Compositions and methods for detecting a neoplasia

Abstract

The invention provides compositions and methods for detecting a neoplasia (e.g., pancreatic cancer, lung cancer, colon cancer) in a subject sample (e.g., serum, blood, plasma, tissue). In particular embodiments, the invention provides methods for detecting BNC1 and ADAMTS1 promoter methylation in circulating DNA in serum.

1 . A method for detecting or characterizing a neoplasia in a biologic sample of a subject, the method comprising detecting the methylation of a BNC1 and/or ADAMTS1 gene, wherein detection of methylation detects or characterizes the presence of a neoplasia in the sample. 
     
     
         2 . The method of  claim 1 , wherein the method detects an increase in methylation relative to a reference. 
     
     
         3 . The method of  claim 1 , wherein the method detects promoter methylation or methylation of exon 1. 
     
     
         4 . The method of  claim 1 , wherein the neoplasia is a cancer selected from the group consisting of pancreatic cancer, gastrointestinal cancer, lung cancer, colon cancer, duodenal cancer, colorectal carcinoma, neuroendocrine carcinoma, cholangiocarcinomas, and ampullary tumors. 
     
     
         5 . The method of  claim 1 , wherein the biologic sample is a tissue or biologic fluid sample. 
     
     
         6 . The method of  claim 1 , wherein the biologic fluid is selected from the group consisting of blood, serum, plasma, urine, pancreatic juice, pancreatic cyst fluid, or lung lavage. 
     
     
         7 . The method of  claim 2 , wherein the reference is the level of methylation present at the promoter in a control sample. 
     
     
         8 . The method of  claim 7 , wherein the control sample is derived from a healthy subject. 
     
     
         9 . The method of  claim 1 , wherein the methylation is detected by quantitative methylation-specific PCR (QMSP). 
     
     
         10 - 20 . (canceled) 
     
     
         21 . A method for detecting or characterizing pancreatic cancer in a serum or plasma sample derived from a subject, the method comprising detecting the methylation of BNC1 and ADAMTS1, wherein detection of methylation detects or characterizes pancreatic cancer in the subject. 
     
     
         22 . The method of  claim 21 , wherein the method detects an increase in methylation relative to a reference. 
     
     
         23 . The method of claim  17 , further comprising imaging the subject, and localizing the cancer. 
     
     
         24 . The method of  claim 21 , further comprising detecting an alteration in the sequence or expression of a Brca1, Brca2, p16, K-ras, APC, PalB2, and/or DPC4 gene or polypeptide relative to a reference. 
     
     
         25 - 27 . (canceled) 
     
     
         28 . A method of monitoring a subject diagnosed as having a neoplasia, the method comprising detecting an alteration in promoter methylation level in a BNC1 and/or ADAMTS1 gene in a subject sample relative to a reference, wherein an altered level indicates an altered severity of neoplasia in the subject; or
 A method for selecting a treatment for a subject diagnosed as having a neoplasia, the method comprising detecting methylation of a BNC1 and/or ADAMTS1 gene, wherein detection of methylation indicates that epigenetic therapy should be selected for treatment of said subject.   
     
     
         29 - 32 . (canceled) 
     
     
         33 . The method of  claim 1 , wherein the subject is a human patient. 
     
     
         34 . The method of  claim 1 , wherein the methylation is quantified by methylation on beads or quantitative methylation-specific PCR. 
     
     
         35 - 36 . (canceled) 
     
     
         37 . A kit for the analysis of promoter methylation, the kit comprising at least one primer capable of distinguishing between methylated and unmethylated BNC1 and ADAMTS1 promoter sequences. 
     
     
         38 . The kit of  claim 37 , further comprising a pair of primers for amplifying the promoter sequence of a reference gene. 
     
     
         39 . The kit of  claim 37 , further comprising a detectable probe, wherein the probe is capable of binding to the promoter sequence. 
     
     
         40 . The kit of  claim 39 , wherein the probe is detected by fluorescence, by autoradiography, by an immunoassay, by an enzymatic assay, or by a colorimetric assay.