DIAGNOSTIC ASSAY FOR TISSUE TRANSPLANTATION STATUS

A method of detecting circulatory nucleic acids from a transplanted tissue in a transplant recipient, the method comprising: amplifying circulatory nucleic acids from a transplanted tissue in a blood sample from the transplant recipient, and detecting amplification of a copy number deletion (CND) polymorphism from the transplanted tissue, and related methods for determining the status of a donor tissue transplanted into a recipient.

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Description
FILING DATA

This application is a continuation of application Ser. No. 14/349,832, filed Apr. 4, 2014, which is the U.S. National Phase of International Application No. PCT/AU2012/001210, filed Oct. 5, 2012, designating the U.S. and published as WO 2013/049892 A1 on Apr. 11, 2013, which claims priority from Australian Provisional Patent Application No. 2011904235, filed on Oct. 7, 2011, entitled “Diagnostic assay for tissue transplantation status,” the entire contents of which, are incorporated herein by reference.

FIELD

The present disclosure relates generally to tissue, including organ, transplantation. Taught herein is a genetic-based diagnostic assay to ascertain the status of a tissue transplantation procedure in a recipient based on a characterization of circulating or other cell free nucleic acid material. The instant disclosure enables kits, primers and protocols for ascertaining the status of a transplantation procedure.

BACKGROUND

Bibliographic details of the publications referred to by author in this specification are collected alphabetically at the end of the description.

Reference to any prior art in this specification is not, and should not be taken as, an acknowledgment or any form of suggestion that this prior art forms part of the common general knowledge in any country.

Tissue, including organ, transplantation is an important medical procedure to replace diseased or traumatized tissue in a recipient patient with donor tissue from a genetically or histocompatibility matched donor. The success or otherwise of a transplantation procedure is currently determined mainly by an invasive histological examination of biopsied material. However, histological examination has a high degree of sampling error, is invasive, has low sensitivity, can potentially cause tissue damage, requires a high degree of technical expertise and is consequently expensive.

Worldwide, the number of patients requiring an organ transplant far exceeds the availability of suitable organs. An ability to identify early rejection of the transplanted organ would enable a physician to intervene with an appropriate immunosuppressive treatment and save the organ and potentially the patient's life. Reducing the level of organ failure due to rejection increases the availability of donor organs for other patients and significantly reduces the overall cost.

Kidney transplants account for over 50% of all organ transplants in Australia. This will likely increase over time with the number of patients receiving dialysis increasing at a rate of approximately 60% per year. In 2010, the cost of providing dialysis and kidney transplant services was approximately AU$1 billion (Howard et al. (2009) Nephrology 14:123-132; Cass et al. (2010) Kidney Health Australia 27).

The average cost of providing dialysis is AU$61,659 per person per year. This compares to AU$81,549 for a kidney transplant with subsequent costs of AU$11,770 per year. Hence, the ability to facilitate successful kidney transplants has significant economic benefits quite apart from the improved life expectancy and superior quality of life for successful kidney transplant recipients compared to those on dialysis.

The presence of circulating or cell-free DNA was first reported by Mandel et al. (1948) C.R. Acad. Sci Paris 142:241-243. Circulating DNA can arise following processes such as apoptosis and necrosis of tissue (Giacona et al. (1998) Pancreas 17:89-97). In patients with cancer, the circulating DNA can be identified as emanating from cancer cells on the basis of oncogenes, microsatellite altercations and other genetic biomarkers in the DNA (Diehl et al. (2005) Proc. Natl. Acad. Sci USA 102:16368-16373; Diehl et al. (2008) Nat. Med. 14:985-990). Hence, circulating DNA has been used in genotyping studies to detect disease conditions and as an indicator of the health of a person or a fetus.

International Patent Publication No. WO 2011/057061 proposed a genetic approach to monitor for the presence of DNA from donor tissue in a sample from the recipient. The method was based on determining a genetic profile of recipient and a donor DNA whereby the detection of free donor DNA provides an indication that donor cells were being destroyed. The approach proposed required, however, the genotyping of both the recipient and the donor in order to determine an appropriate genetic marker which was definitively donor nucleic acid. Furthermore, the genetic profile was principally focused on mutations or polymorphisms such as single nucleotide polymorphisms, variable number tandem repeats, minisatellites, di-, tri- and tetra-nucleotide polymorphisms and the like.

Lee et al. (2006) Transfusion 46:1870-1878 used bi-allelic insertion-deletion polymorphisms to characterize microchimerism. Subsequently, Abbott Laboratories produced a real-time PCR-based assay to detect 34 bi-allelic insertion-deletion polymorphisms.

Wu et al. (2009) Nature Medicine 15(2):215-219 used polymorphic deletion probes to identify and monitor cellular chimerism between recipient and donor tissue, mainly to ascertain the success or otherwise of stem cell engraftment. The authors proposed that deletion polymorphic detection would complement but not replace established techniques used for monitoring genetic chimerism. It was found that FISH-based polymorphic deletion probe analysis was not as sensitive as PCR-based short tandem-recipient analysis to detect levels of chimerization of less than 5%.

However, insertion-deletion polymorphisms are typically associated with small nucleotide deletions followed by a small number of nucleotide insertions (a few to tens of bp). In terms of their detection by PCR methodologies there is generally sharing of sequence identity between wild-type and indel alleles, which impacts (negatively) on the signal-to-noise ratio for quantification of DNA chimerism.

