Detection of polymorphisms in the human 5-lipoxygenase gene

Abstract

The present invention is based at least in part on the discovery of polymorphisms within the 5-lipoxygenase gene which are included in a haplotype. Accordingly, the invention provides nucleic acid molecules having a nucleotide sequence of an allelic variant of a 5-LO gene. The invention also provides methods for identifying specific alleles of polymorphic regions of a 5-LO gene, methods for determining whether a patient has a more or less severe phenotype of an inflammatory disease or disorder such as asthma, methods for determining whether a patient will be more or less responsive to treatment with 5′LO inhibitors, forensic methods based on detection of polymorphisms within the 5-LO gene, and kits for performing such methods.

1 . An isolated nucleic acid molecule comprising an allelic variant of a polymorphic region of a 5-LO gene, wherein the allelic variant comprises one or more nucleotide sequences selected from the group consisting of those set forth in SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6, or the complement thereof.  
     
     
         2 . The method of  claim 1 , wherein the allelic variant further comprises one or more nucleotide sequences selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:8, or the complement thereof.  
     
     
         3 . The isolated nucleic acid molecule of claims  1  or  2 , further comprising at least one variant Spl binding site, or the complement thereof.  
     
     
         4 . An isolated nucleic acid molecule comprising a haplotype, wherein the haplotype comprises one or more of SEQ ID NO: 4, SEQ ID NO: 5, and SEQ ID NO: 6, one or more of SEQ ID NO: 7 and SEQ ID NO: 8, or the complements thereof, and wherein the nucleic acid molecule is a 5-LO gene.  
     
     
         5 . An isolated nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO:1, or a portion thereof, wherein said nucleic acid molecule comprises one or more nucleotide residues selected from the group consisting of an adenine at residue 1000 of SEQ ID NO:1, deleted residues 472-477 of SEQ ID NO:1, and an adenine at residue 559 of SEQ ID NO:1, or the complements thereof.  
     
     
         6 . The isolated nucleic acid molecule of  claim 5 , further comprising one or more nucleotide residues selected from the group consisting of an adenine at residue 84 of SEQ ID NO:1, and an adenine at residue 137 of SEQ ID NO:1, or the complements thereof.  
     
     
         7 . The isolated nucleic acid molecule of  claim 5 , further at least one non-wild-type Spl binding site allele, or the complement thereof.  
     
     
         8 . A kit comprising a probe or primer which is capable of hybridizing to the nucleic acid molecule of any of claims  1 ,  2 ,  4 ,  5 ,  6 , or 7.  
     
     
         9 . The kit of  claim 8 , wherein the probe or primer comprises a nucleotide sequence from about 15 to about 30 nucleotides.  
     
     
         10 . The kit of  claim 8 , wherein the probe or primer comprises a nucleotide sequence selected from the group consisting of nucleic acids having a nucleotide sequence set forth in SEQ ID NOs: 9-60.  
     
     
         11 . The kit of  claim 8 , wherein the probe or primer is labeled.  
     
     
         12 . A method for determining whether an asthma patient will be responsive to treatment with a 5-LO inhibitor, comprising 
 a) obtaining a nucleic acid sample from the asthma patient;    b) determining the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO:1; and    c) determining whether the asthma patient will be responsive to treatment with a 5-LO inhibitor based on the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO: 1, wherein the allelic variant comprises one or more nucleotide sequences selected from the group consisting of those set forth in SEQ ID NO: 4, SEQ ID NO:5, and SEQ ID NO:6, or the complement thereof.    
     
     
         13 . The method of  claim 12 , wherein the allelic variant further comprises one or more nucleotide sequences selected from the group consisting of SEQ ID NO: 7 and SEQ ID NO: 8, or the complement thereof.  
     
     
         14 . The method of  claim 12  or  13 , wherein the allelic variant further comprising at least one non-wild-type Spl binding site allele, or the complement thereof.  
     
     
         15 . A method for determining whether an asthma patient has a more or less severe asthma phenotype, comprising 
 a) obtaining a nucleic acid sample from the asthma patient;    b) determining the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO: 1; and    c) determining whether the asthma patient has a more or less severe asthma phenotype based on the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO: 1, wherein the allelic variant comprises one or more nucleotide sequences selected from the group consisting of those set forth in SEQ ID NO: 4, SEQ ID NO:5, and SEQ ID NO:6, or the complement thereof.    
     
