Polymorphisms in known genes associated with inflammatory autoimmune disease, methods of detection and uses thereof

• US 6,900,016 B1
• Filed: 09/10/2001
• Issued: 05/31/2005
• Est. Priority Date: 09/08/2000
• Status: Expired due to Fees

• Current Assignee: Celera Corporation (Quest Diagnostics Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Venter, J. Craig, Zhang, Jinghui N., Rowe, William, Naik, Ashwinikumar, Woodage, Trevor, Kalush, Francis, Subramanian, Gangadharan, Liu, Xiangjun, Cravchik, Anibal
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US09/949,002
• Time in Patent Office: 1,359 Days
• Field of Search: 435/6, 435/91.2, 435/320.1, 530/350, 536/23.4
• US Class Current: 435/6.14
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The present invention is based on the discovery of novel polymorphisms (SNPs) in the genes known in the art to contribute to inflammatory and autoimmune disorders. Such polymorphisms can lead to a variety of disorders that are mediated/modulated by a variant inflammatory and autoimmune disorders associated protein. The present invention provides reagents used for detecting and expressing the variant nucleic acid/protein sequence as well as methods of identifying and using these variants.

Claims

1. A detection reagent selected firm the group consisting of:

(a) a detection reagent comprising at least about 15 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 15 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

G’

;

(b) a detection reagent comprising at least about 15 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 15 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

T’

; and

(c) a detection reagent which is entirely complementary to the detection reagent of (a) or (b).

13. The detection reagent of claim 1 wherein position 301 of SEQ ED NO:

1574 is about at the center of the detection reagent.

14. The detection reagent of claim 1 wherein position 301 of SEQ ID NO:

1574 is about at the 3′

end of the detection reagent.

15. The detection reagent of claim 1 wherein the detection reagent is detectably labeled.

16. The detection reagent of claim 15, wherein the detection reagent is labeled with a reporter.

17. The detection reagent of claim 16, wherein the reporter is fluorescent.

18. The detection reagent of claim 16, wherein the detection reagent is further labeled with a quencher.

19. The detection reagent of claim 1, wherein the detection reagent is bound to a solid support.

20. The detection reagent of claim 19, wherein the solid support comprises a nucleic acid array.

2. An isolated polynucleotide selected from the group consisting of:

(a) an isolated polynucleotide consisting of a segment of SEQ ID NO;

1574, wherein the segment comprises at least about 12 contiguous nucleotides of SEQ ID NO;

1574, and wherein the at least about 12 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

G’

,

(b) an isolated polynucleotide consisting of a sent of SEQ ID NO;

1574, wherein the segment comprises at least about 12 contiguous nucleotides of SEQ ID NO;

1574, and wherein the at least about 12 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

T’

; and

(c) an isolated polynucleotide which is entirely complementary to the isolated polynucleotide of (a) or (b).

3. A detection reagent selected from the group consisting of:

(a) a detection reagent comprising at least about 20 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 20 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

G’

;

(b) a detection reagent comprising at least about 20 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 20 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

T’

; and

(c) a detection reagent which is entirely complementary to the detection reagent of (a) or (b).

4. An isolated polynucleotide consisting of a nucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence of SEQ ID NO;

1574, wherein position 301 of SEQ ID NO;

1574 is ‘

G’

;

(b) the nucleotide sequence of SEQ ID NO;

1574, wherein position 301 of SEQ ID NO;

1574 is ‘

T’

; and

(c) a nucleotide sequence which is entirely complementary to the nucleotide sequence of (a) or (b).

5. An isolated polynucleotide consisting of a segment of a nucleotide sequence selected from the group consisting of SEQ ID NOS:

602 and 764, wherein the segment comprises a nucleotide sequence selected from the group consisting of;

(a) the nucleotide sequence of SEQ ID NO;

1574, wherein position 301 of SEQ ID NO;

1574 is ‘

G’

;

(b) the nucleotide sequence of SEQ ID NO;

1574, wherein position 301 of SEQ ID NO;

1574 is ‘

T’

; and

(c) a nucleotide sequence which is entirely complementary to (a) or (b).

6. An amplified polynucleotide selected from the group consisting of:

(a) an amplified polynucleotide comprising at least about 30 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 30 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

G’

;

(b) an amplified polynucleotide comprising at least about 30 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 30 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

T’

; and

(c) an amplified polynucleotide which is entirely complementary to the amplified polynucleotide of (a) or (b).

11. The extension primer of claim 6, wherein the ddNTP is delectably labeled.

12. The extension primer of claim 11, wherein the ddNTP is labeled with a mass tag.

7. An extension primer selected from the group consisting of:

(a) an extension primer comprising at least about 12 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 12 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

G’

, and wherein position 301 of SEQ ID NO;

1574 is a ddNTP at the 3′

end of the extension prier, and

(b) an extension primer which is entirely complementary to the extension primer of (a).

8. An extension primer selected from the group consisting of:

(a) an extension primer comprising at least about 20 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 20 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

G’

, and wherein position 301 of SEQ ID NO;

1574 is a ddNTP at the 3′

end of the extension primer; and

(b) an extension primer which is entirely complementary to the extension primer of (a).

9. An extension primer selected from the group consisting of:

(a) an extension primer comprising at least about 12 contiguous nucleotides of SEQ ID NO;

1574, wherein the at least about 12 contiguous nucleotides include position 301 of SEQ ID NO;

1574, and wherein position 301 of SEQ ID NO;

1574 is ‘

T’

, and wherein position 301 of SEQ ID NO;

1574 is a ddNTP at the 3′

end of the extension primer, and

(b) an extension primer which is entirely complementary to the extension primer of (a).

10. An extension primer selected from the group consisting of:

(a) an extension primer comprising at least about 20 contiguous nucleotides of SEQ ID NO;

1574, wherein the at let about 20 contiguous nucleotides include position 301 of SEQ ID NO;

574, and wherein position 301 of SEQ ID NO;

1574 is ‘

T’

, and wherein position 301 of SEQ ID NO;

1574 is a ddNTP at the 3′

end of the extension primer; and

(b) an extension primer which is entirely complementary to the extension primer of (a).