There is a clear need, therefore, to better manage tissue, including organ, transplantation procedures to ensure a high rate of transplant organ survival. This need is met by an ability to detect rejection at an early stage using a sensitive genetic-based approach.

SUMMARY

The present disclosure teaches a method for determining the status of donor tissue transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulating nucleic acids which have a copy number variant (CNV) polymorphism which indicates the nucleic acids are donor-derived nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or minimal or clinically acceptable cellular damage. In an embodiment, the CNV is a copy number deletion (CND) polymorphism which is one of a panel of CND polymorphisms wherein a given recipient is characterized by having a null genotype for at least one CND polymorphism in the panel and the donor transplant as having a non-null genotype for this CND polymorphism. In an embodiment, the genotype of the donor with respect to CND polymorphisms does not have to be directly determined. Furthermore, the presence or absence of the polymorphism need not be determined by nucleotide sequencing nor by bi-allelic microchimerism. Examples of CNV polymorphisms are listed in Table 2. In an embodiment, the CNVs are CNDs as listed in Table 3.

CNV is defined as a DNA sequence that varies in copy number within individuals in the population, the length of DNA sequence affected may vary from a few hundred base pairs to several million base pairs. Contrastingly, sequence-level deletions involve shorter sequences of DNA, typically in the range 1 bp to 100 bp. Insertion-deletion is described as a deletion of DNA sequence (usually a few base pairs) followed by an insertion of DNA sequence (usually a few base pairs) after the deleted nucleotides.

The use of CNV-deletion loci enables interrogation of large DNA sequences (by qPCR or other molecular methodology) that are absent in the recipient, thus completely avoiding the issue of distinguishing donor DNA from background recipient DNA and leading to improvements in the signal-to-noise ratio for measurement of target DNA levels.

Reference to “tissue” includes an organ, limb and appendage as well as microtissues and stem cells. Examples of organs include a kidney, heart, lung, pancreatic islet, liver, intestine and skin

Examples of limbs include a leg, arm, hand and foot. Examples of an appendage include a toe, nose and ear. Examples of stem cells include adult and embryonic stem cells. The sample which is screened for free nucleic acids is selected from plasma, whole blood, serum, urine, pus, respiratory fluid, lymph fluid, feces, bile, saliva, sputum, semen, vaginal flow, cerebrospinal fluid, brain fluid, ascites, milk, secretions from the genitourinary tract and a lavage of a tissue or organ (e.g. a lung) In an embodiment, the sample is plasma, whole blood or serum. In an embodiment, the sample is urine. A “free” nucleic acid includes a circulating nucleic acid and refers to nucleic acid released following cell damage. Cell damage may result from processes such as apoptosis or necrosis, drug cytotoxicity or an immunologically-based rejection reaction.

Another aspect enabled herein is a transplantation protocol for transplanting tissue from a donor to a recipient, the protocol comprising transplanting the tissue and then monitoring a sample from the recipient for the presence of circulating nucleic acids which are from donor cells wherein if donor nucleic acids are detected, the recipient is subjected to immunosuppression therapy or, if the patient is on immunosuppression therapy, the therapy may be altered.

The subject disclosure further teaches an assay to monitor the balance between immunosuppression and tissue damage such as due to rejection or pharmaceutical cytotoxicity. Hence, the subject disclosure teaches a method of treating a subject who has undergone a transplantation procedure by monitoring for changes in the levels of donor nucleic acids. Such changes may be relative to a control. The control includes pre-transplantation levels of free recipient nucleic acids or a change in the ratio of total nucleic acids to donor nucleic acids.

Further provided is the use of a panel of CNVs such as CNDs which identifies a nucleic acid as being of donor origin or, by deduction, non-recipient origin in the manufacture of a diagnostic assay to detect the status of transplanted tissue in the recipient. In an embodiment, one of the recipient or donor has a null genotype with respect to at least one of the CND polymorphisms and the other of the recipient or donor does not.

Table 2 provides a list of common CNVs which are characteristic of in recipient DNA. The list in Table 2 should be read in conjunction with, and includes, other known CNVs such as those defined in Conrad et al. (2010) Nature 464:704-712; McCarroll et al. (2008) Nat Genet 40(10):1166-1174. One group of 10 CNVs, in the form of CNDs is listed in Table 3. In an embodiment, at least one CND null genotype is present in any given recipient. The donor need not be genotyped as CND polymorphisms are selected such that there is approximately a 50% probability that if a recipient has a null-CND genotype, the donor will not. In transplant recipients experiencing variable clinical signs of rejection, the donor-specific plasma nucleic acid concentrations may vary which correlates with the immunologic mechanism of rejection (i.e. humoral versus cellular) as well as the medical category of rejection (i.e. acute versus chronic).

The following abbreviations used in the specification are defined in Table 1.

TABLE 1 Abbreviations Abbreviation Definition AP-PCR Arbitrarily primed PCR cfDNA Circulating, free DNA CND Copy number deletion CNV Copy number variant CP-PCR Consensus sequence primed PCR DOP-PCR Degenerate oligonucleotide-primer PCR MF-PCR Multiplex fluorescent PCR PCR Polymerase chain reaction PCR/RFLP Restriction fragment length PCR q-PCR Quantitative PCR qf-PCR Quantitative fluorescent PCR RT-PCR Real time PCR NABSA Nucleic acid based sequence amplification Null genotype Zero copies of a genetic marker (nullisomic) SRY Sex-determining region Y

BRIEF DESCRIPTION OF THE FIGURES

Reference is made to a “CND_0X” were X is a numeral from 1 to 10. These are CNVs which are defined in Table 3 and are selected from Table 2.

