Method of detecting genetic translocations identified with chromosomal abnormalities

• US 6,280,929 B1
• Filed: 06/07/1995
• Issued: 08/28/2001
• 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: Tkachuk, Douglas, Pinkel, Daniel, Gray, Joe W.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/487,974
• Time in Patent Office: 2,274 Days
• Field of Search: 435/6, 435/810, 436/501, 536/23.1, 536/24.1, 536/24-3, 536/33, 536/25.3, 935/77.78
• US Class Current: 435/6.11
• 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 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. A method of staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of at least 40 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations, wherein each probe comprises a distinct fluorescent label;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization; and

(c) observing the proximity or overlap of the regions stained by each probe, to determine whether said translocation is present in the interphase cell.

2. The method according to claim 1, wherein the translocation is associated with a cancer.

3. The method according to claim 2, wherein said cancer is CML and a first probe is substantially complementary to at least a part of a BCR gene on chromosome 22 and a second probe is substantially complementary to at least a part of a ABL gene on chromosome 9.

4. The method according to claim 3, wherein the BCR probe comprises 18 kb and comprises part of, and extends centromeric to, the 5.8 kb breakpoint cluster region of the BCR gene.

5. The method according to claim 3, wherein the ABL probe comprises 35 kb and is telomeric to the 200 kb region of ABL between exons IB and II.

6. The method according to claim 3, wherein the BCR probe is labeled with biotin and the ABL probe is labeled with dioxigenin.

7. The method according to claim 3, wherein the BCR probe is labeled with dioxigenin and the ABL probe is labeled with biotin.

8. The method according to claim 3, wherein the BCR hybridization complex and the ABL hybridization complex are than 1 micron from each other.

9. The method according to claim 1, further comprising adding blocking nucleic acid that comprises fragments which are substantially complementary to repetitive segments in the targeted chromosomal DNA.

10. The method according to claim 1, wherein the hybridization capacity of repetitive segments of the nucleic acid is disabled.

11. The method according to claim 1, wherein the probes are labeled such that a dual color fluorescence is produced.

12. The method according to claim 1, wherein the translocation is associated with Burkitts lymphoma.

13. The method according to claim 1, wherein said probes have a combined complexity of between about 40 kb and 750 kb.

14. The method according to claim 13, wherein said probes have a combined complexity of between about 50 kb and 400 kb.

15. The method according to claim 1, wherein said probe is labeled with a direct label or an affinity label.

23. The method according to claim 1, wherein said probes have a combined complexity of between about 50 kb and 1 Mb.

28. The method according to claim 1, wherein said probes have a combined complexity of between about 50 kb and 750 kb.

16. A method of distinguishing normal and malignant cells comprising staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities of malignant cells, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of at least 40 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations, wherein each probe comprises a distinct fluorescent label;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization;

(c) observing the proximity or overlap of the regions stained by each probe to determine whether said translocation is present in the interphase cell, wherein said translocation is indicative of a malignant cell.

17. A method of determining prognosis for a patient and/or determining the effectiveness of a therapy comprising staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities of malignant cells, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of at least 40 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations, wherein each probe comprises a distinct fluorescent label;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization;

(c) observing the proximity or overlap of the regions stained by each probe to determine whether said translocation is present in the interphase cell, wherein the occurrence of a translocation is indicative of the prognosis of the patient and/or the effectiveness of therapy.

18. A method according to claim 17, wherein the therapy is selected from the group consisting of chemotherapy, radiation, surgery and transplantation.

19. A method of staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of at least 40 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization;

(c) adding a distinct fluorescent label to each of said nucleic acid probes; and

(d) observing the proximity or overlap of the regions stained by each probe, to determine whether said translocation is present in the interphase cell.

20. The method according to claim 19, wherein said label is a direct label or an affinity label.

21. The method according to claim 19, wherein one of said nucleic acid probes is labeled with biotin.

22. The method according to claim 19, wherein one of said nucleic acid probes is labeled with dioxigenin.

24. The method according to claim 19, wherein said probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank breakpoint regions known to be associated with genetic translocations.

25. The method according to claim 19, wherein said probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that extend partially across breakpoint regions known to be associated with genetic translocations.

26. The method according to claim 19, wherein said probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that extend fully across breakpoint regions known to be associated with genetic translocations.

27. A method of staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of about 50 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations, wherein each probe comprises a distinct fluorescent label;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization; and

(c) observing the proximity or overlap of the regions stained by each probe, to determine whether said translocation is present in the interphase cell.

29. A method of distinguishing normal and malignant cells comprising staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities of malignant cells, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of about 50 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations, wherein each probe comprises a distinct fluorescent label;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization;

(c) observing the proximity or overlap of the regions stained by each probe to determine whether said translocation is present in the interphase cell, wherein said translocation is indicative of a malignant cell.

30. A method of determining prognosis for a patient and/or determining the effectiveness of a therapy comprising staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities of malignant cells, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of about 50 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations, wherein each probe comprises a distinct fluorescent label;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization;

(c) observing the proximity or overlap of the regions stained by each probe to determine whether said translocation is present in the interphase cell, wherein the occurrence of a translocation is indicative of the prognosis of the patient and/or the effectiveness of therapy.

31. A method of staining target chromosomal DNA to detect in an interphase cell one or more genetic translocations identified with chromosomal abnormalities, said method comprising:

(a) providing a heterogeneous mixture of two or more nucleic acid probes having a combined complexity of about 50 kb, which probes contain nucleic acid segments which are substantially complementary to nucleic acid segments that flank and/or extend partially or fully across breakpoint regions known to be associated with genetic translocations;

(b) reacting the heterogeneous mixture with the targeted chromosomal DNA by in situ hybridization;

(c) adding a distinct fluorescent label to each of said nucleic acid probes; and

(d) observing the proximity or overlap of the regions stained by each probe, to determine whether said translocation is present in the interphase cell.