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

FIELD OF THE INVENTION 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 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 a result of genomic instability, cancer cells accumulate both random and causal alterations at multiple levels from point mutations to whole-chromosome aberrations. DNA copy number changes include, but are not limited to, loss of heterozygosity (LOH) and homozygous deletions, which can result in the loss of tumor suppressor genes, and gene amplification events, wh...

AI Technical Summary

Benefits of technology

Methods for estimating the copy number of a genomic region in a genomic sample are disclosed. In one embodiment a sample comprising genomic DNA is fragmented and a subset of the fragments are amplified, thereby reducing the complexity of the genomic DNA in the sample. The amplified fragments are hybridized to an array of probes comprises comprising at least 400,000 different oligonucleotide probes organized into a plurality of probe sets. An experimental hybridization pattern for the sample is obtained from the array and an intensity measurement is calculated for a plurality of the probe sets. The calculated intensity measurement for at least one probe set is compared to an intensity measurement from a reference source to estimate the copy number of the region targeted by that probe set.

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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