FIG. 1a is a diagrammatic and photographic representation of CND_01 internal PCR: Shaded region indicates the deleted segment. Lanes 2-22 are 21 control samples (12/21—null copy, 9/21—1 or 2 copy), lanes 1 and 24—Marker VIII and lane 23-blank. FIG. 1b is a diagrammatic and photographic representation of CND_01 flanking PCR: Lanes 2-22 are the same 21 control samples (19/21 are null or 1 copy; 2/21 are 2 copy wild-type (arrowed); lane 1 and 24—Marker VIII and lane 23—blank.

FIG. 2 is a photographic representation of internal PCR on cellular and plasma DNA for CND_02: —For 4 control samples, cellular and plasma DNA sample were tested in alternate lanes (lane 2 to 9). Difference in the band intensity is due to the different amounts of DNA in plasma and cellular sample (Cellular DNA is equivalent to ˜19000 GE, whereas plasma DNA is equivalent to ˜250 GE in the reaction).

FIG. 3 is a photographic representation of sensitivity of CNV deletion genotyping. The sensitivity was as low as 1%.

FIG. 4 is a graphical representation of the detection of non-self sex-determining region Y (SRY). DNA in recipient blood plasma using quantitative PCR (q-PCR).

FIGS. 5a through c are graphical representations of CND_01, CND_02 and CND_03 showing accurate, precise and robust measurements of rare DNA.

FIG. 6 is a photographic representation of internal PCR on cellular and plasma DNA for patient sample. Lanes 2-5 CND_02 (uninformative as both recipient and donor are ‘null’) lane 7-10 CND_03 (informative), lane 12-15 CND_08 (informative).

FIGS. 7a and b are graphical representations of plasma transplant-derived cDNA (a) and total cfDNA (b) for 35 transplant recipients. In the transplant recipients experiencing variable clinical signs of rejection, the donor-specific plasma DNA concentrations were found to vary and this appeared to correlate with the immunologic mechanism of rejection (i.e. humoral versus cellular mediated) as well as the medical category of rejection (i.e. acute versus chronic).

FIGS. 8a and b are graphical representations of plasma-derived cfDNA (a) and total plasma cfDNA (b) in pre-transplant and post-transplant recipients.

 DETAILED DESCRIPTION

Throughout this specification, unless the context requires otherwise, the word “comprise” or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element or integer or method step or group of elements or integers or method steps but not the exclusion of any element or integer or method step or group of elements or integers or method steps.

As used in the subject specification, the singular forms “a”, “an” and “the” include singular and plural aspects unless the context clearly dictates otherwise. Thus, for example, reference to “copy number variant” includes a single copy number variant, as well as two or more different copy number variants; reference to “an organ” includes a single organ, as well as two or more organs; reference to “the disclosure” includes single or multiple aspects taught by the disclosure; and so forth. The aspects taught and enabled herein are encompassed by the term “invention”. All such aspects are enabled within the width of the claims.

The present disclosure teaches a non-invasive assay to assess the outcome of a tissue transplantation procedure. The assay relies on the identification of non-recipient nucleic acids (i.e. donor nucleic acids) in a biological sample from the recipient of transplanted tissue from the donor. By “identification” includes characterization and quantitation. The assay characterizes a copy number variant (CNV) polymorphism, such as a copy number deletion (CND), which identifies donor nucleic acid in a mixture of recipient nucleic acid in the sample. The CNV such as CND does not require sequence analysis or bi-allelic microchimerism analysis. Damage to a transplanted tissue elicits release of donor nucleic acids from the transplanted cells into the circulatory system and other fluids of the recipient. The status of the transplanted tissue can be monitored and early signs of cellular damage identified leading to appropriate clinical intervention to save the tissue. Cellular damage can result from inter alia immunological-based rejection, apoptosis, necrosis, pharmacological cytotoxicity, trauma, blood flow ischemia and infection. The clinical intervention may involve the administration of immunosuppressive drugs, if the patient is on immunosuppression therapy, a change in dose of the drug or the type of drug. Other interventions include anti-pathogen therapy, drugs to improve blood flow or protocols to reduce swelling or trauma to the tissue. The assay may be universally applied to all transplantation procedures without need of directly determining a donor's CNV polymorphism genotype. The detection of a CNV polymorphism enables a highly sensitive approach of identifying non-recipient human DNA. In an embodiment, the recipient has a null genotype with respect to the CNV polymorphism and the donor does not. Alternatively, the donor has a null genotype with respect to the CNV polymorphism and the recipient does not.

A CNV is a structural genomic variant, measuring 1 kb in length or larger (e.g. 1 kb-108 kb), that results in confined copy number changes in a specific chromosomal region. If its population allele frequency is less than 1%, it is referred to as variants (CNVs) include insertions and deletions as well as more complex changes that involve gains and losses at the same locus. CNV was originally defined as insertions and deletions greater than 1 kb in size (Feuk et al. (2006) Nature Rev 7:85-97). Over time, with the wealth of data emerging from the sequencing of human genomes (The 1000 Genomes Project Consortium (2010) Nature 467:1061-1073), the operational spectrum of copy number variant (CNVs) has widened to include much smaller events (for example, those >50 bp in length). These are distinguished from small sequence deletion polymorphisms (also called single base changes) by their genomic size (Weber et al. (2002) Am J Human Genet 71:854-862).

