Array-based detection of genetic alterations associated with disease

• US 6,210,878 B1
• Filed: 08/08/1997
• Issued: 04/03/2001
• Est. Priority Date: 08/08/1997
• Status: Expired due to Term

• 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., Albertson, Donna G.
• Primary Examiner(s): CANELLA, KAREN A
• Application Number:
  US08/908,855
• Time in Patent Office: 1,334 Days
• Field of Search: 435/6, 435/7.23, 435/810, 435/975, 436/64, 436/813, 536/24.31
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 33/57415 of breast
• CPC Class Codes: Y10S 435/81 Packaged device or kit
• CPC Class Codes: Y10S 435/975 Kit
• CPC Class Codes: Y10S 436/813 Cancer

Abstract

The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.

Claims

1. A method of screening for the presence of breast cancer cells in a sample, the method comprising:

contacting a nucleic acid sample from a human patient with a probe which binds selectively to a target polynucleotide sequence on a region in which copy number is altered in breast cancer cells and is selected from the group consisting of Flpter 0.603, 0.646, 0.675 0.694, 0.772 or 0.867 on chromosome 20, wherein the probe is contacted with the sample under conditions in which the probe binds selectively with the target polynucleotide sequence to form a stable hybridization complex; and

detecting the formation of a hybridization complex.

2. The method of claim 1, wherein the step of detecting the hybridization complex comprises determining the copy number of the target sequence.

3. The method of claim 1, wherein the probe is labeled with digoxigenin or biotin.

4. The method of claim 1, wherein the step of detecting the hybridization complex is carried out by detecting a fluorescent label.

5. The method of claim 4, wherein the fluorescent label is FICT or Texas red.

6. The method of claim 1, wherein the sample is a tissue section.

7. The method of claim 1, wherein the sample comprises a metaphase cell.

8. The method of claim 1, wherein the sample comprises an interphase cell.

9. The method of claim 1, wherein the sample nucleic acids are from a test cell and a reference cell.

10. The method of claim 1, wherein the probe is a member of a nucleic acid array.

11. A kit for the detection of a chromosome abnormality correlated with breast cancer, the kit comprising a compartment which contains more than one nucleic acid probe which binds selectively to a target polynucleotide sequence in a region of a chromosome correlated with breast cancer, wherein the probes bind selectively with the target polynucleotide sequence selected from the group consisting of Flpter 0.603, 0.646, 0.675, 0.694, 0.722 and 0.867 on chromosome 20.