Non-invasive diagnosis of graft rejection in organ transplant patients

Abstract

The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

1 - 35 . (canceled) 
     
     
         36 . A method of detecting and treating transplant rejection in a solid organ transplant recipient comprising:
 a) obtaining a biological sample from said solid organ transplant recipient, wherein said biological sample comprises circulating cell-free nucleic acids comprising transplant-specific circulating cell-free nucleic acids;   b) performing high throughput sequencing on said circulating cell-free nucleic acids and producing sequencing reads of said circulating cell-free nucleic acids;   c) using said sequencing reads of said circulating cell-free nucleic acids to detect at least 100 single nucleotide polymorphisms that are distinguishable from recipient-specific single nucleotide polymorphisms, wherein said transplant-specific single nucleotide polymorphisms are selected from the group consisting of heterozygous single nucleotide polymorphisms, homozygous single nucleotide polymorphisms, and both heterozygous and homozygous single nucleotide polymorphisms;   d) using said at least 100 single nucleotide polymorphisms that are distinguishable from recipient-specific single nucleotide polymorphisms to obtain a quantitative value for said transplant-specific circulating cell-free nucleic acids in said biological sample from said solid organ transplant recipient;   e) detecting transplant rejection in said solid organ transplant recipient based on said quantitative value for said transplant-specific circulating cell-free nucleic acids in said biological sample; and   f) treating said detected transplant rejection in said solid organ transplant recipient by administering an immunosuppressive drug to said solid organ transplant recipient.   
     
     
         37 . The method of  claim 36 , wherein said quantitative value for said transplant-specific circulating cell-free nucleic acids in said biological sample from said solid organ transplant recipient incorporates a quality score associated with said sequencing reads of said circulating cell-free nucleic acids. 
     
     
         38 . The method of  claim 36 , wherein said at least 100 single nucleotide polymorphisms that are distinguishable from recipient-specific single nucleotide polymorphisms comprise heterozygous single nucleotide polymorphisms. 
     
     
         39 . The method of  claim 36 , wherein said at least 100 single nucleotide polymorphisms that are distinguishable from recipient-specific single nucleotide polymorphisms comprise homozygous single nucleotide polymorphisms. 
     
     
         40 . The method of  claim 36 , wherein said at least 100 single nucleotide polymorphisms that are distinguishable from recipient-specific single nucleotide polymorphisms comprise heterozygous and homozygous single nucleotide polymorphisms. 
     
     
         41 . The method of  claim 36 , wherein said biological sample is a urine sample. 
     
     
         42 . The method of  claim 36 , wherein said biological sample is a sample selected from the group consisting of a blood sample, a plasma sample, and a serum sample. 
     
     
         43 . The method of  claim 36 , wherein said biological sample is a plasma sample. 
     
     
         44 . The method of  claim 36 , wherein said high-throughput sequencing is sequencing-by-synthesis sequencing. 
     
     
         45 . The method of  claim 36 , wherein said sequence reads comprise sequence reads with lengths of at least about 36 base pairs. 
     
     
         46 . The method of  claim 36 , wherein said transplant rejection is acute transplant rejection. 
     
     
         47 . The method of  claim 36 , wherein said transplant rejection is chronic transplant rejection. 
     
     
         48 . The method of  claim 36 , wherein said solid organ comprises an organ selected from the group consisting of kidney, pancreas, liver, heart, lung, and combinations thereof. 
     
     
         49 . The method of  claim 36 , wherein said immunosuppressive drug comprises rapamycin. 
     
     
         50 . The method of  claim 36 , wherein said immunosuppressive drug comprises cyclosporin A. 
     
     
         51 . The method of  claim 36 , wherein said quantitative value is a preset threshold value.