The CNV polymorphisms are selected on the basis that due to their high incidence in the population, a recipient will be characterized as having nucleic acids with at least one CNV genotype and a 50% likelihood that if a recipient or donor has a given CNV genotype, then the other of the recipient or donor will not. In an embodiment, the recipient nucleic acid is characterized as being nullisomic for at least one of the CNV sites and the donor is not.

Accordingly, the present disclosure teaches a method for determining the status of a donor tissue transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulating nucleic acids which have a copy number variant (CNV) polymorphism which indicates it is donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level. An “acceptable level” means minimal adverse clinical side effects.

The detection of donor nucleic acids means the detection of non-recipient-derived nucleic acid material which in turn is indicative of transplant rejection or other damage to the transplant including apoptosis, necrosis, ischemia, trauma or infection. The damage may also be due to a drug administered to the patient such as an immunosuppression drug. The absence of donor nucleic acids means that non-recipient nucleic acid material is not being released which is indicative of a successful or healthy transplantation. The CNV polymorphism genotype of the donor does not need to be determined for the assay to be effective. A panel of CNV polymorphisms is screened on the basis that any given recipient will have or not have at least one of these polymorphisms and the donor will have or not have one polymorphism different from the recipient. In an embodiment, the recipient is nullisomic for at least one of the CNV sites in the panel and the donor is not. In another embodiment, the donor is nullisomic for at least one of the CNV sites in the panel and the recipient is not. Furthermore, in transplant recipients experiencing variable clinical signs of rejection, the donor-specific plasma nucleic acid concentrations may vary which correlates with the immunologic mechanism of rejection (i.e. humoral versus cellular) as well as the medical category of rejection (i.e. acute versus chronic).

Consequently, the present specification is instructional for a method for determining the status of a donor tissue transplanted into a recipient, the method comprising screening circulating nucleic acids in sample from the recipient for the presence of a CNV polymorphism selected from a panel of polymorphisms wherein the donor nucleic acids comprise the presence or absence of at least one polymorphism not shared by the recipient wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level for such as but not limited to the continued health of a patient.

In a related embodiment, the present specification enables a method for determining the status of a donor tissue transplanted into a recipient, the method comprising selecting a panel of from 1 to 200 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms, screening a sample from the recipient for the presence of circulating nucleic acids with the presence of nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the donor nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level. In an embodiment, the panel comprises 1 to 100 oligonucleotide pairs targeting from 1 to 100 CNV polymorphisms. In an embodiment, there are from 1 to 10 oligonucleotide pairs targeting 1 to 10 CNV polymorphisms. By “1 to 200” means 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199 or 200.

Reference to “tissue” with regards to transplantation includes an organ, limb, appendage and skin as well as microtissue and stem cells. Examples of organs include kidney, heart, lung, pancreatic islet, liver, intestine and skin. A limb includes a leg, arm, hand and foot. An appendage includes a toe, nose and ear.

In an embodiment, the tissue is an organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver, intestine and skin.

Hence, the present disclosure teaches a method for determining the status of donor organ transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulating nucleic acids which have a CNV polymorphism which indicates it is not the recipient's nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The present specification is further instructional for a method for determining the status of a donor organ transplanted into a recipient, the method comprising screening circulating nucleic acids in a sample from the recipient for the presence of CNV polymorphism selected from a panel of polymorphisms wherein the recipient's nucleic acids comprise the presence or absence of at least one polymorphism not shared by the donor wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of a donor organ transplanted into a recipient, the method comprising selecting a panel of from 1 to 200 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms, screening a sample from the recipient for the presence of circulating nucleic acids with the presence of nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the donor on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of a donor organ transplanted into a recipient, the method comprising selecting a panel of from 1 to 100 oligonucleotide primer pairs which target from 1 to 100 known CNV polymorphisms, screening a sample from the recipient for the presence of circulating nucleic acids with the presence of nucleic acids with the from 1 to 100 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the donor on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of a donor organ transplanted into a recipient, the method comprising selecting a panel of from 1 to 10 oligonucleotide primer pairs which target from 1 to 10 known CNV polymorphisms, screening a sample from the recipient for the presence of circulating nucleic acids with the presence of nucleic acids with the from 1 to 10 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the donor on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the tissue is an organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver, intestine and skin.

In an embodiment, the organ is a kidney.

Accordingly, the present disclosure teaches a method for determining the status of a donor kidney transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulating nucleic acids which have a CNV polymorphism which indicates it is not the recipient's nucleic acids wherein the presence of non-recipient nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level for the continued health of a patient. By “non-recipient” means “donor”.

The present specification is also instructional for a method for determining the status of a donor kidney transplanted into a recipient, the method comprising screening circulating nucleic acids in sample from the recipient for the presence of CNV polymorphism selected from a panel of polymorphisms wherein the recipient's nucleic acids comprise the presence or absence of at least one polymorphism not shared by the donor wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of a donor kidney transplanted into a recipient, the method comprising selecting a panel of from 1 to 200 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms, screening a sample from the recipient for the presence of circulating nucleic acids with the presence of nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level for the continued health of a patient.

In an embodiment, the present specification enables a method for determining the status of a donor kidney transplanted into a recipient, the method comprising selecting a panel of from 1 to 100 oligonucleotide primer pairs which target from 1 to 100 known CNV polymorphisms, screening a sample from the recipient for the presence of circulating nucleic acids with the presence of nucleic acids with the from 1 to 100 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level for the continued health of a patient.

