Method for detecting cell proliferative disorders

Abstract

The present invention relates to the detection of a cell proliferative disorder associated with alterations of microsatellite DNA in a sample. The microsatellite DNA can be contained within any of a variety of samples, such as urine, sputum, bile, stool, cervical tissue, saliva, tears, or cerebral spinal fluid. The invention is a method to detect an allelic imbalance by assaying microsatellite DNA. Allelic imbalance is detected by observing an abnormality in an allele, such as an increase or decrease in microsatellite DNA which is at or corresponds to an allele. An increase can be detected as the appearance of a new allele. In practicing the invention, DNA amplification methods, particularly polymerase chain reactions, are useful for amplifying the DNA. DNA analysis methods can be used to detect such a decrease or increase. The invention is also a method to detect genetic instability of microsatellite DNA. Genetic instability is detected by observing an amplification or deletion of the small, tandem repeat DNA sequences in the microsatellite DNA which is at or corresponds to an allele. The invention is also a kit for practicing these methods.

1 . A method for detecting a cell proliferative disorder in a subject, the method comprising: a) obtaining from the subject a sample comprising microsatellite DNA; and b) detecting an allelic imbalance, wherein an allelic imbalance is indicative of a cell proliferative disorder. 
     
     
         2 . The method of  claim 1 , wherein the allelic imbalance is detected as a decrease in the level of DNA corresponding to an allele. 
     
     
         3 . The method of  claim 2 , wherein the level of DNA corresponding to the allele is less than 50% of the level of DNA of a corresponding allele in a microsatellite DNA sample of a subject that lacks the cell proliferative disorder. 
     
     
         4 . The method of  claim 1 , wherein the allelic imbalance is detected as an increase in the level of DNA corresponding to an allele. 
     
     
         5 . The method of  claim 4 , wherein the increase is detected as the presence of a new allele. 
     
     
         6 . The method of  claim 1 , wherein detection comprises size fractionation of the DNA. 
     
     
         7 . The method of  claim 6 , wherein the DNA is fractionated by gel electrophoresis. 
     
     
         8 . The method of  claim 1 , wherein the cell proliferative disorder is a neoplasm. 
     
     
         9 . The method of  claim 8 , wherein the neoplasm is selected from the group consisting of head, neck, lung, esophageal, stomach, small bowel, colon, bladder, kidney, and cervical neoplasms. 
     
     
         10 . The method of  claim 1 , wherein the sample is selected from the group consisting of urine, sputum, bile, stool, cervical tissue, saliva, tears, cerebral spinal fluid, serum, plasma, and lymphocytes. 
     
     
         11 . The method of  claim 1 , wherein the DNA is amplified by means of nucleotides which hybridize to the flanking regions of the microsatellite DNA before detecting. 
     
     
         12 . The method of  claim 11 , wherein the amplification comprises a polymerase chain reaction. 
     
     
         13 . The method of  claim 1 , wherein the microsatellite DNA comprises a locus selected from the group consisting of DRPLA, UT762, IFNA, D9S200, D9S156, D3S1284, D3S1238, CHRNB1, D17S86, D9S747, D9S171, D16S476, D4S243, D14S50, D21S1245, FgA, D8S3G7, THO, D115488, D135802, D175695, D175654, and D20548. 
     
     
         14 . The method of  claim 11 , wherein the nucleotide sequences of the flanking region to which the oligonucleotide primers hybridize are selected from the group consisting of SEQ ID NO:1-31 and SEQ ID NO:32. 
     
     
         15 . The method of  claim 14 , wherein oligonucleotide primers are selected from the group consisting of SEQ ID NO:33-63 and SEQ ID NO:64. 
     
     
         16 . A method for detecting a cell proliferative disorder in a subject, the method comprising: a) obtaining a sample from the subject of microsatellite DNA; and b) detecting genetic instability in the sample of microsatellite DNA, wherein genetic instability is indicative of a cell proliferative disorder. 
     
     
         17 . The method of  claim 16 , wherein the instability is detected as an amplification of nucleotide repeats in the DNA. 
     
     
         18 . The method of  claim 16 , wherein the instability is detected as a deletion of nucleotide repeats in the DNA. 
     
     
         19 . The method of  claim 16 , wherein the DNA is amplified before detecting. 
     
     
         20 . The method of  claim 16 , wherein the cell proliferative disorder is not due to a repair gene defect. 
     
     
         21 . The method of  claim 20 , wherein the cell proliferative disorder is a neoplasm. 
     
     
         22 . The method of  claim 20 , wherein the neoplasm is selected from the group consisting of the head, neck, lung, and bladder neoplasms. 
     
     
         23 . The method of  claim 21 , wherein the neoplasm is benign. 
     
     
         24 . The method of  claim 21 , wherein the neoplasm is malignant. 
     
     
         25 . The method of  claim 16 , wherein the sample is selected from the group consisting of urine, sputum, bile, stool, cervical tissue, saliva, tears, cerebral spinal fluid, serum, plasma, and lymphocytes. 
     
     
         26 . A kit for detecting a cell proliferative disorder, the kit comprising oligonucleotide primers that are complementary to a nucleotide sequence that flanks nucleotide repeats of microsatellite DNA. 
     
     
         27 . The kit of  claim 26 , further comprising a detectably labeled deoxyribonucleotide. 
     
     
         28 . The kit of  claim 26 , wherein nucleotide sequences that flank nucleotide repeats of microsatellite DNA to which the oligonucleotide primers are complementary are selected from the group consisting of SEQ ID NO:1-31 and SEQ ID NO:32. 
     
     
         29 . The kit of  claim 28 , wherein the oligonucleotide primers are selected from the group consisting of SEQ ID NO:33-63 and SEQ ID NO:64.