Screening methods and sequences relating thereto

• US 7,622,258 B2
• Filed: 03/14/2008
• Issued: 11/24/2009
• Est. Priority Date: 08/03/2001
• Status: Expired due to Fees

• Current Assignee: Myriad Genetics
• Original Assignee: Cardiff University
• Inventors: Cheadle, Jeremy Peter, Sampson, Julian R.
• Primary Examiner(s): Aeder; Sean E
• Application Number:
  US12/048,728
• Publication Number:
  US 20080213784A1
• Time in Patent Office: 620 Days
• Field of Search: 435/6
• US Class Current: 435/6.18
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

A screening method for identifying an individual having a pre-disposition towards having a cancer is disclosed, which screening method comprises the steps of:

• • (a) obtaining a test sample comprising a nucleotide sequence comprised in a gene in a base excision repair (BER) pathway of the individual or an amino acid sequence of a polypeptide expressed thereby; and
  • (b) comparing a region of the test sample sequence with the corresponding region of the wild type sequence,
    whereby a difference between the test sample sequence and the wild type sequence signifies that the individual is pre-disposed to having the cancer; and
  • wherein the difference comprises a specified variation. The specified variation can be the known mutation in the human MYH protein, G382D-hMYH or a nucleotide sequence encoding it, or it can be one or more novel variations, namely, Y165C, E466X, and Y90X, or the respective corresponding nucleotide sequences. The method is particularly suitable for determining a pre-disposition towards bowel cancer.

Claims

1. A method for predicting in an individual the likelihood of developing colorectal cancer, comprising:

determining from a sample obtained from the individual whether the individual has a nucleotide variant in an MYH gene of the individual that results in the amino acid variant G382D, wherein the presence of said nucleotide variant is indicative of an increased likelihood of developing colorectal cancer, wherein if the individual has said nucleotide variant, determining whether the individual is homozygous for said nucleotide variant.

2. The method according to claim 1, wherein said nucleotide variant is at position 1145.

3. The method according to claim 2, wherein said nucleotide variant at position 1145 is G→

A.

4. The method according to claim 1, wherein if the individual has said nucleotide variant, determining whether the individual is compound heterozygous for any other mutations.

5. The method according to claim 1, further comprising determining whether the individual has a second nucleotide variant in the MYH gene of the individual that results in the amino acid variant Y165C, wherein the presence of said second nucleotide variant is also indicative of an increased likelihood of developing colorectal cancer.

6. The method according to claim 5, wherein said second nucleotide variant is at position 494.

7. The method according to claim 6, wherein said second nucleotide variant at position 494 is A→

G.

8. The method according to claim 1, further comprising identifying an individual with colorectal adenomas or cancer, having at least one family member diagnosed with colorectal cancer, or with an increased risk for colorectal cancer.

9. The method according to claim 8, wherein said identifying step is performed before said determining step.

10. The method according to claim 1, wherein said determining step comprises amplifying, from said sample obtained from the individual, the MYH gene, or a portion thereof.

11. The method according to claim 10, further comprising sequencing the amplified MYH gene, or a portion thereof, of the individual.

12. The method according to claim 1, further comprising:

determining whether the individual has a mutation in a second gene, other than the MYH gene, associated with familial adenomatous polyposis (FAP), attenuated FAP (AFAP), or hereditary non-polyposis colorectal cancer (HNPCC) syndrome.

13. The method according to claim 12, wherein said second gene is the APC gene.

19. The method according to claim 1, wherein said determining step comprises hybridizing the MYH gene, or a portion thereof, obtained from a sample from the individual, with an oligonucleotide.

14. A method of genotyping, comprising:

identifying an individual with colorectal adenomas or cancer, having at least one family member diagnosed with colorectal cancer, or with an increased risk for colorectal cancer; and

determining subsequently, from a sample obtained from said identified individual, whether said identified individual has a nucleotide variant in an MYH gene of the individual that results in the amino acid variant G382D.

15. The method according to claim 14, wherein said determining step comprises hybridizing the MYH gene, or a portion thereof, obtained from said sample, with an oligonucleotide.

16. The method according to claim 14, wherein said determining step comprises amplifying, from said sample, the MYH gene, or a portion thereof.

17. The method according to claim 16, further comprising sequencing the amplified MYH gene, or a portion thereof, of the individual.

18. The method according to claim 14, wherein said nucleotide variant comprises a germ-line nucleotide variant.

20. The method according to claim 14, wherein said nucleotide variant is at position 1145.

21. The method according to claim 20, wherein said nucleotide variant at position 1145 is G→

A.

22. The method according to claim 14, wherein if said identified individual has said nucleotide variant, determining whether said identified individual is homozygous for said nucleotide variant.

23. The method according to claim 14, wherein if said identified individual has said nucleotide variant, determining whether said identified individual is compound heterozygous for any other mutations.

24. The method according to claim 14, further comprising determining whether the individual has a second nucleotide variant in the MYH gene of the individual that results in the amino acid variant Y165C.

25. The method according to claim 24, wherein said second nucleotide variant is at position 494.

26. The method according to claim 25, wherein said second nucleotide variant at position 494 is A→

G.

27. A method of genotyping, comprising:

determining from a sample obtained from an individual identified with colorectal adenomas or cancer, having at least one family member diagnosed with colorectal cancer, or with an increased risk for colorectal cancer sample, whether said individual has a nucleotide variant in an MYH gene of the individual that results in the amino acid variant G382D.

28. The method according to claim 27, wherein said determining step comprises hybridizing the MYH gene, or a portion thereof, obtained from said sample, with an oligonucleotide.

29. The method according to claim 27, wherein said determining step comprises amplifying, from said sample, the MYH gene, or a portion thereof.

30. The method according to claim 29, further comprising sequencing the amplified MYH gene, or a portion thereof, of said individual.

31. The method according to claim 27, wherein said nucleotide variant is 1145G→

A.

32. The method according to claim 27, wherein if said individual has said nucleotide variant, determining whether said individual is homozygous for said nucleotide variant.

33. The method according to 27, wherein if said individual has said nucleotide variant, determining whether said individual is compound heterozygous for any other mutations.