Methods for detecting a polymorphism in the nfkb1 gene promoter

Abstract

The present invention discloses a functional relationship between a recognized disease condition and a polymorphism in the nucleotide factor kappa B promoter (NFKB1). This relationship provides a platform for methods of altering promoter activity and for determining similar relationships between specific pathologies and identified polymorphisms. A statistically significant risk of developing ulcerative colitis was shown to be correlated with the presence of an ATTG insertion/deletion in the NFKB1 promoter and is likely to apply also to a variety of other inflammatory diseases.

1 . An isolated polynucleotide probe for detecting a functional polymorphism in a human NFKB1 promoter, comprising a nucleic acid segment that binds to the functional polymorphic allele position in the promoter but does not bind to wildtype NFKB promoter allele. 
     
     
         2 . An isolated polynucleotide probe for detecting an ATTG D allele polymorphism of a human NFKB1 promoter, wherein said probe specifically binds to the ATTG D allele but exhibits little or no binding to the ATTG W allele of the NFKB1 promoter. 
     
     
         3 . An isolated polynucleotide probe for detecting an ATTG W polymorphism in a mammalian NFKB1 promoter, wherein said probe specifically binds to the ATTG W allele of said promoter but exhibits little or no binding to the ATTG D allele of the NFKB1 promoter. 
     
     
         4 . The isolated polynucleotide probe of  claim 2 , which has an oligonucleotide sequence of about 10-30 nucleotides complementary to a NFKB1 promoter region comprising an ATTG D allele. 
     
     
         5 . The isolated polynucleotide probe of  claim 2  wherein the ATTG D allele polymorphism is a −94 ins/del ATTG in SEQ ID NO:1. 
     
     
         6 . The isolated polynucleotide probe of  claim 2  selected from the group consisting of SEQ ID NO:3, SEQ ID NO:4 and SEQ ID NO:5. 
     
     
         7 . The isolated polynucleotide probe of  claim 3  that has the sequence of SEQ ID NO:2. 
     
     
         8 . The isolated polynucleotide probe of  claim 2  or  claim 3  further comprising a detectable label. 
     
     
         9 . The isolated polynucleotide probe of  claim 8  wherein the detectable label is selected from the group consisting of a fluorescent, colorimetric, radio-, and antibody label. 
     
     
         10 . The isolated polynucleotide probe of  claim 9  wherein the label is a radioactive label. 
     
     
         11 . The isolated oligonucleotide probe of  claim 3  wherein the promoter is a human NFKB1 promoter. 
     
     
         12 . The isolated oligonucleotide probe of  claim 2  wherein the ATTG-D allele is an ATTG singlet polymorphism at position −94 of SEQ ID NO:1. 
     
     
         13 . The isolated oligonucleotide probe of  claim 3  wherein the ATTG-W allele is a duplet polymorphism at position −94 of SEQ ID NO:1. 
     
     
         14 - 23 . (canceled) 
     
     
         24 . A kit for detecting a −94ins/del ATTG polymorphism in a NFKB1 promoter, said kit comprising at least one oligonucleotide probe that selectively hybridizes to a −94delATTG, optionally at least one oligonucleotide probe that selectively hybridizes to a −94insATTG polymorphism, and directions for use. 
     
     
         25 . The kit of  claim 24  wherein the oligonucleotide probe is detectably labeled. 
     
     
         26 . The kit of  claim 25  wherein the detectable label is a fluorescent, radio-, antibody or colorimetric label. 
     
     
         27 . The kit of  claim 25  wherein the oligonucleotide probe for detecting the −94delATTG polymorphism is selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:4. 
     
     
         28 . The kit of  claim 25  wherein the oligonucleotide probe for detecting the −94insATTG polymorphism is a probe having the sequence of SEQ ID NO:5. 
     
     
         29 - 35 . (canceled) 
     
     
         36 . An isolated human NFKB1 promoter gene comprising a nucleic acid sequence that selectively binds to SEQ ID NO:4. 
     
     
         37 . The promoter of claim  35  that selectively binds to SEQ ID NO:5. 
     
     
         38 . The promoter of claim  35  that comprises a −94del ATTG deletion in SEQ ID NO:1. 
     
     
         39 . The promoter of claim  35  that comprises an ATTG (SEQ ID NO:1 from position −91 to position −96) insertion/deletion. 
     
     
         40 . The promoter gene of claim  35  consisting essentially of SEQ ID NO: 1 and complements thereof. 
     
     
         41 . An isolated oligonucleotide comprising a contiguous nucleotide sequence of human NKFB1 promoter comprising an ATTG singlet as a polymorphism −94ins/delATTG of SEQ ID NO:1 wherein said sequence maintains NKFB1 promoter function. 
     
     
         42 - 43 . (canceled)