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.

What is claimed is: 
     
         1 . A method of detecting transplant rejection in a solid organ transplant recipient, the method comprising:
 (a) generating a single nucleotide polymorphism (SNP) profile of the solid organ transplant recipient by genotyping the solid organ transplant recipient and selecting SNPs that have an allele frequency of 0.1 or greater;   (b) providing a biological sample from the solid organ transplant recipient after the solid organ transplant recipient has received a solid organ transplant from a solid organ transplant donor, wherein the biological sample comprises cell-free nucleic acids from the solid organ transplant; and   (c) determining an amount of solid organ transplant-derived cell-free nucleic acids in the biological sample by detecting and quantifying a homozygous or a heterozygous SNP within the transplant-derived cell-free nucleic acids by performing a high-throughput sequencing reaction (HTS) or digital polymerase chain reaction (dPCR), and   (d) detecting transplant rejection if the amount of solid organ transplant-derived cell-free nucleic acids exceeds a predetermined threshold.   
     
     
         2 . The method of  claim 1 , wherein the biological sample is selected from the group consisting of blood, plasma, serum, urine. 
     
     
         3 . The method of  claim 1 , wherein the biological sample is plasma. 
     
     
         4 . The method of  claim 1 , wherein the biological sample is blood. 
     
     
         5 . The method of  claim 1 , wherein the biological sample is urine. 
     
     
         6 . The method of  claim 1 , wherein the solid organ transplant received by the solid organ transplant recipient is selected from the group consisting of: a kidney transplant, a heart transplant, a liver transplant, a lung transplant, a skin transplant, an intestine transplant, a pancreas transplant, a pancreas after kidney transplant, a simultaneous pancreas-kidney transplant, and any combination thereof. 
     
     
         7 . The method of  claim 1 , wherein the SNP profile comprises informative homozygous and heterozygous SNPs. 
     
     
         8 . The method of  claim 1 , wherein the homozygous or the heterozygous SNP is a nucleotide insertion, a repeat, or a deletion. 
     
     
         9 . The method of  claim 1 , further comprising a step of administering an immunosuppressant treatment. 
     
     
         10 . The method of  claim 1 , further comprising a step of adjusting immunosuppressant treatment. 
     
     
         11 . The method of  claim 1 , wherein an amplification reaction is performed on the cell-free nucleic acids in the biological sample prior to determining the amount of solid organ transplant-derived cell-free nucleic acids from the solid organ transplant in the biological sample. 
     
     
         12 . The method of  claim 1 , further comprising generating a single nucleotide polymorphism (SNP) profile of the solid organ transplant donor by genotyping the solid organ transplant donor and selecting SNPs that have an allele frequency of 0.2 or greater. 
     
     
         13 . The method of  claim 1 , wherein the method comprises using a computer to access data reflecting the amount of solid organ transplant-derived cell-free nucleic acids from the solid organ transplant in the biological sample. 
     
     
         14 . The method of  claim 1 , wherein the amount of solid organ transplant-derived cell-free nucleic acids in the biological sample is determined as a percentage of solid organ transplant-derived cell-free nucleic acids amongst solid organ transplant recipient-derived cell-free nucleic acids. 
     
     
         15 . The method of  claim 1 , wherein the amount of solid organ transplant-derived cell-free nucleic acids in the biological sample is determined as a percentage of solid organ transplant-derived cell-free nucleic acids amongst total cell-free nucleic acids. 
     
     
         16 . The method of  claim 1 , wherein the amount of solid organ transplant-derived cell-free nucleic acids in the biological sample is determined as a concentration. 
     
     
         17 . The method of  claim 1 , wherein the cell-free nucleic acids comprise DNA, RNA, mRNA, miRNA, double-stranded DNA, single-stranded DNA, single-stranded DNA hairpins, DNA/RNA hybrids, RNA hairpins, organ-specific RNA transcripts, or a combination thereof. 
     
     
         18 . The method of  claim 1 , wherein the cell-free nucleic acids comprise DNA. 
     
     
         19 . The method of  claim 1 , wherein the solid organ transplant-derived cell-free nucleic acids from the solid organ transplant in the biological sample comprise DNA.