In an embodiment, the present specification enables a method for determining the status of a donor kidney transplanted into a recipient, the method comprising selecting a panel of from 1 to 10 oligonucleotide primer pairs which target from 1 to 10 known CNV polymorphisms, screening a sample from the recipient for the presence of circulating nucleic acids with the presence of nucleic acids with the from 1 to 10 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level for the continued health of a patient.

The “status” of the transplanted tissue means the presence or absence of any cellular damage to transplanted tissue. The presence of tissue damage is indicated by release of nucleic acids from cells of the donor tissue transplanted into the recipient. The status is the outcome of the assay. The released nucleic acids are referred to herein as “free” or “circulating” nucleic acids (e.g. circulating, free DNA [cfDNA]). The sample includes plasma, whole blood, serum, urine, pus, respiratory fluid, lymph fluid, feces, bile, saliva, sputum, semen, vaginal flow, cerebrospinal fluid, brain fluid, ascites, milk, secretions from the genitourinary tract and a lavage of a tissue or organ (e.g. a lung). In an embodiment, the sample is plasma, whole blood or serum. In an embodiment, the sample is urine. Hence, aspects contemplated herein include assaying biological fluid for circulating, free nucleic acids, such as cfDNA.

A “free” nucleic acid includes a circulating nucleic acid (e.g. cfDNA) and refers to nucleic acid released following cell damage. Cell damage may result from processes such as inter alia apoptosis or necrosis, drug cytotoxicity or an immunologically-based rejection reaction.

The assay is based on detection at the level of presence or absence of non-recipient (i.e. donor-derived) nucleic acids. The levels of donor-derived nucleic acids may also be monitored over time such as following transplantation or following administration of immunosuppression drugs or other therapies. Detection of donor-derived nucleic acids may also be used to assess the likelihood that the transplanted tissue will survive or will require removal and/or to assess the toxicity of a drug being given to a patient. Tissue damage includes immunological rejection, apoptosis, necrosis, trauma, ischemic injury, infection by a pathogen, perioperative ischemia, reperfusion injury, hypertension, injuries due to reactive oxygen species and pharmaceutical toxicity.

Terms such as “diagnosis”, “prognosis”, “determination”, “monitor”, “assay” and the like may be used to describe the methodology of detecting donor nucleic acids or nucleic acids which are not of recipient origin. The diagnostic assay may also be used in a protocol to monitor the health of a patient with respect to the status of the transplanted tissue and/or the level of toxicity of any drugs being administered to the patient.

Hence, the method enabled herein provides a means for assessing the transplant status or outcome. The status or outcome may range from transplant rejection to transplant tolerance or to any form of cellular damage. Tissue damage is evidenced by detection of non-recipient (i.e. donor tissue-derived) nucleic acids. These are released into various fluids in the recipient following apoptosis of cells of the donor tissue. Transplantation tolerance or non-damage tissue is evidenced by an absence of donor-derived nucleic acids or a level of donor-derived nucleic acids which relative to a control is indicative of minimal cell damage or a level of cell damage which is clinically acceptable for the continued health of the patient. Evidence for transplantation tolerance provides an indication that the transplant will likely survive or is at least healthy at any given time period.

As used herein, the diagnosis or prognosis of transplant status includes predicting, assessing, determining and diagnosing transplant status or outcome and in some cases the likelihood that a patient will survive a transplantation procedure or post-transplantation medical protocol.

The CNV polymorphism may be a deletion, insertion or an expansion. In an embodiment, it is a CNV deletion, referred to herein as a copy number deletion CND or CND polymorphism.

A panel of CNV deletions is selected which is expected to have approximate null frequencies of 40-50% in the general population. This is done by in silico analysis of public data (Conrad et al. (2010) supra; McCarroll et al. (2008) supra). These CNV regions are polymorphic and have no intrinsic clinical significance. CNV selection and frequency calculations are performed as follows: The HapMap data set includes trio-data for each CNV. For frequency calculations, only singleton and parental samples are included. CNVs with only 0, 1 and 2 copy genotypes are selected for analysis (i.e. CNVs of more than 2 copy and Chromosomes X and Y CNVs are excluded). For each selected CNV, frequencies of 0, 1 and 2 copy genotypes are calculated. CNVs in the form of CNDs overlapping with segmental duplications were excluded. CNVs with 0.4-0.5 null copy frequency and less than 3 kb in size were selected from Table 2. An example is the CNDs listed in Table 3.

Table 2 provides a list of common CNV sites which are commonly present in recipient nucleic acid. The list in Table 2 should be read in conjunction with, and includes, other known CNVs such as those defined in Conrad et al. (2010) supra; McCarroll et al. (2008) supra. Included herein is an aspect whereby the recipient is nullisomic for at least one of the CND sites and the donor is not. In another embodiment, the donor is nullisomic for a CND site and the recipient is not. The donor need not be genotyped as there is a 1 in 2 chance (50% probability) that if a recipient has a given CND site, the donor will not or vice versa. Table 3 is an example of a panel of suitable CND sites useful in the practice of the present assay. The CNDs in Table 3 are referred to as “CND_0X” where X is a numeral from 1 to 10. These correlate to a CNP ID in Table 2 via their CNP_id. in Table 3.

