Chromosome-specific staining to detect genetic rearrangements

• US 20040235039A1
• Filed: 06/09/2004
• Published: 11/25/2004
• Est. Priority Date: 03/20/1990
• Status: Abandoned Application

• Current Assignee: Regents of the University of California (University of California)
• Original Assignee: Regents of the University of California (University of California)
• Inventors: Pinkel, Daniel, Gray, Joe W., Tkachuk, Douglas
• Application Number:
  US10/863,370
• Publication Number:
  US 20040235039A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2539/101 Subtraction analysis
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Claims

1-126. -126. (Canceled).

127. A method of detecting a chromosomal translocation resulting in a fusion gene between BCR and ABL, said fusion gene associated with cancer, said method comprising:

(a) preparing at least two nucleic acid probes, each labeled with a distinguishable label, wherein a first of said probes hybridizes to the BCR gene side of the translocation, and the second probe hybridizes to a part of the ABL gene;

(b) contacting said probes to chromosomes under conditions of appropriate stringency to allow specific hybridization of the probes to complementary DNA sequences in the chromosomes;

(c) detecting the presence of hybridized probes; and

(d) identifying the chromosomal translocation by the labeling pattern of the probes relative to the chromosomes;

wherein said translocation results in a fusion gene that encodes either of two proteins designated as p190 and p210.