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 for determining whether a patient diagnosed with myelodysplastic syndrome (MDS) or leukemia characterized by a mutation in FLT3 kinase is in remission, comprising:
 obtaining a human nucleic acid sample from a myelodysplastic syndrome (MDS) or leukemia patient having a mutation in FLT3 kinase;   amplifying a portion of a nucleic acid encoding a polypeptide having FLT3 kinase activity from the sample, thereby generating an amplicon; and   ascertaining the presence or absence of at least one tandem duplication in the amplicon in a genomic region defined by SEQ ID NOs 26 and 33;   wherein the absence of the tandem duplication is indicative of remission.   
     
     
         2 . The method of  claim 1 , wherein the ascertaining step comprises comparing the length of the amplicon to an expected length of an amplicon lacking a tandem duplication. 
     
     
         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 the amplification 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. 
     
     
         6 . The method of  claim 1 , wherein the nucleic acid sample is genomic DNA. 
     
     
         7 . The method of  claim 6 , wherein the genomic DNA is obtained from one or more myelocytes. 
     
     
         8 . The method of  claim 1 , wherein the amplicon comprises a region defined by SEQ ID NO: 26 and SEQ ID NO: 27 or a partial portion thereof. 
     
     
         9 . A method of predicting relapse of acute myeloid leukemia (AML) comprising:
 obtaining a nucleic acid sample from a human subject in remission of AML;   determining whether or not the nucleic acid sample is positive for a marker of poor prognosis, wherein said marker comprises a length mutation falling within a region of FLT3 defined by SEQ ID NO: 26 and SEQ ID NO: 33; and   correlating the presence of said marker with a increased likelihood of relapse; or   correlating the absence of said marker with decreased likelihood of relapse.   
     
     
         10 . The method of  claim 9 , wherein the length mutation comprises one or more tandem duplications of all or a partial portion of the nucleotides in the region of FLT3 defined by SEQ ID NO: 26 and SEQ ID NO: 33. 
     
     
         11 . The method of  claim 10 , wherein the length mutation further comprises one or more nucleotide insertions. 
     
     
         12 . The method of  claim 9 , wherein the length mutation comprises one or more tandem duplications of all or a partial portion of the nucleotides in the region of FLT3 defined by SEQ ID NO: 26 and SEQ ID NO: 27. 
     
     
         13 . The method of  claim 12 , wherein the length mutation further comprises one or more nucleotide insertions. 
     
     
         14 . The method of  claim 9 , wherein the length mutation is detected as an increase in length of a gene amplification reaction product of the sample compared to an expected length of a wild-type gene amplification reaction product. 
     
     
         15 . The method of  claim 9 , wherein the nucleic acid sample is genomic DNA. 
     
     
         16 . The method of  claim 15 , wherein the genomic DNA is obtained from one or more myelocytes. 
     
     
         17 . The method of  claim 9 , wherein nucleic acid samples obtained from the human subject prior to treatment were positive for said marker. 
     
     
         18 . The method of  claim 9 , wherein said marker comprises a length mutation falling within a region of FLT3 corresponding to the region defined by SEQ ID NO: 26 and SEQ ID NO: 33. 
     
     
         19 . A marker of poor prognosis of leukemic disease, comprising an isolated nucleic acid of FLT3 kinase that differs in length or in sequence from a nucleic acid encoding a polypeptide having FLT3 kinase activity, wherein the marker differs in length or in sequence of a region defined by SEQ ID NO: 26 and SEQ ID NO: 33. 
     
     
         20 . The marker of  claim 19 , wherein the difference in length or in sequence is attributable to a tandem duplication mutation within the region defined by SEQ ID NO: 26 and SEQ ID NO: 33. 
     
     
         21 . The marker of  claim 20 , wherein the difference in length or in sequence is attributable to a tandem duplication within a region defined by SEQ ID NO: 26 and SEQ ID NO: 27.