Bcr-abl truncation mutations

Abstract

Truncation variants of BCR-ABL mRNA that produces BCR-ABL proteins with a truncated C-terminus and its role in resistance to treatment with kinase inhibitors is described. Vectors for expressing the truncated gene products are described as well as recombinant cells that express the truncated gene products from cDNA constructs. Also provided are methods compositions and kits for detecting the BCR-ABL truncation variants. Also provided are methods for determining the prognosis of a patient diagnosed as having myeloproliferative disease, and methods for predicting the likelihood for resistance to a treatment with tyrosine kinase inhibitor in a patient diagnosed as having myeloproliferative disease. Additionally, methods for screening BCR-ABL tyrosine kinase domain inhibitors which rely on the recombinant cells are also disclosed.

What is claimed is: 
     
         1 . A kit for detecting the presence or absence of one or more BCR-ABL truncation mutations comprising a first primer and a second primer, wherein the first primer binds to a portion of ABL exon 4 and the second primer binds to a portion of the junction of ABL exon 9 and exon 10, wherein the first and second primers in an amplification reaction are capable of generating an amplicon. 
     
     
         2 . The kit of  claim 1 , wherein the first primer is SEQ ID NO: 23 or a complement thereof. 
     
     
         3 . The kit of  claim 2 , wherein the second primer is SEQ ID NO: 22 or a complement thereof. 
     
     
         4 . The kit of  claim 3 , further comprising a third primer that binds to a portion of BCR exon b2. 
     
     
         5 . The kit of  claim 4 , wherein the third primer is SEQ ID NO: 21 or a complement thereof. 
     
     
         6 . The kit of  claim 5 , wherein at least on primer is labeled with a detectable label. 
     
     
         7 . The kit of  claim 6 , wherein the detectable label is a radioisotope, a fluorophore, a protein, or an enzyme. 
     
     
         8 . The kit of  claim 7 , wherein the fluorophore is a fluorescent moiety. 
     
     
         9 . The kit of  claim 8 , further comprising a probe selected from the group consisting of SEQ ID NOs: 8, 13, and 18. 
     
     
         10 . The kit of  claim 9 , wherein the one or more BCR-ABL truncation mutations is selected from 2417insCAGG, Del 2596-2597, and C2506T. 
     
     
         11 . A kit for detecting the presence or absence of one or more BCR-ABL truncation mutations comprising:
 (a) a first primer and a second primer, wherein the first primer binds to a portion of ABL exon 4 and the second primer binds to a portion of the junction of ABL exon 9 and exon 10, wherein the first and second primers in an amplification reaction are capable of generating an amplicon; and   (b) one or more detectably labeled probes capable of hybridizing to said amplicon.   
     
     
         12 . The kit of  claim 11 , wherein the one or more probes is selected from at least 20 contiguous nucleotides of SEQ ID NO: 8, at least 20 contiguous nucleotides of SEQ ID NO: 13, or at least 20 contiguous nucleotides of SEQ ID NO: 18. 
     
     
         13 . The kit of  claim 12 , wherein the first primer is SEQ ID NO: 23 or a complement thereof. 
     
     
         14 . The kit of  claim 13 , wherein the second primer is SEQ ID NO: 22 or a complement thereof. 
     
     
         15 . The kit of  claim 14 , further comprising a third primer that binds to a portion of BCR exon b2. 
     
     
         16 . The kit of  claim 15 , wherein the third primer is SEQ ID NO: 21 or a complement thereof. 
     
     
         17 . The kit of  claim 16 , wherein the first, second, and third primers are labeled with a detectable label. 
     
     
         18 . The kit of  claim 17 , where the detectable label is a radioisotope, a fluorophore, a protein,