Rapid Comparative Genome Hybridization

• US 20090069191A1
• Filed: 01/26/2006
• Published: 03/12/2009
• Est. Priority Date: 01/27/2005
• Status: Active Grant

• Current Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Original Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Inventors: McCaskill, Christopher, Mohammed, Mansoor S., Dzidic, Natasa
• Granted Patent: US 8,021,888 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 2523/313 Irradiation, e.g. UV irradiation
• CPC Class Codes: Y10S 436/80 Fluorescent dyes, e.g. rhodamine
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Disclosed is a method for performing nucleic acid hybridization assays, such as assays used for detecting and mapping chromosomal or genetic abnormalities associated with various diseases or associated with predisposition to various diseases. In a particular aspect, the present method relates to the use of rapid nucleic acid hybridization methods for comparing nucleic acid segments of one genome to corresponding nucleic acid segments in another genome(s).

Claims

1. A method for performing nucleic acid hybridization to immobilized nucleic acid, comprising the following steps:

a) contacting a solid support comprising one or more immobilized nucleic acid probe molecules under hybridization conditions with a non-specific blocking nucleic acid at a concentration of at least about 1 mg/ml, said one or more immobilized nucleic acid probe molecules capable of hybridizing with a sequence complementary thereto;

b) contacting the solid support under hybridization conditions with a test sample containing nucleic acid target molecules;

c) applying acoustic surface waves to the hybridization of step a) or step

b) or both; and

d) determining whether the one or more nucleic acid probes of the solid support have hybridized to test sample nucleic acid target molecules.

2. The method of claim 1 further comprising the step of washing following step a), b) or both step a) and b).

3. The method of claim 2 wherein said washing further includes application of acoustic surface waves to the washing step.

4. The method of claim 1 wherein hybridization in step b) further comprises addition of a non-specific blocking nucleic acid.

5. The method of claim 4 wherein said non-specific blocking nucleic acid is added at a concentration of at least about 1 mg/ml.

6. The method of claim 5, wherein the non-specific blocking nucleic acid comprises Cot-1 DNA.

7. The method of claim 1, wherein step a) and b) are performed for less than about 3 hours.

8. The method of claim 2, wherein said washing is performed for less than about 1 hour.

9. The method of claim 1, wherein step a) or b) is performed for less than about 1 hour.

10. The method of claim 1, wherein the method is performed in less than about 5 hours.

11. The method of claim 1, further comprising labeling the one or more nucleic acid target molecules.

12. The method of claim 1, wherein the method is performed in less than about 8 hours.

13. The method of claim 1, wherein the one or more nucleic acid probes comprises one or more bacterial artificial chromosomes.

14. The method of claim 1, wherein the non-specific blocking nucleic acid comprises Cot-1 DNA.

15. The method of claim 1 further comprising contacting with one or more reference sample nucleic acid target molecules in the hybridization of step b).

16. The method of claim 15 wherein said reference sample and said test sample nucleic acid target molecules are labeled.

17. The method of claim 1 wherein the support comprises an array of immobilized nucleic acid probe molecules.

18. A method for performing nucleic acid hybridization to immobilized nucleic acid, comprising the following steps:

a) contacting a solid support containing one or more immobilized nucleic acid probe molecules under hybridization conditions with a nucleic acid test sample containing one or more nucleic acid target molecules, said one or more immobilized nucleic acid probe molecules capable of hybridizing with a sequence complementary thereto;

b) applying acoustic surface waves to the hybridization of step a); and

c) determining whether the one or more nucleic acid probes of the solid support have hybridized to test sample nucleic acid target molecules.

19. The method of claim 18 further comprising the step of washing following step a).

20. The method of claim 19 where said washing further includes application of acoustic surface waves to the solid support during the washing step.

21. The method of claim 18 wherein step a) is performed for less than about 3 hours.

22. The method of claim 19 wherein said washing is performed for less than about 1 hour.

23. The method of claim 18 wherein step a) is performed for less than about 1 hour.

24. The method of claim 18 wherein the method is performed in less than about 5 hours.

25. The method of claim 18 further comprising labeling the one or more nucleic acid target molecules.

26. The method of claim 18 wherein the method is performed in less than about 8 hours.

27. The method of claim 18 wherein the immobilized nucleic acid probes comprises one or more bacterial artificial chromosomes.

28. The method of claim 18 wherein said hybridization further comprises non-specific blocking nucleic acid

29. The method of claim 28 wherein said non-specific blocking nucleic acid is added at a concentration of at least about 1 mg/ml.

30. The method of claim 28 wherein the non-specific blocking nucleic acid comprises Cot-1 DNA.

31. The method of claim 18 wherein a reference sample nucleic acid is included in the hybridization.

33. The method of claim 18 wherein the solid support is prehybridized to a non-specific blocking nucleic acid prior to the hybridization step of step a).

34. The method of claim 33 wherein said non-specific blocking nucleic acid is added at a concentration of at least about 1 mg/ml.

35. The method of claim 33 wherein the non-specific blocking nucleic acid comprises Cot-1 DNA.

36. The method of claim 33 further comprising the step of washing following the prehybridization.

37. The method of claim 33 where said washing following prehybridization further includes application of acoustic surface waves.

38. The method of claim 18 wherein the support comprises an array of immobilized nucleic acid probe molecules.

32. The method of claim 32 wherein said reference sample and said test sample are labeled.