Non-invasive diagnosis of graft rejection in organ transplant patients

• US 9,845,497 B2
• Filed: 02/24/2014
• Issued: 12/19/2017
• Est. Priority Date: 11/06/2009
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Quake, Stephen R., Snyder, Thomas M., Valantine, Hannah
• Primary Examiner(s): Bunker, Amy M
• Application Number:
  US14/188,455
• Publication Number:
  US 20150337361A1
• Time in Patent Office: 1,394 Days
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16H 20/40 relating to mechanical, radiation or invasive therapies, e.g. surgery, laser therapy, dialysis or acupuncture
• CPC Class Codes: G16H 50/20 for computer-aided diagnosis, e.g. based on medical expert systems

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.

Claims

1. A method of detecting donor-specific circulating cell-free nucleic acids in a solid organ transplant recipient, the method comprising:

(a) genotyping a solid organ transplant donor to obtain a single nucleotide polymorphism (SNP) profile of the solid organ transplant donor;

(b) genotyping a solid organ transplant recipient to obtain a SNP profile of the solid organ transplant recipient, wherein the solid organ transplant recipient is selected from the group consisting of;

a kidney transplant, a heart transplant, a liver transplant, a pancreas transplant, a lung transplant, a skin transplant, and any combination thereof;

(c) obtaining a biological sample from the solid organ transplant recipient after the solid organ transplant recipient has received the solid organ transplant from the solid organ transplant donor, wherein the biological sample is selected from the group consisting of blood, serum and plasma, and wherein the biological sample comprises circulating cell-free nucleic acids from the solid organ transplant; and

(d) determining an amount of donor-specific circulating cell-free nucleic acids from the solid organ transplant in the biological sample by detecting a homozygous or a heterozygous SNP within the donor-specific circulating cell-free nucleic acids from the solid organ transplant in at least one assay, wherein the at least one assay comprises high-throughput sequencing or digital polymerase chain reaction (dPCR), and

wherein the at least one assay detects the donor-specific circulating cell-free nucleic acids from the solid organ transplant when the donor-specific circulating cell-free nucleic acids make up at least 0.03% of the total circulating cell-free nucleic acids in the biological sample.

2. The method of claim 1, wherein the biological sample is blood.

3. The method of claim 1, wherein the at least one assay is a high-throughput sequencing assay that generates at least 1,000 sequence reads per hour.

4. The method of claim 3, wherein the high-throughput sequencing assay comprises a next-generation sequencing assay.

5. The method of claim 4, wherein the high-throughput sequencing assay generates sequencing reads of at least 36 bases.

6. The method of claim 1, wherein at least ten different homozygous or heterozygous SNPs are detected.

7. The method of claim 1, further comprising a step of administering a therapeutic regimen to treat the solid organ transplant recipient.

8. The method of claim 7, wherein the therapeutic regimen comprises administering an immunosuppressant treatment.

9. The method of claim 1, wherein the solid organ transplant recipient is a human subject.

10. The method of claim 1, wherein an amplification reaction is performed on the donor-specific circulating cell-free nucleic acids in the biological sample prior to determining the amount of donor-specific circulating cell-free nucleic acids from the solid organ transplant in the biological sample.

11. The method of claim 3, wherein the high-throughput sequencing assay is a shotgun sequencing assay.

12. The method of claim 1, wherein the donor-specific circulating cell-free nucleic acids from the solid organ transplant in the biological sample are DNA, RNA, mRNA, miRNA, double-stranded DNA, single-stranded DNA, single-stranded DNA hairpins, DNA/RNA hybrids, RNA hairpins, or a combination thereof.

13. The method of claim 1, wherein the donor-specific circulating cell-free nucleic acids from the solid organ transplant in the biological sample are RNA.

14. The method of claim 13, wherein the donor-specific circulating cell-free nucleic acids from the solid organ transplant are organ-specific RNA transcripts.

15. The method of claim 1, further comprising genotyping the solid organ transplant donor, the solid organ transplant recipient, or both the solid organ transplant donor and the solid organ transplant recipient prior to the determining in step (d).

16. The method of claim 1, further comprising genotyping the solid organ transplant donor, the solid organ transplant recipient, or both the solid organ transplant donor and the solid organ transplant recipient simultaneously with the determining in step (d).

17. The method of claim 1, wherein the SNP profile comprises informative homozygous and heterozygous SNPs.

18. The method of claim 17, wherein the method further comprises multiplying the number of informative heterozygous SNP molecules from the solid organ transplant by a factor of two.

19. The method of claim 1, wherein sensitivity of the method is greater than 56%.

20. The method of claim 1, wherein the determining comprises detecting donor-specific circulating cell-free nucleic acids from the solid organ transplant wherein the donor-specific circulating cell-free nucleic acids from the solid organ transplant make up between 0.03% and 8.0% of the total circulating cell-free nucleic acids in the biological sample.

21. The method of claim 1, wherein the high-throughput sequencing assay has a sequencing error rate of less than 1.5% for detecting donor-specific circulating cell-free nucleic acids from the solid organ transplant.

22. The method of claim 1, wherein the high-throughput sequencing assay has resequencing error rate of less than 0.003% for detecting donor-specific circulating cell-free nucleic acids from the solid organ transplant.

23. The method of claim 1, wherein the detecting of the homozygous or heterozygous SNP comprises using a quality score.

24. The method of claim 1, wherein the homozygous or heterozygous SNP comprises one or more base changes selected from the list consisting of an insertion, a repeat, and a deletion.

25. The method of claim 1, wherein the homozygous or heterozygous SNP comprises a marker having at least two alleles, each occurring at a frequency greater than 1% of the population.

26. The method of claim 1, wherein the high-throughput sequencing assay comprises mapping one or more of the donor-specific circulating cell-free nucleic acids from the solid organ transplant in the biological sample with a genome sequence of the solid organ transplant donor.

27. The method of claim 1, wherein the biological sample is plasma.

28. The method of claim 1, wherein the biological sample is serum.

29. The method of claim 8, wherein the immunosuppressant regimen is selected from the group consisting of rapamycin, cyclosporin A, and anti-CD40L monoclonal antibody.

30. The method of claim 1, wherein the method comprises using a computer to access data reflecting the amount of donor-specific circulating cell-free nucleic acids from the solid organ transplant in the biological sample.

31. The method of claim 1, wherein the at least one assay detects the donor-specific circulating cell-free nucleic acids from the solid organ transplant when the donor-specific circulating cell-free nucleic acids make up less than 8% of the total circulating cell-free nucleic acids in the biological sample.

32. The method of claim 1, wherein the at least one assay detects the donor-specific circulating cell-free nucleic acids from the solid organ transplant when the donor-specific circulating cell-free nucleic acids make up 2% of the total circulating cell-free nucleic acids in the biological sample.

33. The method of claim 1, wherein the at least one assay detects the donor-specific circulating cell-free nucleic acids from the solid organ transplant when the donor-specific circulating cell-free nucleic acids make up 0.03% of the total circulating cell-free nucleic acids in the biological sample.