Hence, the subject specification teaches a method for determining the status of donor tissue transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulatory nucleic acids which have or do not have a CND polymorphism which indicates it is donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

Further taught here is a method for determining the status of donor tissue transplanted into a recipient, the method comprising screening circulatory nucleic acids in sample from the recipient for the presence of CNV polymorphism selected from a panel of polymorphisms wherein the recipient's nucleic acids comprise the presence or absence of at least one polymorphism not shared by the donor wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of donor tissue transplanted into a recipient, the method comprising selecting a panel of from 1 to 200 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms, screening a sample from the recipient for the presence of nucleic acids with the presence of circulatory nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of apoptosis of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of donor tissue transplanted into a recipient, the method comprising selecting a panel of from 1 to 100 oligonucleotide primer pairs which target from 1 to 100 known CNV polymorphisms, screening a sample from the recipient for the presence of nucleic acids with the presence of circulatory nucleic acids with the from 1 to 100 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of apoptosis of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of donor tissue transplanted into a recipient, the method comprising selecting a panel of from 1 to 10 oligonucleotide primer pairs which target from 1 to 10 known CNV polymorphisms, screening a sample from the recipient for the presence of nucleic acids with the presence of circulatory nucleic acids with the from 1 to 10 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of apoptosis of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the CNV polymorphism panel is selected from the list in Table 2 wherein the recipient is characterized by having the null genotype for at least one CNV region in the panel wherein the presence of nucleic acids characterized by not having the null genotype for at least one CNV region in the panel indicates the nucleic acids are non-recipient nucleic acids wherein the presence of donor (non-recipient) nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor (non-recipient) nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

An example of a panel of CNVs is the CND panel set forth in Table 3.

Accordingly, the present disclosure teaches a method for determining the status of donor organ transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulatory nucleic acids which have a CNV polymorphism selected from the list in Table 2 wherein nucleic acids characterized by not having the null genotype for at least one CNV region in the panel indicates nucleic acids are donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present disclosure teaches a method for determining the status of donor organ transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulatory nucleic acids which have a CND polymorphism selected from the list in Table 3 wherein nucleic acids characterized by not having the null genotype for at least one CND region in the panel indicates nucleic acids are donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The present specification enables a method for determining the status of donor organ transplanted into a recipient, the method comprising selecting a panel of from 1 to 200 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms selected from the list set forth in Table 2, screening a sample from the recipient for the presence of nucleic acids with the presence of circulatory nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of non-recipient nucleic acids or a level of non-recipient nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The present specification is further instructional for a method for determining the status of donor organ transplanted into a recipient, the method comprising screening circulatory nucleic acids in sample from the recipient for the presence of CNV polymorphism selected from a panel of polymorphisms as set forth in Table 2 wherein the recipient's nucleic acids comprise the presence or absence of at least one polymorphism not shared by the donor wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the tissue is an organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver and intestine.

The present disclosure also teaches a method for determining the status of a donor kidney transplanted into a recipient, the method comprising screening a sample from the recipient for the presence or absence of circulatory nucleic acids which have a CNV polymorphism selected from the list set forth in Table 2 wherein the presence of nucleic acids not having the null genotype for at least one CNV region in the panel indicates the nucleic acids are donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The present specification enables a method for determining the status of donor tissue transplanted into a recipient, the method comprising selecting a panel of from 1 to 50 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms such as selected from the list set forth in Table 2, screening a sample from the recipient for the presence of circulatory nucleic acids with the presence of nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The present specification is further instructional for a method for determining the status of a donor kidney transplanted into a recipient, the method comprising screening circulatory nucleic acids in sample from the recipient for the presence of CNV polymorphism selected from a panel of polymorphisms as set forth in Table 2 wherein the presence of nucleic acids not having the null genotype for at least one CNV region in the panel indicates the nucleic acids are donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The biological sample includes a body fluid such as plasma, whole blood, serum, urine, pus, respiratory fluid, lymph fluid, feces, bile, saliva, sputum, semen, vaginal flow, cerebrospinal fluid, brain fluid, ascites, milk, secretions from the genitourinary tract and a lavage of a tissue or organ (e.g. a lung).

In an embodiment, the sample is blood plasma.

In an embodiment, the CNV is a CND. Examples of CNDs are listed in Table 3.

The present disclosure teaches a method for determining the status of donor tissue transplanted into a recipient, the method comprising screening a blood plasma sample from the recipient for the presence or absence of nucleic acids which have a CNV polymorphism including a CND polymorphism such as a CND listed in Table 2 or 3 which indicates it is donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

An example of an acceptable level of donor nucleic acids is a level which enables the health of the patent to be maintained.

