BRAF mutation T1796A in thyroid cancers

• US 7,378,233 B2
• Filed: 04/09/2004
• Issued: 05/27/2008
• Est. Priority Date: 04/12/2003
• Status: Active Grant

• Current Assignee: Johns Hopkins University
• Original Assignee: Johns Hopkins University
• Inventors: Cohen, Yoram, Xing, Mingzhao, Sidransky, David
• Primary Examiner(s): Canella; Karen A.
• Application Number:
  US10/821,203
• Publication Number:
  US 20050048533A1
• Time in Patent Office: 1,509 Days
• Field of Search: None
• US Class Current: 435/4
• 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
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The BRAF gene has been found to be activated by mutation in human cancers, predominantly in malignant melanoma. We tested 476 primary tumors, including 214 lung, 126 head and neck, 54 thyroid, 27 bladder, 38 cervical, and 17 prostate cancers, for the BRAF T1796A mutation by polymerase chain reaction (PCR)-restriction enzyme analysis of BRAF exon 15. In 24 (69%) of the 35 papillary thyroid carcinomas examined, we found a missense thymine (T)→adenine (A) transversion at nucleotide 1796 in the BRAF gene (T1796A). The T1796A mutation was detected in four lung cancers and in six head and neck cancers but not in bladder, cervical, or prostate cancers. Our data suggest that activating BRAF mutations may be an important event in the development of papillary thyroid cancer. Moreover, BRAF mutation reliably predicts a poor prognosis for papillary thyroid carcinomas.

Claims

1. A method for distinguishing malignant papillary from benign thyroid samples, comprising:

determining presence of a T→

A transversion at nucleotide 1796 of BRAF according to SEQ ID NO;

1 in a thyroid sample of a human, wherein presence of the transversion indicates a malignant papillary neoplasm and absence of the transversion indicates a benign neoplasm or sample.

2. The method of claim 1 wherein the thyroid sample is a fine needle aspirate (FNA).

3. The method of claim 1 wherein the thyroid sample is a tissue sample.

4. The method of claim 1 wherein the thyroid sample is a cytological sample.

5. The method of claim 1 further comprising:

providing a diagnosis based on the presence or absence of the transversion.

6. The method of claim 1 further comprising:

providing a prognosis based on the presence or absence of the transversion.

7. The method of claim 6 wherein if the human has the transversion the prognosis indicates that the human has a higher risk of neck lymph node metastasis than a human without the transversion, and if the human does not have the transversion the prognosis indicates that the human has a lower risk of neck lymph node metastasis than a human with the transversion.

8. The method of claim 6 wherein if the human has the transversion the prognosis indicates that the human has a higher risk of cancer recurrence than a human without the transversion, and if the human does not have the transversion the prognosis indicates that the human has lower risk of cancer recurrence than a human with the transversion.

9. The method of claim 1 further comprising:

determining a therapeutic regimen for the human using as a factor the presence or absence of the transversion.

10. The method of claim 3 wherein the sample has a follicular morphology.

11. The method of claim 3 wherein the sample as a papillary morphology.

12. A method of detecting a malignant papillary thyroid neoplasm in a human suspected of having a thyroid neoplasm, comprising:

determining presence of a T→

A transversion at nucleotide 1796 of BRAF according to SEQ ID NO;

1 in a blood sample of a human suspected of having a thyroid neoplasm, wherein presence of the transversion indicates a malignant papillary thyroid neoplasm in the human and absence of the transversion indicates a benign thyroid neoplasm or no neoplasm.

13. A method for detecting a T→

A transversion mutation at nucleotide 1796 of BRAF according to SEQ ID NO;

1, comprising;

amplifying all or part of exon 15 of BRAF from a thyroid test sample to form amplified products, wherein said part comprises at least nucleotides 1792 to 1799 of BRAF;

digesting the amplified products with restriction endonuclease TspRI to form digested products;

identifying a mutation at nucleotide 1796 if the digested products contain;

one fragment fewer than digested products formed when using wild-type BRAF as a template for amplifying and digesting;

or

one additional fragment compared to digested products formed when using wild-type BRAF as a template for amplifying or digesting.

14. The method of claim 13 wherein the test sample is an FNA from a thyroid.

15. The method of claim 13 wherein the test sample is a tissue sample from a thyroid.