Method to determine responsiveness of cancer to epidermal growth factor receptor targeting treatments

Patent metadata

Field	Value
Publication number	US-10000815-B2
Application number	US-201514638779-A
Country	US
Kind code	B2
Filing date	Mar 4, 2015
Priority date	Mar 31, 2004
Publication date	Jun 19, 2018
Grant date	Jun 19, 2018

Abstract

Disclosed herein are methods and reagents for determining the responsiveness of cancer to an epidermal growth factor receptor (EGFR) targeting treatment. The detection of these mutations will allow for the administration of gefitinib, erlotinib and other tyrosine kinase inhibitors to those patients most likely to respond to the drug.

First claim

What is claimed is:

1. A kit comprising:
at least one primer pair designed to anneal to an EGFR nucleic acid, wherein one primer of the pair comprises a sequence that selectively hybridizes to at least one nucleotide variance under high stringency conditions and amplifies the nucleotide variance sequence but does not amplify a corresponding wild type EGFR sequence, wherein the nucleotide variance comprises:
i) a substitution in exon 18 that results in an amino acid change consisting of a substitution of cysteine for glycine at position 719 (G719C) of SEQ ID NO:512, a substitution of serine for glycine at position 719 (G719S) of SEQ ID NO:512, or a substitution of alanine for glycine at position 719 (G719A) of SEQ ID NO:512;
ii) an in-frame deletion in exon 19 that results in one or more amino acid changes comprising a deletion of at least amino acids leucine, arginine, and glutamic acid at position 747, 748, and 749 of SEQ ID NO:512;
iii) a substitution in exon 20 that results in an amino acid change at position 790 of SEQ ID NO:512; or
iv) a substitution in exon 21 that results in an amino acid change consisting of a substitution of arginine for leucine at position 858 (L858R) of SEQ ID NO:512, or a substitution of glutamine for leucine at position 861 (L861Q) of SEQ ID NO:512;
wherein one or more primers comprise at least one non-naturally occurring nucleobase, peptide nucleic acid, or a label, and the at least one primer pair is located in one or more containers.

2. The kit of claim 1 , wherein the nucleotide variance is a substitution in exon 18 that results in an amino acid change consisting of a substitution of cysteine for glycine at position 719 (G719C) of SEQ ID NO:512.

3. The kit of claim 1 , wherein the nucleotide variance is a substitution in exon 18 that results in an amino acid change consisting of a substitution of serine for glycine at position 719 (G719S) of SEQ ID NO:512, or is a substitution in exon 18 that results in an amino acid change consisting of a substitution of alanine for glycine at position 719 (G719A) of SEQ ID NO:512.

4. The kit of claim 1 , wherein the nucleotide variance is a mutation that results in an in-frame deletion in exon 19 of the EGFR gene consisting of a deletion within codons 746 to 753 that results in amino acid changes comprising a deletion of at least amino acids leucine, arginine, and glutamic acid at position 747, 748, and 749 of SEQ ID NO:512.

5. The kit of claim 1 , wherein the nucleotide variance is a substitution in exon 21 that results in an amino acid change consisting of a substitution of arginine for leucine at position 858 (L858R) of SEQ ID NO:512.

6. The kit of claim 1 , wherein the nucleotide variance is a substitution of glutamine for leucine at position 861 (L861Q) of SEQ ID NO:512.

7. The kit of claim 1 , wherein one or more of the primers comprises a label.

8. The kit of claim 7 , wherein the label comprises a fluorescent molecule, a chemiluminescent moiety or a bioluminescent moiety.

9. The kit of claim 1 , wherein one or more of the primers is affixed to the surface of a solid support.

10. The kit of claim 9 , wherein the solid support is a microarray.

11. The kit of claim 1 , further comprising reagents for PCR amplification.

12. The kit of claim 1 , wherein the kit comprises at least two primer pairs to detect at least two different variances.

13. The kit of claim 12 , wherein the at least two primer pairs are differentially labeled to differentiate between the variances.

14. The kit of claim 1 , further comprising an allele specific oligonucleotide probe specific for a nucleotide variance, wherein the probe comprises a detectable label.

