• and
• (d) identifying a quantitative difference in the copy number of at least one nucleic acid sequence in said at least two genomic sources using said data.

A method for comparing the copy number of at least one nucleic acid sequence in at least two genomic sources, said method comprising:

• (a) preparing at least a first collection of nucleic acid molecules from a first genomic source and a second collection of nucleic acid molecules from a second genomic source, wherein said first and second genomic collections have a complexity of 1×108 base pairs or more;
• (b) contacting said first and second collections of nucleic acid molecules with one or more pluralities of distinct oligonucleotide features bound to a surface of a solid support, wherein said one or more pluralities of distinct oligonucleotide features comprise oligonucleotides that range in size from 20 nt to 200 nt in length and said contacting occurs under stringent assay conditions;
• (c) measuring the binding of the first and second collections of nucleic acid molecules to said features to produce data;
• and
• (d) identifying a quantitative difference in the copy number of at least one nucleic acid sequence in said at least two genomic sources using said data.