Method of screening for susceptibility to drug-induced cardiac arrhythmia

Abstract

Isolated polynucleotide molecules, and peptides encoded by these molecules, are used in the analysis of human cardiac potassium channel minK subunit variants, as well as in screening and diagnostic applications relating to a D85N polymorphism in the KCNE1 gene encoding the human cardiac potassium channel minK subunit polypeptide. By analyzing biological samples from a subject, it is possible to type a human cardiac potassium channel minK subunit with regard to the KCNE1-D85N polymorphism, for example, in the context of screening for susceptibility to drug-induced cardiac arrhythmias.

What is claimed is:  
     
         1 . A method of screening for susceptibility to a drug-induced cardiac arrhythmia in a subject, the method comprising: 
 (a) obtaining a biological sample from the subject; and    (b) detecting a D85N polymorphism of a KCNE1 gene encoding a cardiac potassium channel minK subunit polypeptide in the biological sample from the subject, the presence of the D85N polymorphism indicating the susceptibility of the subject to a drug-induced cardiac arrhythmia.    
     
     
         2 . The method of  claim 1 , wherein the biological sample comprises a nucleic acid sample.  
     
     
         3 . The method of  claim 2 , wherein the D85N polymorphism of the KCNE1 gene comprises a G to A transition at nucleotide 281 of a cDNA that corresponds to the KCNE1 gene.  
     
     
         4 . The method of  claim 3 , wherein the G to A transition at nucleotide 281 of the cDNA that corresponds to the KCNE1 gene further comprises a change in a triplet code from GAC to AAC or GAT to AAT, which encodes a minK polypeptide having an asparagine moiety at amino acid 85.  
     
     
         5 . The method of  claim 2 , wherein the polymorphism is detected by amplifying a target nucleic acid in the nucleic acid sample from the subject using an amplification technique.  
     
     
         6 . The method of  claim 5 , wherein the polymorphism is detected by amplifying a target nucleic acid in the nucleic acid sample from the subject using an oligonucleotide pair, wherein a first oligonucleotide of the pair hybridizes to a first portion of the KCNE1 gene, wherein the first portion includes the D85N polymorphism of the KCNE1 gene, and wherein the second of the oligonucleotide pair hybridizes to a second portion of the KCNE1 gene that is adjacent to the first portion.  
     
     
         7 . The method of  claim 6 , wherein the first portion of the KCNE1 gene includes nucleotide 281 of a cDNA that corresponds to the KCNE1 gene.  
     
     
         8 . The method of  claim 7 , wherein the first and the second oligonucleotides each further comprise a detectable label, and wherein the label of the first oligonucleotide is distinguishable from the label of the second oligonucleotide.  
     
     
         9 . The method of  claim 8 , wherein said label of said first oligonucleotide is a radiolabel, and wherein said label of said second oligonucleotide is a biotin label.  
     
     
         10 . The method of  claim 2 , wherein the polymorphism is detected by sequencing a target nucleic acid in the nucleic acid sample from the subject.  
     
     
         11 . The method of  claim 10 , wherein the sequencing comprises dideoxy sequencing.  
     
     
         12 . The method of  claim 2 , wherein the step of detecting the polymorphism is detected by contacting a target nucleic acid in the nucleic acid sample from the subject with a reagent that detects the presence of the D85N polymorphism and detecting the reagent.  
     
     
         13 . The method of  claim 12 , wherein the reagent detects a G to A transition at nucleotide 281 of a cDNA that corresponds to the KCNE1 gene.  
     
     
         14 . The method of  claim 12 , wherein the reagent comprises an allele specific oligonucleotide.  
     
     
         15 . The method of  claim 14 , wherein the allele specific oligonucleotide has a sequence as set forth in SEQ ID NO:9.  
     
     
         16 . The method of  claim 1  or  2 , wherein the subject is a human subject.  
     
     
         17 . The method of  claim 1 , wherein the biological sample comprises a polypeptide sample.  
     
     
         18 . An oligonucleotide pair, wherein a first oligonucleotide of the pair hybridizes to a first portion of the KCNE1 gene, wherein the first portion includes a D85N polymorphism of the KCNE1 gene, and wherein the second of the oligonucleotide pair hybridizes to a second portion of the KCNE1 gene that is adjacent to the first portion.  
     
     
         19 . The oligonucleotide pair of  claim 18 , wherein the first portion of the KCNE1 gene includes nucleotide 281 of a cDNA that corresponds to the KCNE1 gene.  
     
