Methods for detecting circulating mutant BRAF DNA

• US 7,442,507 B2
• Filed: 01/24/2006
• Issued: 10/28/2008
• Est. Priority Date: 01/24/2005
• Status: Active Grant

• Current Assignee: Sloan-Kettering Institute For Cancer Research (Memorial Sloan-Kettering Cancer Center), New York University
• Original Assignee: Memorial Sloan-Kettering Cancer Center, New York University School of Medicine (New York University)
• Inventors: Chapman, Paul B., Polsky, David, Osman, Iman
• Primary Examiner(s): Benzion; Gary
• Assistant Examiner(s): CALAMITA, HEATHER
• Application Number:
  US11/338,615
• Publication Number:
  US 20060246476A1
• Time in Patent Office: 1,008 Days
• Field of Search: None
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism

Abstract

The present invention relates to a method for detecting the presence of circulating mutant BRAF DNA, which may be present in circulating melanoma cells or as DNA shed from tumor cells. Methods, compositions and kits which employ one or more sets of BRAF mutant specific primer pairs for detection of circulating mutant BRAF DNA are presented. Also provided are methods for diagnosing and/or determining stage/progression of a melanoma in a mammal based on detection of a BRAF mutant nucleic acid sequence. Such methods are also well suited to monitoring disease activity in patients with active disease or those in remission.

Claims

1. A method for diagnosing metastatic melanoma in a subject, said method comprising:

(a) isolating a blood sample from said subject, wherein the blood sample comprises DNA sequences;

(b) performing an amplification reaction of said DNA sequences of said blood sample, wherein said amplification reaction comprises a first primer capable of annealing specifically to a BRAF mutant sequence at a first position in a BRAF DNA sequence wherein said first primer is SEQ ID NO;

6 and a second primer capable of annealing specifically at a second position in a BRAF DNA sequence, wherein said first and second primers anneal to different strands of double stranded BRAF DNA sequence, wherein the amplification reaction is capable of producing a BRAF mutant specific amplification product when the DNA sequences of the sample comprise a BRAF DNA sequence comprising a mutant sequence at said first position of said BRAF DNA sequence; and

(c) visualizing amplification products produced by said amplification reaction, wherein detection of a BRAF mutant specific amplification product is a positive indicator of metastatic melanoma in said subject.

2. The method of claim 1, wherein the blood sample is peripheral blood.

3. The method of claim 2, further comprising removing erythrocytes from said peripheral blood prior to step (b) to produce a population of erythrocyte-depleted peripheral blood cells.

4. The method of claim 1, further comprising isolating DNA sequences from said blood sample.

5. The method of claim 1, wherein said BRAF mutant sequence at a first position in a BRAF nucleic acid sequence comprises a T1799A mutation in BRAF exon 15.

6. The method of claim 1, wherein said second primer capable of annealing specifically at a second position in a BRAF nucleic acid sequence is SEQ ID NO:

4 or SEQ ID NO;

5.

7. The method of claim 1, wherein said method further comprises a preliminary amplification reaction of said DNA sequences of said sample performed prior to the amplification reaction of step (b), and wherein said preliminary amplification reaction comprises first and second primers capable of annealing specifically to a BRAF DNA sequence, wherein said first and second primers anneal to different strands of double stranded BRAF DNA sequence;

and said preliminary amplification reaction produces a BRAF amplification product capable of amplification using said first and second primers of step (b).

8. The method of claim 1, wherein at least one of said first or second primers is fluorescently labeled and amplification products produced by said amplification reaction are fluorescently labeled.

9. A method for detecting metastatic melanoma in a subject, said method comprising:

(a) isolating a blood sample from said subject, wherein the blood sample comprises DNA sequences;

(b) performing an amplification reaction of said DNA sequences of said sample, wherein said amplification reaction comprises a first primer capable of annealing specifically to a BRAF mutant sequence at a first position in a BRAF DNA sequence, wherein said first primer is SEQ ID NO;

6 and a second primer capable of annealing specifically at a second position in a BRAF DNA sequence, wherein said first and second primers anneal to different strands of double stranded BRAF DNA sequence, wherein the amplification reaction is capable of producing a BRAF mutant specific amplification product when the DNA sequences of the sample comprise a BRAF DNA sequence comprising a mutant sequence at said first position of said BRAF DNA sequence; and

(c) visualizing amplification products produced by said amplification reaction, wherein detection of a BRAF mutant specific amplification product is a positive indicator of metastatic melanoma in said subject.

10. The method of claim 9, wherein the blood sample is peripheral blood.

11. The method of claim 9, further comprising removing erythrocytes from said peripheral blood prior to step (b) to produce a population of erythrocyte-depleted peripheral blood cells.

12. The method of claim 9, further comprising isolating DNA sequences from said blood sample.

13. The method of claim 9, wherein said BRAF mutant sequence at a first position in a BRAF nucleic acid sequence comprises a T1799A mutation in BRAF exon 15.

14. The method of claim 9, wherein said second primer capable of annealing specifically at a second position in a BRAF nucleic acid sequence is SEQ ID NO:

4 or SEQ ID NO;

5.

15. The method of claim 9, wherein said method further comprises a preliminary amplification reaction of said DNA sequences of said sample performed prior to the amplification reaction of step (b), and wherein said preliminary amplification reaction comprises first and second primers capable of annealing specifically to a BRAF DNA sequence, wherein said first and second primers anneal to different strands of double stranded BRAF DNA sequence;

and said preliminary amplification reaction produces a BRAF amplification product capable of amplification using said first and second primers of step (b).

16. The method of claim 9, wherein at least one of said first or second primers is fluorescently labeled and amplification products produced by said amplification reaction are fluorescently labeled.

17. A primer comprising the nucleic acid sequence of SEQ ID NO:

6.

18. A primer according to claim 17, wherein said primer is fluorescently labeled.

19. A composition comprising at least one BRAF mutant specific primer and a biologically compatible salt solution, wherein said BRAF mutant specific primer is the primer of claim 17.

20. A method for detecting BRAF mutant status in a subject, said method comprising:

(a) isolating a sample from said subject, wherein said sample is a tumor sample or a blood sample and comprises DNA sequences;

(b) performing an amplification reaction of said DNA sequences of said sample, wherein said amplification reaction comprises a first primer capable of annealing specifically to a BRAF mutant sequence at a first position in a BRAF DNA sequence, wherein said first primer is SEQ ID NO;

6 and a second primer capable of annealing specifically at a second position in a BRAF DNA sequence, wherein said second primer is SEQ ID NO;

4 or SEQ ID NO;

5 wherein said amplification reaction is capable of producing a BRAF mutant specific amplification product when said DNA sequences of said sample comprise a BRAF DNA sequence comprising a mutant sequence at said first position of said BRAF DNA sequence; and

(c) visualizing amplification products produced by said amplification reaction, wherein detection of a BRAF mutant specific amplification product indicates that a BRAF mutant allele is present in said subject.