     
         16 . The method of  claim 15 , wherein the allelic variant further comprises one or more nucleotide sequences selected from the group consisting of SEQ ID NO: 7 and SEQ ID NO: 8, or the complement thereof.  
     
     
         17 . The method of  claim 15  or  16 , wherein the allelic variant further comprising at least one non-wild-type Spl binding site allele, or the complement thereof.  
     
     
         18 . A method for selecting the appropriate drug to administer to a patient who has asthma, comprising 
 a) obtaining a nucleic acid sample from the patient;    b) determining the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO:1; and    c) selecting the appropriate drug to administer to a patient who has an inflammatory disease or disorder based on the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO:1, wherein the allelic variant comprises one or more nucleotide sequences selected from the group consisting of those set forth in SEQ ID NO: 4, SEQ ID NO:5, and SEQ ID NO:6, or the complement thereof.    
     
     
         19 . The method of  claim 18 , wherein the allelic variant further comprises one or more nucleotide sequences selected from the group consisting of SEQ ID NO:7 and SEQ ID NO:8, or the complement thereof.  
     
     
         20 . The method of  claim 18  or  19 , wherein the allelic variant further comprising at least one non-wild-type Spl binding site allele, or the complement thereof.  
     
     
         21 . The method of  claim 18 , wherein the drug is a 5-LO inhibitor.  
     
     
         22 . A method of identifying a patient who is a candidate for effective treatment with a 5-LO inhibitor comprising the steps of: 
 a) obtaining a nucleic acid sample from the patient;    b) determining the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO:1; and    c) identifying a patient who is a candidate for effective treatment with a 5-LO inhibitor based on the presence of an allelic variant which differs from the reference sequence set forth in SEQ ID NO:1, wherein the allelic variant comprises one or more nucleotide sequences selected from the group consisting of those set forth in SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6, or the complement thereof.    
     
     
         23 . The method of  claim 22 , wherein the allelic variant further comprises one or more nucleotide sequences selected from the group consisting of SEQ ID NO: 7 and SEQ ID NO:8, or the complement thereof.  
     
     
         24 . The method of  claim 22  or  23 , wherein the allelic variant further comprising at least one non-wild-type Spl binding site allele, or the complement thereof.  
     
     
         25 . The method of  claim 22 , wherein the patient has an inflammatory disease or disorder.  
     
     
         26 . The method of  claim 22 , wherein the patient has asthma.  
     
     
         27 . A method for determining the identity of an allelic variant of a 5-LO gene in a nucleic acid obtained from a patient, wherein the sample comprises a 5-LO gene sequence, comprising contacting a sample nucleic acid from the patient with a probe or primer having a sequence which is complementary to a 5-LO gene sequence, wherein the probe or primer is selected from the group consisting of nucleic acids having a nucleotide sequence set forth in SEQ ID NO: 4, SEQ ID NO:5, or SEQ ID NO:6, or the complement thereof, and wherein the allelic variant comprises one or more nucleotide sequences selected from the group consisting of those set forth in SEQ ID NO: 4, SEQ ID NO:5, and SEQ ID NO:6, or the complements thereof, thereby determining the identity of the allelic variant.  
     
     
         28 . The method of  claim 27 , wherein determining the identity of the allelic variant comprises determining the identity of at least one nucleotide at any one of the nucleotide residues selected from the group consisting of: residue 1000 of SEQ ID NO:1, any one of residues 472-477 of SEQ ID NO:1, and residue 559 of SEQ ID NO:1.  
     
     
         29 . The method of  claim 27 , wherein determining the nucleotide content comprises sequencing the nucleotide sequence.  
     
     
         30 . The method of  claim 27 , wherein determining the identity of the allelic variant comprises performing a restriction enzyme site analysis.  
     
     
         31 . The method of  claim 27 , wherein determining the identity of the allelic variant is carried out by single-stranded conformation polymorphism.  
     
     
         32 . The method of  claim 27 , wherein determining the identity of the allelic variant is carried out by allele specific hybridization.  
     
     
         33 . The method of  claim 27 , wherein determining the identity of the allelic variant is carried out by primer specific extension.  
     
     
         34 . The method of  claim 27 , wherein determining the identity of the allelic variant is carried out by an oligonucleotide ligation assay.  
     
     
         35 . The method of  claim 27 , wherein the probe or primer comprises a nucleotide sequence from about 15 to about 30 nucleotides.  
     
     
         36 . The method of  claim 27 , wherein the probe or primer is labeled.