     
         20 . The oligonucleotide pair of  claim 18 , wherein said first and said second oligonucleotides each further comprise a detectable label, and wherein said label of said first oligonucleotide is distinguishable from said label of said second oligonucleotide.  
     
     
         21 . The oligonucleotide pair of  claim 20 , wherein said label of said first oligonucleotide is a radiolabel, and wherein said label of said second oligonucleotide is a biotin label.  
     
     
         22 . A set of oligonucleotide primers comprising an anti-sense primer and a sense primer, wherein said oligonucleotide primer set is suitable for amplifying a portion of the KCNE1 gene, wherein the portion includes a D85N polymorphism of the KCNE1 gene.  
     
     
         23 . The oligonucleotide set of  claim 22 , wherein the first portion of the KCNE1 gene includes nucleotide 281 of a cDNA that corresponds to the KCNE1 gene.  
     
     
         24 . The oligonucleotide primer set of  claim 22 , wherein said anti-sense primer has a nucleotide sequence selected from the group consisting of SEQ ID NO:6 and SEQ ID NO:8 and wherein said sense primer has a nucleotide sequence selected from the group consisting of SEQ ID NO:5 and SEQ ID NO:7.  
     
     
         25 . A kit for detecting a D85N polymorphism in a KCNE1 gene encoding cardiac potassium channel minK subunit in a subject, the kit comprising: 
 (a) a reagent for detecting the presence of a D85N polymorphism of the KCNE1 gene in a biological sample from the subject; and    (b) a container for the reagent.    
     
     
         26 . The kit of  claim 25 , wherein the reagent for detecting the presence of the D85N polymorphism of the KCNE1 gene comprises a reagent which detects a G to A transition at nucleotide 281 of a cDNA that corresponds to the KCNE1 gene.  
     
     
         27 . The kit of  claim 25 , further comprising a reagent for amplifying a nucleic acid molecule containing a D85N polymorphism of the KCNE1 gene.  
     
     
         28 . The kit of  claim 27 , wherein the amplifying reagent comprises a polymerase enzyme suitable for use in a polymerase chain reaction and a pair of oligonucleotides.  
     
     
         29 . The kit of  claim 28 , wherein a first oligonucleotide of the pair of oligonucleotides hybridizes to a first portion of the KCNE1 gene, wherein the first portion includes the D85N polymorphism of the KCNE1 gene, and wherein the second of the oligonucleotide pair hybridizes to a second portion of the KCNE1 gene that is adjacent to the first portion.  
     
     
         30 . The kit of  claim 29 , wherein the first portion of the KCNE1 gene includes nucleotide 281 of a cDNA that corresponds to the KCNE1 gene.  
     
     
         31 . The kit of  claim 25 , further comprising a reagent for extracting a nucleic acid sample from a biological sample obtained from a subject.  
     
     
         32 . An assay kit for detecting the presence of a D85N polymorphism of a KCNE1 gene encoding a cardiac potassium channel minK subunit polypeptide in a biological sample, the kit comprising a first container containing a first antibody capable of immunoreacting with a cardiac potassium channel minK subunit polypeptide having an aspartate to aspargine transition at amino acid 85, wherein the first antibody is present in an amount sufficient to perform at least one assay.  
     
     
         33 . The assay kit of  claim 32 , further comprising a second container containing a second antibody that immunoreacts with the first antibody.  
     
     
         34 . The assay kit of  claim 33 , wherein the first antibody and the second antibody comprise monoclonal antibodies.  
     
     
         35 . The assay kit of  claim 33 , wherein the first antibody is affixed to a solid support.  
     
     
         36 . The assay kit of  claim 33 , wherein the first and second antibodies each comprise an indicator.  
     
     
         37 . The assay kit of  claim 36 , wherein the indicator is a radioactive label or an enzyme.  
     
     
         38 . An assay kit for detecting the presence, in a biological sample, of an antibody immunoreactive with a cardiac potassium channel minK subunit polypeptide characterized by a D85N polymorphism of a KCNE1 gene encoding the cardiac potassium channel minK subunit polypeptide, the kit comprising a first container containing a cardiac potassium channel minK subunit polypeptide having an aspartate to asparagine transition at amino acid 85 that immunoreacts with the antibody, with the polypeptide present in an amount sufficient to perform at least one assay.  
     
     
         39 . The method of  claim 38 , wherein the minK polypeptide comprises an amino acid sequence as set forth in SEQ ID NO:4.