DDR2 mutations in squamous cell lung cancer

Patent metadata

Field	Value
Publication number	US-10385403-B2
Application number	US-201615294068-A
Country	US
Kind code	B2
Filing date	Oct 14, 2016
Priority date	Apr 2, 2012
Publication date	Aug 20, 2019
Grant date	Aug 20, 2019

Abstract

Methods for treating patients with squamous cell lung cancer, including detecting the presence of mutations in the discoidin domain receptor 2 (DDR2) gene.

First claim

What is claimed is:

1. A method comprising:
performing an assay to determine a nucleic acid sequence of all or part of a discoidin domain receptor 2 (DDR2) gene in a sample comprising nucleated cells from a squamous cell carcinoma (SCC) in a subject,
wherein the assay comprises contacting the DDR2 gene with a nucleic acid probe that specifically hybridizes with a sequence encoding at least one amino acid variation relative to a reference amino acid sequence, and wherein the at least one amino acid variation is L63V, 1120M, D125Y, G253C, G505S, C580Y, T765P, G774V, or G774E; and
detecting in the sample the nucleic acid sequence encoding at least one amino acid variation of L63V, 1120M, D125Y, G253C, G505S, C580Y, T765P, G774E, or G774V in the DDR2 gene.

2. The method of claim 1 , wherein the subject is human and the reference amino acid sequence comprises SEQ ID NO:1.

3. The method of claim 1 , wherein the reference sequence is obtained from non-cancerous cells of the same subject.

4. The method of claim 1 , wherein the at least one amino acid variation comprises a non-conservative amino acid substitution.

5. The method of claim 1 , wherein the at least one amino acid variation is within a kinase domain or discoidin domain of DDR2.

6. The method of claim 1 , comprising determining a nucleic acid sequence of a coding region of a discoidin domain receptor 2 (DDR2) gene.

7. A method comprising:
performing an assay to determine a nucleic acid sequence of all or part of a discoidin domain receptor 2 (DDR2) gene in a sample comprising nucleated cells from a squamous cell carcinoma (SCC) in a subject, wherein the assay comprises contacting the DDR2 gene with an allele-specific oligonucleotide probe that specifically amplifies a sequence encoding at least one amino acid variation of L63V, 1120M, D125Y, G253C, G505S, C580Y, T765P, G774E, or G774V, relative to a reference amino acid sequence of DDR2; and
detecting in the sample the nucleic acid sequence encoding at least one amine acid variation of L63V, 1120M, D125Y, G253C, G505S, C580Y, T765P, G774E, or G774V in the DDR2 gene.

8. The method of claim 7 , wherein the subject is human and the reference amino acid sequence comprises SEQ ID NO:1.

9. The method of claim 7 , wherein the reference sequence is obtained from non-cancerous cells of the same subject.

10. The method of claim 7 , wherein the at least one amino acid variation comprises a non-conservative amino acid substitution.

11. The method of claim 7 , wherein the at least one amino acid variation is within a kinase domain or discoidin domain of DDR2.

12. The method of claim 7 , comprising determining a nucleic acid sequence of a coding region of a discoidin domain receptor 2 (DDR2) gene.

Assignees

• Broad Inst Inc
• Dana Farber Cancer Inst Inc

Inventors

• Meyerson Matthew
• Hammerman Peter
• Ramos Alexis

Classifications

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/68

  involving nucleic acids · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q2600/106

  Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism · CPC title