15. A primer pair designed to anneal to an EGFR nucleic acid, wherein one primer of the pair comprises a sequence that selectively hybridizes to at least one nucleotide variance under high stringency conditions and amplifies the nucleotide variance sequence but does not amplify a corresponding wild type EGFR sequence, wherein the nucleotide variance comprises:
i) a substitution in exon 18 that results in an amino acid change consisting of
a substitution of cysteine for glycine at position 719 (G719C) of SEQ ID NO:512, a substitution of serine for glycine at position 719 (G719S) of SEQ ID NO:512, or a substitution of alanine for glycine at position 719 (G719A) of SEQ ID NO:512;
ii) an in-frame deletion in exon 19 that results in one or more amino acid changes comprising a deletion of at least amino acids leucine, arginine, and glutamic acid at position 747, 748, and 749 of SEQ ID NO:512;
iii) a substitution in exon 20 that results in an amino acid change at position 790 of SEQ ID NO:512; or
iv) a substitution in exon 21 that results in an amino acid change consisting of a substitution of arginine for leucine at position 858 (L858R) of SEQ ID NO:512, or a substitution of glutamine for leucine at position 861 (L861Q) of SEQ ID NO:512;
wherein one or more primers comprise at least one non-naturally occurring nucleobase, peptide nucleic acid, or a label.

16. The primer pair of claim 15 , wherein one or more of the primers comprise a label.

17. The primer pair of claim 16 , wherein the label comprises a fluorescent molecule, a chemiluminescent moiety or a bioluminescent moiety.

18. The primer pair of claim 15 , wherein one or more of the primers is affixed to the surface of a solid support.

19. The primer pair of claim 15 , wherein the solid support is a microarray.

20. The primer pair of claim 15 that is packaged into a container.

21. The primer pair of a claim 15 that is in lyophilized form.

22. The primer pair of claim 15 , wherein the nucleotide variance is a substitution in exon 18 that results in an amino acid change consisting of a substitution of cysteine for glycine at position 719 (G719C) of SEQ ID NO:512.

23. The primer pair of claim 15 , wherein the nucleotide variance is a substitution in exon 18 that results in an amino acid change consisting of a substitution of serine for glycine at position 719 (G719S) of SEQ ID NO:512, or is a substitution in exon 18 that results in an amino acid change consisting of a substitution of alanine for glycine at position 719 (G719A) of SEQ ID NO:512.

24. The primer pair of claim 15 , wherein the nucleotide variance is a mutation that results in an in-frame deletion in exon 19 of the EGFR gene consisting of a deletion within codons 746 to 753 that results in amino acid changes comprising a deletion of at least amino acids leucine, arginine, and glutamic acid at position 747, 748, and 749 of SEQ ID NO:512.

25. The primer pair of claim 15 , wherein the nucleotide variance is a substitution in exon 21 that results in an amino acid change consisting of a substitution of arginine for leucine at position 858 (L858R) of SEQ ID NO:512.

26. The primer pair of claim 15 , wherein the nucleotide variance is a substitution of glutamine for leucine at position 861 (L861Q) of SEQ ID NO:512.

27. A kit comprising:
a) at least one primer pair designed to anneal to an EGFR nucleic acid, wherein one primer of the pair comprises a sequence that selectively hybridizes to at least one nucleotide variance under high stringency conditions and amplifies the nucleotide variance sequence but does not amplify a corresponding wild type EGFR sequence, wherein the nucleotide variance comprises:
i) a substitution in exon 18 that results in an amino acid change co

Assignees

• Massachusetts Gen Hospital
• Dana Farber Cancer Inst Inc
• Massachusetts Gen Hospital
• Dana Farber Cancer Inst Inc

Inventors

• Bell Daphne Winifred
• Haber Daniel A
• Janne Pasi Antero
• Johnson Bruce E
• Lynch Thomas J
• Meyerson Matthew
• Paez Juan Guillermo
• Sellers William R
• Settleman Jeffrey E
• Sordella Raffaella

Classifications

• A61P43/00

  Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00 · CPC title

• A61P35/00

  Antineoplastic agents · CPC title

• G01N33/575

  for cancer · CPC title

• G01N2333/485

  Epidermal growth factor [EGF] (urogastrone) · CPC title

• C12Q1/485

  involving kinase · CPC title