Methods for disease detection

Abstract

The present invention provides methods for detecting disease by analysis of a patient sample to determine the integrity of nucleic acids in the sample.

1 . A method for determining the presence of cancer or precancer in a patient, the method comprising the steps of:
 conducting a plurality of amplification reactions on a nucleic acid to produce a plurality of nucleic acid fragments of different lengths, wherein the nucleic acid is obtained from a sample comprising shed cells or cellular debris from the patient;   qualitatively determining amplification level in the plurality of amplification reactions; and   identifying the patient as having cancer or precancer if the qualitative amplification level is greater than a predetermined threshold level.   
     
     
         2 .- 5 . (canceled) 
     
     
         6 . The method of  claim 1 , wherein said cancer is selected from the group consisting of colon cancer, lung cancer, esophageal cancer, prostate cancer, stomach cancer, pancreatic cancer, liver cancer, and lymphoma. 
     
     
         7 . The method of  claim 16 , wherein said genomic locus is a tumor suppressor gene or oncogene. 
     
     
         8 . The method of  claim 1 , wherein said sample is selected from the group consisting of stool, sputum, pancreatic fluid, bile, lymph, blood, urine, cerebrospinal fluid, seminal fluid, saliva, breast nipple aspirate, and pus. 
     
     
         9 .- 10 . (canceled) 
     
     
         11 . The method of  claim 1 , wherein the step of qualitatively determining comprises:
 assigning a binary score to each reaction such that the binary score indicates if a positive amplification takes place; and   determining a total score indicative of the amplification level for the plurality of amplification reactions based on the binary score in each reaction.   
     
     
         12 .- 13 . (canceled) 
     
     
         14 . The method of  claim 6 , wherein the cancer is colon cancer. 
     
     
         15 . The method of  claim 8 , wherein the sample is stool. 
     
     
         16 . The method of  claim 1 , wherein the plurality of amplification reactions are conducted at a single genomic locus. 
     
     
         17 . The method of  claim 1 , wherein the plurality of amplification reactions are conducted on a plurality of different genomic loci. 
     
     
         18 . The method of  claim 1 , wherein at least one amplified nucleic acid fragment is at least 200 bp in length. 
     
     
         19 . The method of  claim 1 , wherein at least one amplified nucleic acid fragment is at least 400 bp in length. 
     
     
         20 . The method of  claim 1 , wherein at least one amplified nucleic acid fragment is at least 800 bp in length. 
     
     
         21 . The method of  claim 1 , wherein at least one amplified nucleic acid fragment is at least 1.3 kb in length. 
     
     
         22 . The method of  claim 1 , wherein at least one amplified nucleic acid fragment is at least 1.8 kb in length. 
     
     
         23 . The method of  claim 1 , wherein at least one amplified nucleic acid fragment is at least 2.4 kb in length. 
     
     
         24 . The method of  claim 1 , wherein the plurality of nucleic acid fragments of different lengths comprise at least two fragments selected from the group consisting of fragments of about 200 bp, about 400 bp, about 800 bp, about 1.3 kb, about 1.8 lb, and about 2.4 kb in length. 
     
     
         25 . The method of  claim 1 , wherein the plurality of nucleic acid fragments of different lengths comprise fragments of about 200 bp, about 1.3 kb, about 1.8 kb, and about 2.4 kb in length