Methods of monitoring immunosuppressive therapies in a transplant recipient

1. A method of treating transplant rejection in a transplant recipient of an organ transplant from a transplant donor without consideration of genotype information from the transplant recipient or donor, the method comprising:

(a) providing cell-free DNA from a sample obtained from the transplant recipient;

(b) amplifying, in a targeted manner from the cell-free DNA, each single nucleotide polymorphism (SNP) in a panel of two or more SNPs, wherein each SNP in the panel is selected to have greater than 0.4 minor allele frequency and low linkage with each other;

(c) sequencing the amplified SNPs to obtain homozygous or heterozygous allele distribution patterns of the SNPs in the panel;

(d) assaying, without consideration of genotype information from the transplant donor or recipient, variance in homozygous or heterozygous allele distribution patterns of the SNPs in the panel as compared to expected homozygous or heterozygous allele distribution patterns to determine the level of donor-derived cell-free DNA;

(e) diagnosing rejection of the transplanted organ in the transplant recipient by discriminating rejection from non-rejection of the transplanted organ, wherein a level of donor-derived cell-free DNA above a suitable threshold is indicative of transplant rejection, and wherein the transplant recipient is diagnosed as exhibiting transplant rejection; and

(f) treating the transplant rejection by administering an immunosuppressive therapy to the transplant recipient diagnosed as exhibiting transplant rejection;

wherein individual genotyping of the donor and the recipient across the genome as a whole or portions thereof to determine which allele of each SNP in the panel belongs to the donor and the recipient is not performed.

2. The method of claim 1 , wherein the organ transplant is a kidney transplant.

3. The method of claim 1 , wherein the organ transplant is a heart transplant.

4. The method of claim 1 , wherein the organ transplant is selected from the group consisting of a liver transplant, a lung transplant, a pancreas transplant, a cornea transplant, an organ system transplant, a bone marrow transplant, a pancreatic islet cell transplant, a stem cell transplant, a skin tissue transplant, a skin cell transplant, and a xenotransplant.

5. The method of claim 1 , wherein the sample is a plasma sample.

6. The method of claim 1 , wherein each SNP in the panel is selected to have an overall population minor allele frequency of greater than 0.4, a target population minor allele frequency of greater than 0.4, and the lowest polymerase error rate of the 6 potential allele transitions or transversions, and the genomic distance between each independent SNP is >500kb.

7. The method of claim 1 , wherein the sequencing of the amplified SNPs is performed using a multiplex sequencing platform.

8. The method of claim 1 , wherein the method further comprises testing for the presence of an infectious agent.

9. The method of claim 8 , wherein the infectious agent is selected from the group consisting of viruses, bacteria, fungi, and parasites.

10. The method of claim 9 , wherein the method further comprises testing for the presence of a virus selected from the group consisting of Cytomegalovirus, Epstein-Barr virus, Anelloviridae, and BK virus.

11. The method of claim 1 , wherein the method further comprises conducting one or more gene expression profiling assays.

12. The method of claim 11 , wherein a combination score is calculated based on the results of the level of donor-derived cell-free DNA and the results of the gene expression profiling assay.

13. The method of claim 1 , wherein a level of donor-derived cell-free DNA above 1% is indicative of transplant rejection.

14. The method of claim 1 , each SNP in the panel is selected to have greater than 0.4 minor allele frequency, an established rate of DNA polymerase error, and low linkage with each other.

15. The method of claim 1 , wherein the panel of SNPs comprises at least 20 independent SNPs that are selected to have greater than 0.4 minor allele frequency and low linkage with each other.