Nucleic acid marker for cancer

Abstract

The present invention provides using a truncated WT1 gene transcript as a marker for detecting cancer in a subject. The method provides detecting the truncated WT1 gene transcript in a sample from the subject where the truncated gene transcript is characterized by an absence of a 101 base pair segment of intron 5 between nucleic acid positions −101 and −1. Positive detection of the truncated WT1 gene transcript indicates the presence of cancer. The invention provides a truncated WT1 gene transcript characterized by an absence of a 101 base pair segment of intron 5 between nucleic acid positions −101 and −1 and having a length of about two thousand base pairs. The truncated gene transcript is further characterized by containing at their five prime end sequences normally confined to the fifth intron of the WT1 gene, exons six through ten at their three prime end, and an overall length of approximately 2 kb.

What is claimed is:  
     
         1 . A method for detecting cancer in a subject, the method comprising: 
 obtaining a sample from the subject; and    detecting a truncated WT1 gene transcript in the sample, wherein the presence of the truncated WT1 gene transcript indicates the presence of cancer.    
     
     
         2 . The method of    claim 1    wherein the truncated WT1 gene transcript includes a portion of intron 5.  
     
     
         3 . The method of    claim 2    wherein the truncated gene transcript lacks a 101 base pair segment of intron 5 between nucleic acid positions −101 and −1.  
     
     
         4 . The method of    claim 2    wherein the truncated gene transcript includes a truncated region that has the sequence shown in FIG. 4.  
     
     
         5 . The method of    claim 1    wherein the detection of the truncated WT1 gene transcript further includes performing reverse transcriptase-polymerase chain reaction using a 5 prime primer located in intron 5 and a 3 prime primer located in exon 6.  
     
     
         6 . The method of    claim 5    wherein the primer is 5'-GAA CCC TGC ATC TAA AGT GG-3'.  
     
     
         7 . The method of    claim 5    wherein the detection of the truncated WT1 gene transcript further includes probing products from the reverse transcriptase-polymerase chain reaction with an oligonucleotide sense primer in exon 6, wherein the oligonucleotide sense primer is 5'-CCA CAG CAC AGG GTA CGA-3'.  
     
     
         8 . The method of    claim 7    wherein detection of the truncated WT1 gene transcript further includes identifying a 95 base pair fragment representing a product of the truncated WT1 gene transcript.  
     
     
         9 . The method of    claim 1    wherein the truncated gene transcript has a length of about two thousand base pairs.  
     
     
         10 . The method of    claim 1    wherein positive detection indicates the presence of prostate cancer.  
     
     
         11 . The method of    claim 1    wherein positive detection indicates the presence of breast cancer.  
     
     
         12 . The method of    claim 1    wherein positive detection indicates the presence of leukemia.  
     
     
         13 . A method for detecting a truncated WT1 gene transcript, the method comprising: 
 obtaining a nucleic acid sample from a subject suitable for performing reverse transcriptase-polymerase chain reaction;    performing reverse transcriptase-polymerase chain reaction on the nucleic acid sample using a 5 prime primer located in intron 5 and a 3 prime primer located in exon 6;    probing products from the reverse transcriptase-polymerase chain reaction with an oligonucleotide sense primer in exon 6; and    identifying a fragment representing a product of the truncated WT1 gene transcript.    
     
     
         14 . The method of    claim 13    wherein the oligonucleotide sense primer is 5'-CCA CAG CAC AGG GTA CGA-3'.  
     
     
         15 . The method of    claim 14    wherein the primer used for performing reverse transcriptase-polymerase chain reaction is 5'-GAA CCC TGC ATC TAA AGT GG-3'.  
     
     
         16 . The method of    claim 15    wherein the truncated gene transcript includes a truncated region that has the sequence shown in FIG. 4.  
     
     
         17 . The method of    claim 15    wherein the fragment is a 95 base pair fragment.  
     
     
         18 . An isolated nucleic acid comprising a truncated WT1 gene transcript that includes of a portion of intron 5.  
     
     
         19 . The isolated nucleic acid of    claim 18    wherein the truncated WT1 gene transcript includes intron 5 and lacks a 101 base pair segment of intron 5 between nucleic acid positions −101 and −1, wherein the truncated WT1 gene transcript has a length of about two thousand base pairs.  
     
     
         20 . The isolated nucleic acid of    claim 18    wherein the truncated WT1 gene transcript includes a truncated region having the sequence shown in FIG. 4.