Methods for detection of promoter polymorphism in a UGT gene promoter

Abstract

The present invention is directed to methods for detecting the presence of genetic polymorphisms that correlate with altered gene expression. More specifically, the present invention is directed to methods for detecting the genetic polymorphisms located in the UGT1A1 promoter. The invention also provides methods for optimizing drug dosages based upon the presence of the polymorphisms. The invention further provides methods of predicting sensitivity to xenobiotics and diagnostic kits for detecting genetic polymorphisms.

1 . A method for detecting polymorphisms in a uridine diphosphate glucuronosyltransferase (UGT) gene promoter comprising determining the number of thymidine-adenine (TA) repeats in said promoter, wherein the number of TA repeats correlates with expression of the gene.  
     
     
         2 . The method of  claim 1  comprising the steps of 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT1A1 gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         3 . The method of  claim 1  or  2  wherein said promoter is the UGT1A1 promoter.  
     
     
         4 . The method of  claim 3  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         5 . The method of  claim 1  wherein said DNA is amplified by the polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         6 . The method of  claim 1  wherein said DNA is amplified by PCR and said number of TA repeats is determined by sequencing said amplified DNA.  
     
     
         7 . The method of  claim 1  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         8 . The method of  claim 1  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         9 . A method for detecting polymorphisms in the uridine diphosphate glucuronosyltransferase I (UGT1A1) gene promoter comprising determining the number of thymidine-adenine, (TA) repeats in said promoter, wherein the number of TA repeats correlates with expression of the gene.  
     
     
         10 . The method of  claim 9  comprising the steps of: 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         11 . The method of  claim 9  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         12 . The method of  claim 9  wherein said DNA is amplified by polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         13 . The method of  claim 9  wherein said DNA is amplified by PCR and said number of TA repeats is determined by sequencing said amplified DNA.  
     
     
         14 . The method of  claim 9  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         15 . The method of  claim 9  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         16 . A method for screening individuals for variation in glucuronidation activity comprising detecting polymorphisms in a uridine diphosphate glucuronosyltransferase (UGT) gene promoter comprising determining the number of thymidine-adenine (TA) repeats in said promoter, wherein the number of TA repeats correlates with expression of the gene.  
     
     
         17 . The method of  claim 16  comprising the steps of: 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         18 . The method of  claim 16  or  17  wherein said promoter is the UGT1A1 promoter.  
     
     
         19 . The method of  claim 18  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         20 . The method of  claim 16  wherein said DNA is amplified by the polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         21 . The method of  claim 16  wherein said DNA is amplified by PCR and said number of TA repeats is determined by sequencing said amplified DNA.  
     
     
         22 . The method of  claim 16  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         23 . The method of  claim 16  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         24 . A method for screening individuals for variation in glucuronidation activity comprising detecting polymorphisms in a uridine diphosphate glucuronosyltransferase I (UGT1A1) gene promoter, the method comprising determining the number of thymidine-adenine (TA) repeats in said promoter, wherein the number of TA repeats in said promoter correlates with expression of the UGT gene.  
     
     
         25 . The method of  claim 24  comprising the steps of: 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         26 . The method of  claim 24  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         27 . The method of  claim 24  wherein said DNA is amplified by polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         28 . The method of  claim 24  wherein said DNA is amplified by PCR and said number of TA repeats is determined by sequencing said amplified DNA.  
     
     
         29 . The method of  claim 24  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         30 . The method of  claim 24  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         31 . A method for optimizing drug dosages for a patient wherein said drugs are glucuronidated by a uridine diphosphate glucuronosyltransferase (UGT), said method comprising determining the number of thymidine-adenine (TA) repeats in a promoter of the UGT gene wherein the number of TA repeats correlates with expression of said UGT gene, and wherein the activity of said drug is effected by its level of glucuronidation.  
     
     
         32 . The method of  claim 31  comprising the steps of: 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         33 . The method of  claim 31  or  32  wherein said promoter is the UGT1A1 promoter.  
     
     
         34 . The method of  claim 32  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         35 . The method of  claim 31  wherein said DNA is amplified by the polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         36 . The method of  claim 31  wherein said DNA is amplified by PCR and said number of TA repeats is determined and sequencing said amplified DNA.  
     
     
         37 . The method of  claim 31  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         38 . The method of  claim 31  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         39 . A method for optimizing drug dosages wherein said drugs are glucuronidated by uridine diphosphate glucuronosyltransferase I, said method comprising determining the number of thymidine-adenine (TA) repeats in a promoter of the UGT1 gene wherein the number of TA repeats correlates with expression of said UGT gene, and wherein the activity of said drug is effected by its level of glucuronidation.  
     
