Methods for identifying DNA copy number changes

Abstract

Methods of identifying changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.

1 . A method for estimating the copy number of a genomic region in a genomic sample comprising: 
 obtaining a sample comprising genomic DNA;    fragmenting the sample to form fragments;    reducing the complexity of the genomic DNA in the sample by amplifying a subset of the fragments;    hybridizing the amplified fragments to an array of probes wherein the array comprises a plurality of probe sets comprising at least 400,000 different oligonucleotide probes;    detecting an experimental hybridization pattern for the sample from the array;    calculating an intensity measurement for a plurality of probe sets from said experimental hybridization pattern; and    comparing the intensity measurement for a plurality of said probe sets to an intensity measurement from a reference source, to estimate the copy number of at least one genomic region in the sample relative to a reference source.    
     
     
         2 - 50 . (canceled)