Non-invasive diagnosis of graft rejection in organ transplant patients

• US 10,494,669 B2
• Filed: 08/23/2018
• Issued: 12/03/2019
• Est. Priority Date: 11/06/2009
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Quake, Stephen R., Snyder, Thomas M., Valantine, Hannah
• Primary Examiner(s): Bunker, Amy M
• Application Number:
  US16/110,646
• Publication Number:
  US 20180371530A1
• Time in Patent Office: 467 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 heart transplant recipient, the method comprising:

(a) genotyping a heart transplant donor to obtain a single nucleotide polymorphism (SNP) profile of said heart transplant donor;

(b) genotyping a heart transplant recipient to obtain a SNP profile of the heart transplant recipient;

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

(d) performing one or more quantitative polymerase chain reaction (PCR) reactions on said circulating cell-free deoxyribonucleic acid obtained from said biological sample from said heart transplant recipient, wherein said one or more quantitative PCR reactions amplify at least 10 different deoxyribonucleic acid targets, and wherein said at least 10 different deoxyribonucleic acid targets comprise at least 10 informative SNPs; and

(e) quantifying an amount of heart transplant-derived circulating cell-free deoxyribonucleic acid from said heart transplant using markers distinguishable between said heart transplant recipient and said heart transplant donor, wherein said markers distinguishable between said heart transplant recipient and said heart transplant donor are said at least 10 informative SNPs, wherein said quantified amount of heart transplant-derived circulating cell-free deoxyribonucleic acid from said heart transplant using markers distinguishable between said heart transplant recipient and said donor comprises at least 0.03% of the total circulating cell free deoxyribonucleic acid from said biological sample from said heart transplant recipient.

2. The method of claim 1, wherein said at least 10 informative single nucleotide polymorphisms comprise homozygous or heterozygous single nucleotide polymorphisms.

3. The method of claim 1, wherein said at least 10 informative single nucleotide polymorphisms comprise single nucleotide polymorphisms that occur at an allele frequency greater than 1% of a population.

4. The method of claim 1, wherein said quantified amount of said heart transplant-derived circulating cell-free deoxyribonucleic acid is a percentage of said transplant-derived circulating cell-free deoxyribonucleic acid in total circulating cell-free deoxyribonucleic acid.

5. The method of claim 1, wherein said quantified amount of said heart transplant-derived circulating cell-free deoxyribonucleic acid is a ratio of said transplant-derived circulating cell-free deoxyribonucleic acid to total circulating cell-free deoxyribonucleic acid.

6. The method of claim 1, wherein said genotyping said heart transplant donor or said genotyping said heart transplant recipient is separate from (e).

7. The method of claim 1, wherein said circulating cell-free deoxyribonucleic acid is provided from plasma.

8. The method of claim 1, wherein said one or more quantitative PCR reactions comprise a real-time PCR reaction.

9. The method of claim 1, wherein said quantified amount of heart transplant-derived circulating cell-free deoxyribonucleic acid from said heart transplant using markers distinguishable between said heart transplant recipient and said donor comprises between 1.5% and 8% of said total circulating cell free deoxyribonucleic acid from said biological sample from said heart transplant recipient.

10. The method of claim 9, wherein said quantified amount of heart transplant-derived circulating cell-free deoxyribonucleic acid from said heart transplant using markers distinguishable between said heart transplant recipient and said donor comprises at least 0.05% of said total circulating cell free deoxyribonucleic acid from said biological sample from said heart transplant recipient.

11. The method of claim 9, wherein said quantified amount of heart transplant-derived circulating cell-free deoxyribonucleic acid from said heart transplant using markers distinguishable between said heart transplant recipient and said donor comprises at least 2% of said total circulating cell free deoxyribonucleic acid from said biological sample from said heart transplant recipient.

12. The method of claim 9, wherein said quantified amount of heart transplant-derived circulating cell-free deoxyribonucleic acid from said heart transplant using markers distinguishable between said heart transplant recipient and said donor comprises less than 8% of said total circulating cell free deoxyribonucleic acid from said biological sample from said heart transplant recipient.