Method and kit for determining the tissue or cell origin of dna

Abstract

A method of detecting death of a cell type or tissue in a subject is disclosed. The method comprises determining whether cell-free DNA comprised in a fluid sample of the subject is derived from the cell type or tissue, wherein the determining is effected by ascertaining the methylation status of at least four methylation sites on a continuous sequence of the cell-free DNA, the sequence comprising no more than 300 nucleotides, wherein a methylation status of each of the at least four methylation sites on the continuous sequence of the DNA characteristic of the cell type or tissue is indicative of death of the cell type or tissue. Kits for detecting cell death are also disclosed.

1 . A kit for identifying the source of DNA in a sample comprising, oligonucleotides which are capable of detecting the methylation status of at least four methylation sites in a nucleic acid sequence, said nucleic acid sequence being no longer than 300 base pairs and comprising at least four methylation sites which are differentially methylated in a first cell or tissue of interest with respect to a second cell or tissue which is non-identical to said first cell or tissue of interest. 
     
     
         2 . The kit of  claim 1 , wherein said sequence comprises between 50-250 nucleotides. 
     
     
         3 . The kit of  claim 1 , wherein said sequence comprises between 20-200 nucleotides. 
     
     
         4 . The kit of  claim 1 , wherein said DNA is cell-free DNA. 
     
     
         5 . The kit of  claim 1 , wherein said DNA sequence is comprised in a sequence set forth in any one of SEQ NOs: 1-1484. 
     
     
         6 . The kit of  claim 1 , further comprising at least one agent for sequencing said DNA sequence. 
     
     
         7 . The kit of  claim 1 , further comprising DNA having said nucleic acid sequence, wherein said DNA is derived from a known cell of interest. 
     
     
         8 . The kit of  claim 1 , for diagnosing a pathological process. 
     
     
         9 . The kit of  claim 1 , for monitoring a treatment for a pathological process. 
     
     
         10 . The kit of  claim 1 , for monitoring death of a cell type or tissue. 
     
     
         11 . The kit of  claim 1 , further comprising bisulfite 
     
     
         12 . The kit of  claim 1 , wherein said at least one oligonucleotide is labeled with a detectable moiety. 
     
     
         13 . The kit of  claim 1 , wherein a methylation pattern of said at least four methylation sites in said first cell or tissue type of interest is different as compared to a methylation pattern of said at least four methylation sites in the same DNA sequence in the second cell or tissue type of interest. 
     
     
         14 . The kit of  claim 13 , wherein the methylation pattern of said at least four methylation sites is characteristic of said first cell or tissue type of interest. 
     
     
         15 . A kit for identifying the source of DNA in a sample comprising at least oligonucleotides which are capable of amplifying a DNA haying a nucleic acid sequence no longer than 300 base pairs, wherein said nucleic acid sequence comprises at least four methylation sites which are differentially methylated in a first cell of interest with respect to a second cell which is non-identical to said first cell of interest. 
     
     
         16 . The kit of  claim 15 , wherein at least one of said at least two oligonucleotides encodes a bar-code sequence. 
     
     
         17 . The kit of  claim 15 , wherein at least one of said at least two oligonucleotides is labeled with an identifiable moiety. 
     
     
         18 . The kit of  claim 15 , wherein at least one of said at least two oligonucleotides encodes a bar-code sequence. 
     
     
         19 . The kit of  claim 15 , wherein said two oligonucleotides encode sequences which allow for attaching to a flow cell surface. 
     
     
         20 . The kit of  claim 15 , wherein a methylation pattern of said at least four methylation sites in said first cell or tissue type of interest is different as compared to a methylation pattern of said at least four methylation sites in the same DNA sequence in the second cell or tissue type of interest.