Utility of B-RAF DNA mutation in diagnosis and treatment of cancer

1. A method of detecting a wild-type or mutant B-RAF gene in a subject, comprising:

obtaining from a subject a body fluid sample containing DNA; and

detecting a wild-type or mutant B-RAF gene in the sample by hybridizing the wild-type B-RAF gene to a peptide nucleic acid clamp and by hybridizing the mutant B-RAF gene to a locked nucleic acid probe,

wherein the mutant B-RAF gene contains a B-RAF V600E mutation.

2. The method of claim 1 , wherein the body fluid sample is a blood, plasma, serum, or cerebral spinal fluid sample.

3. The method of claim 1 , further comprising, prior to the step of detecting, combining in a vessel the body fluid sample, the peptide nucleic acid clamp, and the locked nucleic acid probe.

4. A method of treating cancer in a subject, comprising:

obtaining from a subject a body fluid sample containing DNA;

detecting whether a mutant B-RAF gene is present in the sample by hybridizing the wild-type B-RAF gene to a peptide nucleic acid clamp and by hybridizing the mutant B-RAF gene to a locked nucleic acid probe;

determining that the subject is likely suffering from cancer when the mutant B-RAF gene is present in the sample; and

administering a cancer therapy to the subject likely suffering from cancer, wherein the mutant B-RAF gene contains a B-RAF V600E mutation.

5. The method of claim 4 , wherein the body fluid sample is a blood, plasma, serum, or cerebral spinal fluid sample.

6. The method of claim 4 , wherein the cancer is melanoma, thyroid cancer, colorectal cancer, lung cancer, or neurocancer.

7. A method of treating cancer based on a predicted outcome, comprising:

obtaining a body fluid sample containing DNA from a test subject suffering from cancer;

detecting whether a mutant B-RAF gene is present in the sample by hybridizing the wild-type B-RAF gene to a peptide nucleic acid clamp and by hybridizing the mutant B-RAF gene to a locked nucleic acid probe;

predicting, when the mutant B-RAF gene is present in the sample, that the test subject has a lower probability to survive or to be a responder to cancer therapy than a subject who suffers from cancer but does not have the mutant B-RAF gene; and

administering a cancer therapy to the subject who suffers from cancer but does not have the mutant B-RAF gene,

wherein the mutant B-RAF gene contains a B-RAF V600E mutation.

8. The method of claim 7 , wherein the tissue sample is a paraffin-embedded tissue sample, and the body fluid sample is a blood, plasma, serum, or cerebral spinal fluid sample.

9. The method of claim 7 , wherein the cancer is melanoma, thyroid cancer, colorectal cancer, lung cancer, or neurocancer.

10. The method of claim 7 , wherein the cancer therapy is a biochemotherapy.

11. The method of claim 7 , wherein the sample is obtained from the test subject prior to or following the therapy.

12. A method of monitoring the treatment of cancer, comprising:

obtaining (i) a first tissue or body fluid sample containing DNA from a subject suffering from cancer prior to treating the subject with a cancer therapy, and (ii) a second tissue or body fluid sample containing DNA from the subject after treating the subject with the cancer therapy;

detecting whether a mutant B-RAF gene is present in the first sample and the second sample by hybridizing the wild-type B-RAF gene to a peptide nucleic acid clamp and by hybridizing the mutant B-RAF gene to a locked nucleic acid probe;

determining that the subject is likely to respond to the therapy when the mutant B-RAF gene is present in a lower amount in the second sample as compared to the first sample; and

administering additional cancer therapy to the subject that is likely to respond to the therapy,

wherein the mutant B-RAF gene contains a B-RAF V600E mutation.

13. The method of claim 12 , wherein the tissue sample is a paraffin-embedded tissue sample, and the body fluid sample is a blood, plasma, serum, or cerebral spinal fluid sample.

14. The method of claim 12 , wherein the cancer is melanoma, thyroid cancer, colorectal cancer, lung cancer, or neurocancer.

15. The method of claim 12 , wherein the cancer therapy is a biochemotherapy.

16. The method of claim 12 , further comprising, after the step of detecting, continuing with the cancer therapy if the amount of B-RAF gene after the cancer therapy is less than the amount of the mutant B-RAF gene before the cancer therapy.

17. A method of treating cancer in a subject based on the status of the cancer, comprising:

obtaining a first body fluid sample containing DNA from a subject suffering from cancer at a first time point;

obtaining a second body fluid sample containing DNA from the subject at a second time point subsequent to the first time point;

detecting whether a mutant B-RAF gene is present in the first sample and the second sample by hybridizing the wild-type B-RAF gene to a peptide nucleic acid clamp and by hybridizing the mutant B-RAF gene to a locked nucleic acid probe;

determining (i) that the cancer has likely progressed in the subject when the mutant B-RAF gene is present in a higher amount in the second sample as compared to the first sample or (ii) that the cancer has likely regressed in the subject when the mutant B-RAF gene is present in a lower amount in the second sample as compared to the first sample; and

administering a cancer therapy to the subject determined to have regressed cancer,

wherein the mutant B-RAF gene contains a B-RAF V600E mutation.

18. The method of claim 17 , further comprising, prior to the step of detecting, combining in a vessel the body fluid sample, the peptide nucleic acid clamp, and the locked nucleic acid probe.