Colorectal cancer associated circulating nucleic acid biomarkers

Abstract

The invention provides methods and reagents for diagnosing colorectal cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated. In some embodiments, the CNA biomarkers are polynucleotide fragments, e.g., DNA fragments, that are present at an elevated level in blood, e.g., in a serum or plasma sample, of a colorectal cancer patient in comparison to the level in blood, e.g., a serum or plasma sample, obtained from a normal individual who does not have colorectal cancer.

1 . A method of analyzing circulating free DNA in a patient sample, comprising detecting, in a sample that is blood, serum or plasma, the level of,
 a first cell-free DNA having a sequence falling within a first chromosomal region set forth in Table 2, and   a second cell-free DNA having a sequence falling within a second chromosomal region set forth in Table 2,   wherein the sequences of said first and second cell-free DNAs are five of repetitive elements.   
     
     
         2 . The method of  claim 1 , wherein said first and second chromosomal regions are different. 
     
     
         3 . The method of  claim 1 , wherein said patient is suspected of having colorectal cancer. 
     
     
         4 . The method of  claim 1 , further comprising determining in said sample a third cell free DNA having a sequence telling within a third chromosomal region set forth in Table 2, wherein said third chromosomal region is different from said first and second chromosomal regions, and the sequence of said third cell free DNA is free of repetitive elements. 
     
     
         5 . The method of  claim 1 , further comprising determining in said sample at least 5, 8, 10, 20, 30, 40, 50, 60, 70, 75, or 79 additional different cell free DNAs each falling within a different chromosomal region set forth in Table 2. 
     
     
         6 . A kit comprising a plurality of oligonucleotides each having a nucleotide sequence falling within one same chromosomal region set forth in Table 2, wherein said plurality includes a number of said oligonucleotides sufficient to detect all circulating cell-free DNA molecules derived from said chromosomal region. 
     
     
         7 .- 10 . (canceled) 
     
     
         11 . A method of diagnosing or screening for colorectal cancer in a patient, comprising:
 detecting, in a sample that is blood, serum or plasma from said patient, the level of a first circulating cell-free DNA having a sequence falling within a first chromosomal region designated as “UP” in Table 2 and a second circulating cell-free DNA having a sequence falling within a second chromosomal region designated as “UP” in Table 2, wherein said first and second chromosomal regions are different, and wherein the sequences of said first and second cell free DNAs are free of repetitive element, and   correlating an increased level of said first and second cell free DNAs with an increased likelihood that said patient ha colorectal cancer; or   detecting, in a sample that is blood, serum or plasma from said patient, the total level of all circulating cell-free DNAs each having a sequence falling within the same one single chromosomal regions designated as “DOWN” in Table 2; and   correlating a decreased total level with an increased likelihood that said patient has colorectal cancer.   
     
     
         12 .- 15 . (canceled) 
     
     
         16 . A system for analyzing circulating cell-free DNA, comprising:
 a sample analyzer for determining the level of a circulating cell-free DNA having a nucleotide sequence of at least 25 nucleotides falling within a chromosomal region set forth in Table 2;   a computer system for automatically receiving and analyzing data obtained in step (1), and for correlating the level of said circulating cell-free DNA with a diagnosis of colorectal cancer, wherein the level of circulating cell-free DNA is determined in accordance with the method of  claim 1 .   
     
     
         17 . The system of  claim 16 , further comprising a display module displaying the result of the correlating step. 
     
     
         18 .- 25 . (canceled)