Methods of diagnosing myelodysplastic syndrome (mds) or leukemia using nucleic acids or fragments encoding flt3 kinase

Abstract

To provide a nucleic acid encoding a receptor protein kinase, wherein the nucleic acid has tandem duplication in a nucleotide sequence of a juxtamembrane and is useful for diagnosis of leukemia; a polypeptide encoded by the nucleic acid; an antibody capable of specifically binding to a region encoded by the nucleic acid having tandem duplication occurring in a nucleotide sequence of a juxtamembrane; a nucleic acid capable of specifically binding to the nucleic acid having tandem duplication occurring in a nucleotide sequence of a juxtamembrane; a method for detection of the nucleic acid encoding a receptor protein kinase; and a kit therefor. A nucleic acid encoding a receptor protein kinase, wherein the nucleic acid has tandem duplication in a nucleotide sequence of a juxtamembrane; a polypeptide encoded by the nucleic acid; an antibody capable of specifically binding to the portion of the polypeptide; a nucleic acid capable of specifically binding to the nucleic acid; a method for detection of the nucleic acid; and a kit for detection.

1 . A method of detecting mutations in FLT3 kinase indicative of a disease state, comprising:
 obtaining a human nucleic acid sample;   amplifying a portion of a nucleic acid encoding a polypeptide having FLT3 kinase activity from the sample, thereby generating an amplicon;   ascertaining the presence of a length mutation in the amplicon, wherein the length mutation is within a region defined by SEQ ID NO: 26 and SEQ ID NO: 33;   wherein the presence of the length mutation is a prognostic for myelodysplastic syndrome (MDS) or leukemia.   
     
     
         2 . The method of  claim 1 , wherein the ascertaining step comprises comparing the length of the amplicon to the length or expected length of an amplicon lacking a length mutation. 
     
     
         3 . The method of  claim 1 , wherein the ascertaining step comprises sequencing the amplicon. 
     
     
         4 . The method of  claim 1 , wherein the nucleic acid sample is selected from the group consisting of genomic DNA, cDNA, or mRNA. 
     
     
         5 . The method of  claim 1 , wherein in the nucleic acid sample is obtained from a patient diagnosed with leukemia. 
     
     
         6 . The method of  claim 1 , wherein the length mutation is not found in a wild-type gene. 
     
     
         7 . The method of  claim 1 , wherein the amplifying step is performed with a primer pair selected from the group consisting of SEQ ID NOs:26 and 27, SEQ ID NOs:30 and 31, and SEQ ID NOs:32 and 33. 
     
     
         8 . The method of  claim 1 , wherein the length mutation is a tandem duplication. 
     
     
         9 . The method of  claim 1 , wherein the leukemia is acute myeloid leukemia. 
     
     
         10 . The method of  claim 9 , wherein the acute myeloid leukemia is sub-classified as M2, M4, or M5 based on the French-American-British (FAB) classification system. 
     
     
         11 . A method of screening a human subject having myelodysplastic syndrome (MDS) or leukemia, comprising:
 obtaining a nucleic acid sample from the subject; and   ascertaining whether the sample includes a length mutation in a region of the FLT3 gene defined by SEQ ID NO: 26 and SEQ ID NO: 33; and wherein the presence of said length mutation is indicative of poor prognosis.   
     
     
         12 . The method of  claim 11 , wherein the length mutation is comprised of one or more tandem duplications of nucleotides. 
     
     
         13 . The method of  claim 12 , wherein the length mutation further comprises one or more nucleotide insertions. 
     
     
         14 . The method of  claim 11 , wherein the nucleic acid sample is selected from the group consisting of genomic DNA, cDNA, or RNA. 
     
     
         15 . The method of  claim 11 , wherein the mutation is detected in a target region defined by a primer pair selected from the group consisting of SEQ ID NOs: 26 and 27, SEQ ID NOs: 30 and 31, and SEQ ID NOs: 32 and 33. 
     
     
         16 . The method of  claim 11 , wherein the presence of a mutation is detected by gel electrophoresis or sequencing. 
     
     
         17 . The method of  claim 11 , wherein the leukemia is acute myeloid leukemia (AML). 
     
     
         18 . The method of  claim 11 , wherein the region of the FLT3 gene is defined by SEQ ID NO: 26 and SEQ ID NO: 27. 
     
     
         19 . A kit for detecting mutations in FLT3 kinase indicative of a disease state comprising nucleic acid oligomers that are capable of priming the amplification of at least a portion of a nucleic acid encoding a polypeptide having FLT3 kinase activity from a human nucleic acid sample, wherein the primers direct the amplification of at least a portion of FLT3 kinase DNA defined by SEQ ID NO: 26 and SEQ ID NO: 33, and wherein the mutations are characterized by one or more tandem duplications. 
     
     
         20 . The kit of  claim 19 , wherein the nucleic acid oligomers are selected to amplify a region defined by at least one of the following primer pairs: SEQ ID NOs:26 and 27, SEQ ID NOs:30 and 31, and SEQ ID NOs:32 and 33. 
     
     
         21 . A kit for detecting mutations in FLT3 kinase indicative of a disease state comprising nucleic acid oligomers that are capable of priming the amplification of a portion of a nucleic acid encoding a polypeptide having FLT3 kinase activity from a human nucleic acid sample, wherein the amplified portion of FLT3 kinase nucleic acid corresponds to the region defined by SEQ ID NO: 26 and SEQ ID NO: 27 or a partial portion thereof, and wherein the mutations are characterized by one or more tandem duplications.