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 diagnosing or predicting transplant status or outcome comprising:
 providing a sample from a subject who has received a transplant from a donor;   determining the presence or absence of one or more nucleic acids from said donor transplant, wherein said one or more nucleic acids from said donor are identified based on a predetermined marker profile; and   diagnosing or predicting transplant status or outcome based on the presence or absence of said one or more nucleic acids.   
     
     
         2 . The method of  claim 1  wherein said transplant status or outcome comprises rejection, tolerance, non-rejection based allograft injury, transplant function, transplant survival, chronic transplant s injury, or titer pharmacological immunosuppression. 
     
     
         3 . The method of  claim 2  wherein said non-rejection based allograft injury is selected from the group of ischemic injury, virus infection, pen-operative ischemia, reperfusion injury, hypertension, physiological stress, injuries due to reactive oxygen species and injuries caused by pharmaceutical agents. 
     
     
         4 . The method of  claim 1  wherein said sample is selected from the group consisting of blood, serum, urine, and stool. 
     
     
         5 . The method of  claim 1  wherein said marker profile is a polymorphic marker profile. 
     
     
         6 . The method of  claim 1  wherein said polymorphic marker profile comprises one or more single nucleotide polymorphisms (SNP's), one or more restriction fragment length polymorphisms (RFLP's), one or more short tandem repeats (STRs), one or more variable number of tandem repeats (VNTR's), one or more hypervariable regions, one or more minisatellites, one or more dinucleotide repeats, one or more trinucleotide repeats, one or more tetranucleotide repeats, one or more simple sequence repeats, or one or more insertion elements. 
     
     
         7 . The method of  claim 1  wherein said polymorphic marker profile comprises one or more SNPs 
     
     
         8 . The method of  claim 1  wherein said transplant is selected from the group consisting of kidney transplant, heart transplant, liver transplant, pancreas transplant, lung transplant, intestine transplant and skin transplant. 
     
     
         9 . The method of  claim 1  wherein said nucleic acid is selected from the group consisting of double-stranded DNA, single-stranded DNA, single-stranded DNA hairpins, DNA/RNA hybrids, RNA and RNA hairpins. 
     
     
         10 . The method of  claim 1  wherein said nucleic acid is selected from the group consisting of double-stranded DNA, single-stranded DNA and cDNA. 
     
     
         11 . The method of  claim 1  wherein said nucleic acid is mRNA. 
     
     
         12 . The method of any of the  claims 9  to  11  wherein said nucleic acid is obtained from circulating donor cells. 
     
     
         13 . The method of  claim 1 , wherein said nucleic acid is circulating cell-free DNA. 
     
     
         14 . The method of  claim 1 , wherein the presence or absence of said one or more nucleic acids is determined by a method selected from the group consisting of sequencing, nucleic acid array and PCR. 
     
     
         15 . The method of  claim 14  wherein said sequencing is shotgun sequencing. 
     
     
         16 . The method of  claim 14  wherein said array is a DNA array. 
     
     
         17 . The method of  claim 16  wherein said DNA array is a polymorphism array. 
     
     
         18 . The method of  claim 17  wherein said polymorphism array is a SNP array. 
     
     
         19 . The method of  claim 1 , further comprising quantitating said one or more nucleic acids. 
     
     
         20 . The method of  claim 19 , wherein the amount of said one or more nucleic acids is indicative of transplant status or outcome. 
     
     
         21 . The method of  claim 20 , wherein the amount of said one or more nucleic acids above a predetermined threshold value is indicative of a transplant status or outcome. 
     
     
         22 . The method of  claim 21 , wherein said threshold is a normative value for clinically stable post-transplantation patients with no evidence of transplant rejection or other pathologies. 
     
     
         23 . The method of  claim 21 , wherein there are different predetermined threshold values for different transplant outcomes or status. 
     
     
         24 . The method of  claim 20  wherein temporal differences in the amount of said one or more nucleic acids are indicative of a transplant status or outcome. 
     
     
         25 . The method of  claim 1 , wherein said marker profile is determined by genotyping said transplant donor. 
     
     
         26 . The method of  claim 25 , further comprising genotyping said subject receiving said transplant. 
     
     
         27 . The method of  claim 26 , further comprising establishing a profile of markers, wherein said markers are distinguishable between said transplant donor and said subject receiving said transplant. 
     
     
         28 . The method of any of the  claims 25  to  27  wherein said genotyping is performed by a method selected from the group consisting of sequencing, nucleic acid array and PCR. 
     
     
         29 . The method of  claim 1  wherein said method has at least 56% sensitivity. 
     
     
         30 . The method of  claim 1  wherein said method has at least 78% sensitivity. 
     
     
         31 . The method of  claim 1  wherein said method has a specificity of about 70% to about 100%. 
     
     
         32 . The method of  claim 1  wherein said method has a specificity of about 80% to about 100%. 
     
     
         33 . The method of  claim 1  wherein said method has a specificity of about 90% to about 100%. 
     
     
         34 . The method of  claim 1  wherein said method has a specificity of about 100%. 
     
     
         35 . A computer readable medium comprising:
 a set of instructions recorded thereon to cause a computer to perform the steps of:
 (i) receiving data from one or more nucleic acids detected in a sample from a subject who has received transplant from a donor, wherein said one or more nucleic acids are nucleic acids from said donor transplant, and wherein said one or more nucleic acids from said donor are identified based on a predetermined marker profile; and 
 (ii) diagnosing or predicting transplant status or outcome based on the presence or absence of said one or more nucleic acids.