Detection of CYP1A1, CYP3A4, CYP2D6 and NAT2 variants by PCR-allele-specific oligonucleotide (ASO) assay

• US 6,183,963 B1
• Filed: 10/23/1998
• Issued: 02/06/2001
• Est. Priority Date: 10/23/1998
• Status: Expired due to Term

• Current Assignee: Autogenomics
• Original Assignee: Signalgene Inc.
• Inventors: Labuda, Damian, Sinnett, Daniel
• Primary Examiner(s): Fredman, Jeffrey
• Assistant Examiner(s): CHAKRABARTI, ARUN K
• Application Number:
  US09/177,359
• Time in Patent Office: 837 Days
• Field of Search: 435/6, 435/91.2, 435/803, 436/501, 536/24.31, 536/24.33
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: Y10S 435/803 Physical recovery methods, e.g. chromatography, grinding

Abstract

The present invention relates to a method of detecting genetic variation in individuals by PCR amplification of the locus of interest, transferring the resulting PCR products to a membrane filter, hybridizing with allele-specific-oligonucleotides (ASOs), and visualizing the results. Such a method is in the field of diagnostics, pharmacogenetics, cancer therapeutics, and drug metabolism. In particular, the present invention relates to the detection of genetic polymorphisms in gene encoding xenobiotics metabolizing enzymes CYP1A1, CYP2D6, CYP3A4, and NAT2.

Claims

1. An isolated oligonucleotide molecule comprising a mutant allele of CYP1A1, which contains a point mutation at one position selected from the group consisting of position 4887, 4889, and 6235.

2. An isolated oligonucleotide molecule of claim 1, wherein said mutation is selected from the group consisting of an adenine at position 4887, a guanine at position 4889 and a cytosine at position 6235.

3. An isolated oligonucleotide molecule of claim 2, wherein said mutant oligonucleotide molecule has a nucleic acid sequence as set forth in SEQ ID NOS:

27, 28 and 31.

4. An isolated oligonucleotide molecule comprising a wild-type allele of CYP1A1, wherein said normal nucleotide is selected from the group consisting of a cytosine at position 4887, a adenine at position 4889 and a thymine at position 6235.

5. An isolated oligonucleotide molecule as claimed in 4, wherein said wild type oligonucleotide molecule has a nucleic acid sequence as set forth in SEQ ID NOS:

26, 29 and 30.

6. An isolated oligonucleotide molecule comprising a mutant allele of CYP3A4, contains a point mutation at position 290.

7. An isolated oligonucleotide molecule of claim 6, wherein said mutation is a guanine.

8. An isolated oligonucleotide molecule of claim 7, wherein said mutant oligonucleotide molecule has a nucleic acid sequence as set forth in SEQ ID NO:

37.

9. An isolated oligonucleotide molecule comprising a mutant allele of CYP2D6, which contains a point mutation at one position selected from the group consisting of position 1934 and 2637.

10. An isolated oligonucleotide molecule of claim 9, wherein said mutation is selected from the group consisting of an adenine at position 1934 and a deletion at position 2637.

11. An isolated oligonucleotide molecule of claim 10, wherein said mutant oligonucleotide molecule has a nucleic acid sequence as set forth in SEQ ID NOS:

33 and 35.

12. An isolated oligonucleotide molecule comprising a wild-type allele of CYP2D6, wherein said normal nucleotide is selected from the group consisting of a guanine at position 1934 and an adenine at position 2637.

13. An isolated oligonucleotide molecule as claimed in 12, wherein said wild type oligonucleotide molecule has a nucleic acid sequence as set forth in SEQ ID NOS:

32 and 34.

14. An isolated oligonucleotide molecule comprising a mutant allele of NAT2, which contains a point mutation at one position selected from the group consisting of position 341, 481, 590, 803, and 857.

15. An isolated oligonucleotide molecule of claim 14, wherein said mutation is selected from the group consisting of a cytosine at position 341, a thymine at position 481, an adenine at position 590, a guanine at position 803, and an adenine at position 857.

16. An isolated oligonucleotide molecule of claim 15, wherein said mutant oligonucleotide molecule has a nucleic acid sequence as set forth in SEQ ID NOS:

16, 18, 20, 23, and 24.

17. An isolated oligonucleotide molecule comprising a wild-type allele of NAT2, wherein said normal nucleotide is selected from the group consisting of a thymine at position 341, a cytosine at position 481, a guanine at position 590, an adenine at position 803, and a guanine at position 857.

18. An isolated oligonucleotide molecule as claimed in 17, wherein said wild type oligonucleotide molecule has a nucleic acid sequence as set forth in SEQ ID NOS:

17, 19, 21, 22, and 25.