Breast cancer associated circulating nucleic acid biomarkers

Abstract

The invention provides methods and reagents for diagnosing breast cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated.

What is claimed is: 
     
         1 . A method of analyzing circulating free DNA in a patient sample, comprising determining, in a sample that is blood, serum or plasma, the presence or absence or the amount of,
 a first cell-free DNA having a sequence falling within a first chromosomal region set forth in Table 2, Table 3, Table 4, Table 5, Table 6, Table 7, or Table 8, and   a second cell-free DNA having a sequence falling within a second chromosomal region set forth in Table 2, Table 3, Table 4, Table 5, Table 6, Table 7, or Table 8,   wherein the sequences of said first and second cell-free DNAs are free of repetitive element.   
     
     
         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 breast cancer. 
     
     
         4 . The method of  claim 1 , further comprising determining in said sample a third cell free DNA having a sequence falling within a third chromosomal region set forth in Table 2, Table 3, Table 4, Table 5, Table 6, Table 7, or Table 8, 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 element. 
     
     
         5 . The method of  claim 1 , further comprising determining in said sample at least 5, 8, 10, 20 or 40 additional different cell free DNAs each falling within a different chromosomal region set forth in Tables 2-8. 
     
     
         6 . The method of  claim 1 , wherein said chromosomal regions are all set forth within the same table chosen from Tables 2-8. 
     
     
         7 . A kit comprising a plurality of oligonucleotides each having a nucleotide sequence falling within one same chromosomal region set forth in a table chosen from Tables 2-8, wherein said plurality includes a number of said oligonucleotides sufficient to detect all circulating cell-free DNA molecules derived from said chromosomal region 
     
     
         8 . A system for analyzing circulating cell-free DNA, comprising:
 a sample analyzer for determining the presence or absence or the amount of, a circulating cell-free DNA having a nucleotide sequence of at least 25 nucleotides falling within a chromosomal region set forth in a table chosen from Tables 2-7;   a computer system for automatically receiving and analyzing data obtained in step (1), and for correlating the presence of, or an increased amount of, said circulating cell- free DNA with a diagnosis of breast cancer.   
     
     
         9 . The system of  claim 8 , further comprising a display module displaying the result of the correlating step.