Compositions and methods for detecting allogeneic matter in a subject

Patent metadata

Field	Value
Publication number	US-11060142-B2
Application number	US-202016795371-A
Country	US
Kind code	B2
Filing date	Feb 19, 2020
Priority date	Mar 1, 2012
Publication date	Jul 13, 2021
Grant date	Jul 13, 2021

Abstract

The present disclosure provides a panel of nucleic acid molecule primers specific for HLA-specific alleles and other genetic polymorphisms, which are useful for quantitatively amplifying these markers to detect, diagnose, and monitor individuals who have or are at risk of certain disease conditions, such as autoimmune disease, proliferative disease, infectious disease, allograft rejection, or pregnancy-related pathologies.

First claim

What is claimed is:

1. A composition, comprising a forward nucleic acid molecule, a reverse nucleic acid molecule, and a probe nucleic acid molecule, wherein the forward, reverse and probe nucleic acid molecules are complementary to HLA-DRB1*01, and wherein the forward nucleic acid molecule has a length of up to 28 nucleotides and comprises the sequence as set forth in SEQ ID NO.:4, the reverse nucleic acid molecule has a length of up to 20 nucleotides and comprises the sequence as set forth in SEQ ID NO.:5, and the probe nucleic acid molecule comprises a nucleic acid sequence, a fluorophore and a quencher, wherein the nucleic acid sequence has a length of up to 40 nucleotides and comprises the sequence as set forth in SEQ ID NO.:6.

2. The composition according to claim 1 , wherein the fluorophore is located at the 5′-end of the probe nucleic acid molecule and the quencher is located at the 3′-end of the probe nucleic acid molecule.

3. The composition of claim 2 , wherein the fluorophore is FAM and the quencher is TAMRA or BHQ.

4. The composition of claim 2 , wherein at least one nucleotide of the probe is a duplex stabilizer.

5. The composition of claim 4 , wherein the duplex stabilizer is at least one LNA or MGB.

6. A kit comprising a nucleic acid composition according to claim 1 .

7. The kit of claim 6 , further comprising one or more reagents for performing PCR.

8. A process for detecting microchimerism, comprising:
(a) amplifying target nucleic acid molecules of a test biological sample using one or more nucleic acid compositions according to claim 1 , wherein the test biological sample comprises a known HLA genotype;
(b) amplifying nucleic acid molecules of a control biological sample using the one or more nucleic acid molecule compositions of (a), wherein the control biological sample comprises a known HLA genotype that is different from the test biological sample; and
(c) detecting the presence of microchimerism when the amplification from the test biological sample and the control biological sample identifies HLA markers in the test biological sample that are also present in the control biological sample.

9. The process of claim 8 , wherein the detection sensitivity is one chimeric genome in 10 5 host genomes.

10. The process of claim 8 , wherein the test biological sample is blood or serum.

11. The process of claim 8 , wherein the microchimerism detected is maternal microchimerism or fetal microchimerism.

12. The process of claim 8 , wherein amplifying comprises performing Q-PCR.

13. A method for detecting incipient allograft rejection, comprising:
(a) obtaining a first biological sample from a subject prior to receiving a transplant from a transplant donor and a second biological sample from the same subject after receiving the transplant during a period of time when there is a risk of rejection;
(b) amplifying target nucleic acid molecules from the biological samples using one or more nucleic acid compositions according to claim 1 , wherein one or more of the nucleic acid compositions comprising the forward, the reverse, and the probe nucleic acid molecules are complementary to target nucleic acid molecules found in the transplant donor and not found in the transplant recipient; and
(c) detecting incipient allograft rejection in the transplant recipient when the presence of amplified target nucleic acid molecules from the transplant donor are detected in the transplant recipient.

14. The method of claim 13 , wherein the first biological sample and/or the second biological sample is blood or serum.

15. The method of claim 13 , wherein the transplant comprises a kidney transplant, a pancreas transplant, an islet cell transplant, a hematopoietic cell transplant, a cord blood transplant or a bone marrow transplant.

16. The method of claim 13 , wherein the subject is human.

17. The method of claim 13 , wherein the subject has a known genotype.

18. The method of claim 13 , wherein amplifying comprises performing Q-PCR.

Assignees

• Hutchinson Fred Cancer Res

Inventors

• Nelson J Lee
• Lambert Nathalie C
• Gadi Vijayakrishna K
• Yan Zhen

Classifications

• C12Q1/6881 Primary

  for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes · CPC title

• C12Q1/6883

  for diseases caused by alterations of genetic material · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q2600/158

  Expression markers · CPC title