Taught herein is a method for determining the status of donor tissue transplanted into a recipient, the method comprising selecting a panel of from 1 to 200 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms such as a CNDs listed in Table 2 or 3, screening a blood plasma from the recipient for the presence of nucleic acids with the presence of nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The present specification is further instructional for a method for determining the status of donor tissue transplanted into a recipient, the method comprising screening nucleic acids in blood plasma from the recipient for the presence of CNV polymorphism such as a CND polymorphism selected from a panel of polymorphisms such as listed in Table 2 or 3 wherein the recipient's nucleic acids comprise the presence or absence of at least one polymorphism not shared by the donor wherein the presence of donor nucleic acids is indicative of apoptosis of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present disclosure teaches a method for determining the status of donor organ transplanted into a recipient the donor organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver and intestine, the method comprising screening a blood plasma from the recipient for the presence or absence of nucleic acids which have a CNV polymorphism which indicates it is from the transplanted tissue of the donor wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of donor organ transplanted into a recipient the donor organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver and intestine, the method comprising selecting a panel of from 1 to 200 oligonucleotide primer pairs which target from 1 to 200 known CNV polymorphisms, screening a blood plasma sample from the recipient for the presence of nucleic acids with the presence of nucleic acids with the from 1 to 200 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of donor organ transplanted into a recipient the donor organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver and intestine, the method comprising selecting a panel of from 1 to 100 oligonucleotide primer pairs which target from 1 to 100 known CNV polymorphisms, screening a blood plasma sample from the recipient for the presence of nucleic acids with the presence of nucleic acids with the from 1 to 100 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the present specification enables a method for determining the status of donor organ transplanted into a recipient the donor organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver and intestine, the method comprising selecting a panel of from 1 to 10 oligonucleotide primer pairs which target from 1 to 10 known CNV polymorphisms, screening a blood plasma sample from the recipient for the presence of nucleic acids with the presence of nucleic acids with the from 1 to 10 oligonucleotide primer pairs wherein the recipient nucleic acids are characterized as having or not having at least one of the known CNV polymorphisms from the panel and the donor nucleic acids are distinguished from the recipient on the basis of having or not having the polymorphism shared by the recipient, wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

The CNVs include CNDs such as those listed in Table 2 as exemplified in Table 3.

The present specification is further instructional for a method for determining the status of donor organ transplanted into a recipient, the donor organ selected from the list consisting of a kidney, heart, lung, pancreatic islet, liver and intestine, the method comprising screening nucleic acids in blood plasma sample from the recipient for the presence of CNV polymorphism selected from a panel of polymorphisms selected from the list in Table 2 wherein the recipient's nucleic acids comprise the presence or absence of at least one polymorphism not shared by the donor wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

In an embodiment, the tissue is an organ is a kidney.

Hence, the present disclosure teaches a method for determining the status of a donor kidney transplanted into a recipient, the method comprising screening a blood plasma from the recipient for the presence or absence of nucleic acids which have a CNV polymorphism selected from the list in Table 2 which indicates it is donor nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

Blood sampling may be accomplished by any technique known in the art such as via syringe, vacuum suction device, pin prick and the like. A blood sample may be further treated or processed such as to concentrate the presence of nucleic acids to remove high abundance molecules, to reduce coagulation, to reduce thrombolysis, to adjust the pH or osmolality or to stabilize the fluid. The blood sample, if treated appropriately, including its storage, may be maintained and assayed from less than one hour to 24 hours to 2 weeks after collection. Alternatively, it is assayed immediately or within a 24 hour period from collection.

The nucleic acids are generally genomic DNA but may also be mRNA or other RNA species. The RNA may be screened for directly or after conversion to DNA such as cDNA.

Methods and kits are taught herein to readily screen a patient following a transplantation procedure. A panel of primers which detail common CNV polymorphisms is used. An example is set forth in Table 2 in relation to CNV polymorphisms. In an embodiment, recipients have the null genotype (i.e. zero copies) for at least one CND site in the panel. Table 3 is an example of a CND subset of CNVs listed in Table 2.

The recipient may express all or some of the CNV polymorphisms. The donor does not have to be genotyped with respect to CNV polymorphisms since any nucleic acids which are not the recipients nucleic acids are presumed to be the donor's nucleic acids. The method enabled herein provides a reliable approach to monitor the success or otherwise of a transplantation procedure and/or a method of treatment to mitigate rejection or other form of tissue injury.

Conveniently, the CNV genotype of fluid nucleic acids is determined by an amplification reaction, such as digital or real time PCR followed by gel electrophoresin, nucleotide sequencing, expression of reporter molecules (Gonzalez et al. (2005) Environ. Michrobiol. 7(7): 1024-1028; DeLa Vega et al. (2005) Mutation Research 573:111-135; Livak et al. (1995) Nature Genetics 9:341-342).

Amplification reactions useful in the practice of the present method include quantitative PCR (q-PCR), quantitative fluorescent PCR (qf-PCR), multiplex fluorescent PCR (MF-PCR), real time PCR (RT-PCR), single cell PCR, restriction fragment length PCR (PCR-RFLP), PCR-RFLP/RT-PCR-RFLP, hot start PCR, nested PCR, in situ polonony PCR, in situ rolling circle amplification, bridge PCR, picotiter PCR and emulsion PCR. Other amplification methods include selective amplification of target polynucleotide sequences, consensus sequence primed PCR (CP-PCR), arbitrarily primed PCR (AP-PCR), degenerate oligonucleotide-primer PCR (DOP-PCR) and nucleic acid based sequence amplification (NABSA).

Following amplification, the CNV genotype is determined such as by electrophoresis which includes capillary, capillary zone, capillary isoelectric focusing and capillary gel electrophoresis as well as capillary electrochromatography, micellar electrokinetic capillary chromatography and transient isotachophoresis by use of arrays, beads, gas chromatography, supercritical fluid chromatography, liquid chromatography (which encompasses partition, adsorption, ion exchange, size exclusion, thin-layer and affinity chromatography). Other techniques include comparative genomic hybridization, microarrays, bead arrays and high through-put genotyping such as with the use of a molecular inversion probe.

Also enabled herein are reagents and kits for screening for or quantitating donor-derived nucleic acids. The subject reagents and kits may vary in form and control. Reagents of interest include reagents specifically designed for (i) genotyping nucleic acid from a recipient; (ii) identification of marker profiles; and (ii) detection and/or quantitation of one or more nucleic acids from a transplant donor in a sample obtained from a transplant recipient.

