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.

Description

RELATED APPLICATIONS [0001] This application is a continuation of U.S. patent application Ser. No. 10 / 712,616 which claims the priority of U.S. Provisional Application No. 60 / 319,685 filed Nov. 11, 2002, 60 / 319,750 filed Dec. 3, 2002 and 60 / 467,105 filed Apr. 30, 2003, the disclosures of which are incorporated herein by reference in their entireties.FIELD OF THE INVENTION [0002] The invention is related to methods of estimating the number of copies of a genomic region that are present in a sample. Specifically, this invention provides methods, computer software products and systems for the detection of regions of chromosomal amplification and deletion from a biological sample. BACKGROUND OF THE INVENTION [0003] The underlying progression of genetic events which transform a normal cell into a cancer cell is characterized by a shift from the diploid to anueploid state (Albertson et al. (2003), Nat Genet, Vol. 34, pp. 369-76 and Lengauer et al. (1998), Nature, Vol. 396, pp. 643-9). As ...

AI Technical Summary

Benefits of technology

The patent describes methods for estimating the copy number of a specific part of DNA in a sample. This is important for understanding the genetic material of an organism. The methods involve breaking down the DNA into smaller fragments and amplifying them, then using a special technique to measure the intensity of the DNA fragments. This intensity measurement is compared to a reference to estimate the copy number of the DNA region. The patent also describes a variation where the DNA fragments are labeled and hybridized to a specific part of the DNA, and the resulting signal is compared to a control to estimate the copy number. Overall, the methods described in the patent make it possible to accurately measure the number of copies of a specific part of DNA in a sample.

Problems solved by technology

One of the continuing challenges to unraveling the complex karyotype of the tumor cell is the development of improved molecular methods that can globally catalogue LOH, gains, and losses with both high resolution and accuracy.

Hybridization to metaphase chromosomes, however, limits the resolution to 10-20 Mb, precluding the detection of small gains and losses.

While the use of arrayed cDNA clones allows analysis of transcriptionally active regions of the genome, the hybridization kinetics may not be as uniform as when using large genomic clones.

Currently, the availability of BAC clones spanning the genome limits the resolution of CGH to 1-2 Mb.

CGH, however, is not well-suited to identify regions of the genome which have undergone LOH such that a single allele is present but there is no reduction in copy number.

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