Detection of amplified or deleted chromosomal regions

DETAILED DESCRIPTION The present invention provides methods and compositions for detecting chromosome abnormalities (such as deletions and amplifications) in a preselected chromosome.
The methods comprise providing a mapped library of labeled probes specific to the chromosome; contacting a chromosome sample from a patient with the library under conditions in which the probes bind selectively with target polynucleotide sequences in the sample to form hybridization complexes; detecting the hybridization complexes; and determining the copy number of each complex.
If the selected chromosome is human chromosome 20 or 17, the preferred libraries are as shown in Table 1 and Table 2, respectively.
The methods are typically carried out using fluorescent in situ hybridization and the probes are labeled with digoxigenin or biotin.
The probes can be used to detect the target sequences in interphase nuclei in the sample.
A reference probe which binds selectively to a sequence within the centromere of the preselected chromosome can be used as a control.
Also provided are methods of detecting specific abnormalities disclosed here.
In particular, methods of detecting an amplification at about position FLpter 0.
85 on human chromosome 20 are disclosed.
The methods comprise contacting a chromosome sample from a patient with a composition consisting essentially of one or more labeled nucleic acid probes each of which binds selectively to a target polynucleotide sequence at about position FLpter 0.
85 on human chromosome 20 under conditions in which the probe forms a stable hybridization complex with the target sequence; and detecting the hybridization complex.
The probes used preferably comprise polynucleotide sequences from cS20.
1.
0A1, cS20.
10B5, cS20.
10H1, or cS20.
10E2.
Also provided are compositions comprising nucleic acid probes which bind selectively to a target polynucleotide sequence at about FLpter 0.
85 on human chromosome 20.
The probes may be labeled for use in the methods of the invention.
The invention further provides kits for the detection of an amplification at about position FLpter 0