Methods for detecting dna originating from different individuals

Abstract

In a first aspect, the present invention features methods for differentiating DNA species originating from different individuals in a biological sample. These methods may be used to differentiate or detect fetal DNA in a maternal sample or to differentiate DNA of an organ donor from DNA of an organ recipient. In preferred embodiments, the DNA species are differentiated by observing epigenetic differences in the DNA species such as differences in DNA methylation. In a second aspect, the present invention features methods of detecting genetic abnormalities in a fetus by detecting fetal DNA in a biological sample obtained from a mother. In a third aspect, the present invention features methods for differentiating DNA species originating from an organ donor from those of an organ recipient. In a fourth aspect, the present invention features kits for differentiating DNA species originating from different individuals in a biological sample.

1 - 38 . (canceled) 
     
     
         39 . A method for determining methylation status of a cell-free human DNA species in a biological sample that (1) contains cell-free human DNA originated from two different human individuals and (2) is obtained from one of the two different human individuals, the method comprising the steps of:
 (a) treating the sample with a reagent that differentially reacts with methylated and unmethylated DNA; and   (b) detecting the presence of a methylated version and/or an unmethylated version of the cell-free human DNA species in the sample, thereby determining methylation status of the human DNA species in the sample.   
     
     
         40 . The method of  claim 39 , further comprising measuring concentration of the methylated or unmethylated version of the human DNA species. 
     
     
         41 . The method of  claim 39 , further comprising purifying the methylated or unmethylated version of the human DNA species. 
     
     
         42 . The method of  claim 39 , wherein the reagent is sodium bisulfate. 
     
     
         43 . The method of  claim 39 , wherein step (b) comprises an amplification reaction. 
     
     
         44 . The method of  claim 43 , wherein the amplification reaction is a polymerase chain reaction (PCR). 
     
     
         45 . The method of  claim 44 , wherein the PCR is a methylation-specific PCR. 
     
     
         46 . The method of  claim 39 , wherein step (b) comprises DNA sequencing. 
     
     
         47 . The method of  claim 39 , wherein step (b) comprises a primer extension assay. 
     
     
         48 . The method of  claim 39 , wherein the sample is a fluid or cellular sample or a mixture thereof. 
     
     
         49 . The method of  claim 39 , wherein the sample is a blood sample. 
     
     
         50 . The method of  claim 39 , wherein the sample is a serum or plasma sample. 
     
     
         51 . The method of  claim 39 , wherein the two different human individuals are a pregnant woman and a fetus the woman is carrying. 
     
     
         52 . The method of  claim 51 , wherein the sample is a maternal blood sample. 
     
     
         53 . The method of  claim 51 , wherein the sample is a maternal serum or plasma sample. 
     
     
         54 . The method of  claim 39 , wherein the different human individuals are a transplant recipient and a transplant donor. 
     
     
         55 . The method of  claim 54 , wherein the transplant is a bone marrow transplant. 
     
     
         56 . The method of  claim 39 , wherein the two different human individuals are one male and one female. 
     
     
         57 . The method of  claim 39 , wherein step (b) is performed inside a cell. 
     
     
         58 . The method of  claim 57 , wherein step (b) comprises an in situ methylation-specific PCR. 
     
     
         59 . The method of  claim 57 , further comprising isolation of cells based on methylation difference of the DNA species.