     
         40 . The method of  claim 39  comprising the steps of: 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         41 . The method of  claim 39  or  40  wherein said promoter is the UGT1A1 promoter.  
     
     
         42 . The method of  claim 39  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         43 . The method of  claim 39  wherein said DNA is amplified by the polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         44 . The method of  claim 39  wherein said DNA is amplified by PCR and said number of TA repeats is determined by sequencing said amplified DNA.  
     
     
         45 . The method of  claim 39  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         46 . The method of  claim 39  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         47 . A method for predicting an individual's sensitivity to xenobiotics wherein said xenobiotics are glucuronidated by a uridine diphosphate glucuronosyltransferase gene product, said method comprising determining the number of thymidine-adenine (TA) repeats in a UGT gene promoter, wherein the number of TA repeats correlates with expression of said UGT gene and wherein the individual's sensitivity to said xenobiotics is effected by glucuronidation activity.  
     
     
         48 . The method of  claim 47  comprising the steps of; 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         49 . The method of  claim 47  or  48  wherein said promoter is the UGT1A1 promoter.  
     
     
         50 . The method of  claim 47  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         51 . The method of  claim 47  wherein said DNA is amplified by the polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         52 . The method of  claim 47  wherein said DNA is amplified by PCR and said number of TA repeats is determined by sequencing said amplified DNA.  
     
     
         53 . The method of  claim 47  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         54 . The method of  claim 47  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         55 . A method for predicting an individual's sensitivity to xenobiotics wherein said xenobiotics are glucuronidated by a uridine diphosphate glucuronosyltransferase I gene product, said method comprising determining the number of thymidine-adenine (TA) repeats in a UGT1 gene promoter, wherein the number of TA repeats correlates with expression of said UGT1 gene and wherein the individual's sensitivity to said xenobiotics is effected by glucuronidation activity.  
     
     
         56 . The method of  claim 55  comprising the steps of: 
 (a) obtaining DNA from an individual;    (b) amplifying all or part of said UGT1 gene promoter contained in said DNA; and    (c) determining the number of TA repeats in said promoter.    
     
     
         57 . The method of  claim 55  or  56  wherein said promoter is the UGT1A1 promoter.  
     
     
         58 . The method of  claim 55  wherein said DNA being amplified comprises all or part of a UGT1A1 promoter.  
     
     
         59 . The method of  claim 55  wherein said DNA is amplified by the polymerase chain reaction (PCR) and said number of TA repeats is determined by gel electrophoresis.  
     
     
         60 . The method of  claim 55  wherein said DNA is amplified by PCR and said number of TA repeats is determined by sequencing said amplified DNA.  
     
     
         61 . The method of  claim 55  wherein said polymorphism comprises an allele, said allele selected from the group consisting of five TA repeats, [TA] 5 , six TA repeats, [TA] 6 , seven TA repeats, [TA] 7  and eight TA repeats, [TA] 8 .  
     
     
         62 . The method of  claim 55  wherein said promoter has a genotype selected from the group consisting of [TA] 5 /[TA] 5 , [TA] 5 /[TA] 6 , [TA] 5 /[TA] 7 , [TA] 5 /[TA] 8 , [TA] 6 /[TA] 8 , [TA] 7 /[TA] 8  and [TA] 8 /[TA] 8 .  
     
     
         63 . A kit for detecting polymorphisms in a uridine diphosphate glucuronosyltransferase (UGT) gene promoter wherein the number of thymidine-adenine (TA) repeats in said UGT gene promoter correlates to expression of said UGT gene, the kit comprising primers for amplifying DNA comprising all or part of the UGT gene promoter to determine the number of TA repeats in said promoter.  
     
     
         64 . The kit of  claim 63  wherein said kit contains one or more additional components selected from the group consisting of deoxynucleoside triphosphates, buffers, labels for detecting said polymorphisms and instructions.  
     
     
         65 . The kit of  claim 63  or  64  wherein the primers are selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4.  
     
     
         66 . The kit of  claim 63  or  64  wherein said promoter is the UGT1A1 promoter.  
     
     
         67 . A kit for detecting polymorphisms in a uridine diphosphate glucuronosyltransferase I (UGT1A1) gene promoter wherein the number of thymidine-adenine (TA) repeats in said UGT1 gene promoter correlates to expression of said UGT1 gene, the kit comprising primers for amplifying DNA comprising all or part of the UGT1 gene promoter to determine the number of TA repeats in said promoter.  
     
     
         68 . The kit of  claim 67  wherein said kit contains one or more additional components selected from the group consisting of deoxynucleoside triphosphates, buffers, labels for detecting said polymorphisms and instructions.  
     
     
         69 . The kit of  claim 67  or  68  wherein the primers are selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4.