Methods and compositions for chromosome-specific staining

• US 6,607,877 B1
• Filed: 06/07/1995
• Issued: 08/19/2003
• Est. Priority Date: 01/16/1986
• 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.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/473,327
• Time in Patent Office: 2,995 Days
• Field of Search: 435/6, 435/810, 436/501, 536/23.1, 536/24.1, 536/24-- 2, 536/25.3, 935/77, 935/78
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• 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 1/6879 for sex determination
• 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 2563/107 fluorescence
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• 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 are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Claims

1. A method of diagnosing a chromosome abnormality in a patient comprising staining target interphase chromosomal DNA with a high complexity nucleic acid probe, wherein the target interphase chromosomal DNA is stained by contacting interphase chromosomal DNA of the patient with a selected DNA probe which comprises a plurality of nucleotide segments complementary to the chromosomal DNA of interest, under conditions appropriate for hybridization of complementary DNA segments to occur, and further wherein the chromosomal DNA is present in a morphologically identifiable cell nucleus during the hybridization;

and detecting hybridization between the interphase chromosomal DNA and the selected DNA probe, the occurrence of hybridization being indicative of the presence of a chromosomal abnormality.

2. The method of claim 1, wherein the chromosome abnormality diagnosed is extra or missing individual chromosomes, extra or missing portions of a chromosome, breaks, rings, or a chromosomal rearrangement.

3. The method of claim 2, wherein the chromosomal rearrangement is a translocation.

4. The method of claim 2, wherein the chromosomal rearrangement is an inversion.

5. The method of claim 1, wherein the chromosomal abnormality is an extra chromosome 21.

6. The method of claim 1, wherein the chromosomal abnormality is a missing chromosome 21.

7. The method of claim 1, wherein the chromosomal abnormality is an extra portion of chromosome 21.

8. The method of claim 1, wherein the chromosomal abnormality is a missing portion of chromosome 21.

9. The method of claim 1, wherein the chromosomal abnormality is a rearrangement of chromosome 21.

10. The method of claim 1, wherein the chromosomal abnormality is a translocation involving chromosome 9 and chromosome 22.

11. The method of claim 1, wherein the chromosomal abnormality is a deletion of chromosome portion 13q14.

12. The method of claim 1, wherein the chromosomal abnormality is a translocation of chromosome 8 and chromosome 14.

13. The method of claim 1, wherein the chromosomal abnormality is an extra chromosome 13, 18, X, or Y.

14. The method of claim 1, wherein the chromosomal abnormality is a translocation of chromosome 4.

15. The method of claim 1, wherein the plurality of nucleotide segments comprises one or more fluorescently-labeled nucleotide segments.

16. The method of claim 1, wherein the plurality of nucleotide segments comprises one or more immunochemically labeled nucleotide segments.

17. The method of claim 1, wherein the plurality of nucleotide segments comprises one or more biotin-labeled nucleotide segments.