Methods for Detection of Promoter Polymorphism in 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 - 69 . (canceled)  
     
     
         70 . A method for predicting an individual's sensitivity to irinotecan comprising 
 a) determining whether the individual has five or eight TA repeats in one or both uridine diphosphate glucuronosyltransferase I (UGT1A1) gene promoters from a sample from the individual, wherein the number of TA repeats correlates with expression of said UGT1A1 gene; and,    b) providing information regarding the individual's sensitivity to irinotecan based on the level of UGT1A1 gene expression, wherein the number of TA repeats correlates with sensitivity to irinotecan.    
     
     
         71 . The method of  claim 70 , wherein determining the number of TA repeats comprises amplifying all or part of the UGT1A1 gene promoter contained in the DNA sample.  
     
     
         72 . The method of  claim 71 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by gel electrophoresis.  
     
     
         73 . The method of  claim 71 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by sequencing the amplified DNA.  
     
     
         74 . The method of  claim 71 , wherein the UGT1A1 gene promoter is amplified using SEQ ID NO:1, SEQ ID NO:2, and/or SEQ ID NO:3.  
     
     
         75 . The method of  claim 70  wherein the DNA sample comprises an 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 .  
     
     
         76 . The method of  claim 70  wherein the individual has a UGT1A1 promoter 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 .  
     
     
         77 . The method of  claim 70 , wherein the individual has cancer.  
     
     
         78 . A method for predicting an individual's sensitivity to irinotecan comprising 
 a) determining the number of thymidine-adenine (TA) repeats in one or both uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene promoters from a DNA sample of the individual, wherein the number of TA repeats correlates with expression of said UGT1A1 gene and irinotecan sensitivity; and    b) predicting the individual's sensitivity to irinotecan using the number of TA repeats.    
     
     
         79 . The method of  claim 78 , wherein determining the number of TA repeats comprises amplifying all or part of the UGT1A1 gene promoter contained in the DNA sample.  
     
     
         80 . The method of  claim 79 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by gel electrophoresis.  
     
     
         81 . The method of  claim 79 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by sequencing the amplified DNA.  
     
     
         82 . The method of  claim 79 , wherein the UGT1A1 gene promoter is amplified using SEQ ID NO:1, SEQ ID NO:2, and/or SEQ ID NO:3.  
     
     
         83 . The method of  claim 78  wherein the DNA sample comprises an 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 .  
     
     
         84 . The method of  claim 78  wherein the individual has a UGT1A1 promoter 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 .  
     
     
         85 . The method of  claim 78 , wherein the individual has cancer.  
     
     
         86 . A method for evaluating glucuronidation activity in a individual comprising: 
 a) determining whether the individual has an absence of alleles [TA] 6  and/or [TA] 7  in one or both uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene promoters from a DNA sample from the individual; and    b) evaluating the level of glucuronidation activity in the individual based on the determination, wherein the level of glucuronidation activity is correlated with the number of TA repeats.    
     
     
         87 . The method of  claim 86 , wherein determining the number of TA repeats comprises amplifying all or part of the UGT1A1 gene promoter contained in the DNA sample.  
     
     
         88 . The method of  claim 87 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by gel electrophoresis.  
     
     
         89 . The method of  claim 87 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by sequencing the amplified DNA.  
     
     
         90 . The method of  claim 87 , wherein the UGT1A1 gene promoter is amplified using SEQ ID NO:1, SEQ ID NO:2, and/or SEQ ID NO:3.  
     
     
         91 . The method of  claim 86  wherein the DNA sample comprises an 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 .  
     
     
         92 . The method of  claim 86  wherein the individual has a UGT1A1 promoter 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 .  
     
     
         93 . The method of  claim 86 , wherein the individual has cancer.  
     
     
         94 . A method for predicting an individual's sensitivity to irinotecan comprising 
 a) having the number of thymidine-adenine (TA) repeats determined in one or both uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene promoters from a DNA sample of the individual; and    b) predicting the individual's sensitivity to irinotecan based on the number of TA repeats in one or both UGT1A1 gene promoters, wherein the number of TA repeats correlates with expression of said UGT1A1 gene and irinotecan sensitivity.    
     
     
         95 . The method of  claim 94 , further comprising obtaining the DNA sample from the individual.  
     
     
         96 . The method of  claim 94 , wherein determining the number of TA repeats comprises amplifying all or part of the UGT1A1 gene promoter contained in the DNA sample.  
     
     
         97 . The method of  claim 96 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by gel electrophoresis.  
     
     
         98 . The method of  claim 96 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by sequencing the amplified DNA.  
     
     
         99 . The method of  claim 96 , wherein the UGT1A1 gene promoter is amplified using SEQ ID NO:1, SEQ ID NO:2, and/or SEQ ID NO:3.  
     
     
         100 . The method of  claim 94  wherein the DNA sample comprises an 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 .  
     
     
         101 . The method of  claim 94  wherein the individual has a UGT1A1 promoter 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 .  
     
     
         102 . The method of  claim 94 , wherein the individual has cancer.  
     
     
         103 . A method for evaluating glucuronidation activity in a individual comprising: 
 a) having a DNA sample from the individual screened for an absence of alleles [TA] 6  and/or [TA] 7  in one or both uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene promoters; and    b) evaluating the level of glucuronidation activity in the individual based on the determination, wherein the level of glucuronidation activity is correlated with the number of TA repeats.    
     
     
         104 . The method of  claim 103 , further comprising obtaining the DNA sample from the individual.  
     
     
         105 . The method of  claim 103 , wherein determining the number of TA repeats comprises amplifying all or part of the UGT1A1 gene promoter contained in the DNA sample.  
     
     
         106 . The method of  claim 105 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by gel electrophoresis.  
     
     
         107 . The method of  claim 105 , wherein the UGT1A1 gene promoter is amplified by polymerase chain reaction (PCR) and the number of TA repeats is determined by sequencing the amplified DNA.  
     
     
         108 . The method of  claim 105 , wherein the UGT1A1 gene promoter is amplified using SEQ ID NO:1, SEQ ID NO:2, and/or SEQ ID NO:3.  
     
     
         109 . The method of  claim 103  wherein the DNA sample comprises an 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 .  
     
     
         110 . The method of  claim 103  wherein the individual has a UGT1A1 promoter 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 .  
     
     
         111 . The method of  claim 103 , wherein the individual has cancer.