One type of such reagents are one or more probes or an array of probes to genotype and/or to detect and/or to quantitate one or more nucleic acids. A variety of different array formats are known in the art, with a wide variety of different probe structures, substrate compositions and attachment technologies. In an example, the CNV polymorphisms listed in Table 2 are screened by a panel of oligonucleotide primers and/or probes. In an example, CND polymorphism listed in Table 3 are screened by a panel of oligonucleotide primers and/or probes.

The kits herein may include arrays or other solid phase platforms. Such kits may additionally comprise one or more therapeutic agents. The kit may further comprise a software package for data analysis, which may include reference profiles for comparison with the test profile.

The kits may comprise reagents such as buffers and H2O or other excipients. The kits may comprise reagents necessary to perform nucleic acid extraction and/or nucleic acid detection using the methods described herein such as PCR and sequencing.

Such kits may also include information, such as scientific literature references, package insert materials, diagnostic trial results, and/or summaries of these and the like, which indicate or establish the activities and/or advantages of the diagnostic assay indicative of the presence of donor nucleic acids in a body sample. Such kits may also include instructions to access a database. Such information may include results of pre-determined trials and controls based on human or animal diagnostic trials. Kits described herein can be provided, marketed and/or promoted to health providers, including physicians, nurses, pharmacists, formulary officials, and the like. Kits may also, in some embodiments, be marketed directly to the consumer. The latter is particularly useful for home care and personalized medicine.

Any of the methods above can be performed by a computer program product that comprises a computer executable logic that is recorded on a computer readable medium. For example, the computer program can execute some or all of the following functions: (i) controlling isolation of nucleic acids from a sample, (ii) pre-amplifying nucleic acids from the sample, (iii) amplifying, sequencing or arraying specific polymorphic regions in the sample, (iv) identifying and quantifying a CNV marker profile in the sample, (v) comparing data on the CNV marker profile detected from the sample with a predetermined threshold, (vi) determining a transplant status or outcome, (vi) declaring normal or abnormal transplant status or outcome. In an embodiment, the computer executable logic can analyze data on the detection and quantity of CND polymorphisms.

The computer executable logic can work in any computer that may be any of a variety of types of general-purpose computers such as a personal computer, network server, workstation, or other computer platform including handheld and portable devices. In an embodiment, a computer program product is described comprising a computer usable medium having the computer executable logic (computer software program, including program code) stored therein. The computer executable logic can be executed by a processor, causing the processor to perform functions described herein. In an other embodiment, some functions are implemented primarily in hardware using, for example, a hardware state machine. Implementation of the hardware state machine so as to perform the functions described herein will be apparent to those skilled in the relevant arts.

The program can provide a method of evaluating a transplant status or outcome in a transplant recipient by accessing data that reflects the genotyping of the transplant recipient and/or the presence or absence of one or more nucleic acids from the transplant donor in the circulation of the transplant patient post-transplantation.

In an embodiment, the computer executing the computer logic herein described may also include a digital input device such as a scanner. The digital input device can provide information on a nucleic acid, e.g. CNV (e.g. CND) presence or quantity. For example, a scanner herein described can provide an image of the CNV (e.g. CND) according to subject assay method. For instance, a scanner can provide an image by detecting fluorescent, radioactive, or other emission; by detecting transmitted, reflected, or scattered radiation; by detecting electromagnetic properties or other characteristics; or by other techniques. The data detected are typically stored in a memory device in the form of a data file. In an embodiment, a scanner may identify one or more labeled targets. For instance, a first CNV polymorphism may be labeled with a first dye that fluoresces at a particular characteristic frequency, or narrow band of frequencies, in response to an excitation source of a particular frequency. A second CNV polymorphism may be labeled with a second dye that fluoresces at a different characteristic frequency. The excitation sources for the second dye may, but need not, have a different excitation frequency than the source that excites the first dye, e.g. the excitation sources could be the same, or different, lasers.

In an embodiment, the subject disclosure teaches 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 the one or more nucleic acids are nucleic acids not from the recipient (i.e. the one or more nucleic acids are from the donor transplant) and wherein the one or more nucleic acids from the donor are identified based on a predetermined CNV marker profile (e.g. CNV profile listed in Table 2); and (ii) diagnosing or predicting transplant status or outcome based on the presence or absence of the one or more nucleic acids.

The present disclosure further enables a transplantation protocol for transplanting tissue from a donor to a recipient, the protocol comprising transplanting the tissue and then monitoring a sample from the recipient for the presence of nucleic acids which are not the recipients wherein if donor nucleic acids are detected, the recipient is subjected to immunosuppression therapy or if the patient is on immunosuppression therapy, the therapy is altered.

Another aspect taught herein is the use of a panel of CNVs which identify a nucleic acid as being of recipient origin or non-recipient origin in the manufacture of a diagnostic assay to detect the status of transplanted tissue in the recipient.

The subject disclosure further teaches an assay to monitor the balance between immunosuppression and tissue damage such as due to rejection or pharmaceutical cytotoxicity. Hence, the subject disclosure teaches a method of treating a subject who has undergone a transplantation procedure by monitoring for changes in the levels of non-recipient nucleic acids. Such changes may be relative to a control. The control includes pre-transplantation levels of free recipient nucleic acids or a change in the ratio of total nucleic acids to non-recipient nucleic acids.

Whilst Table 2 provides a list of CNV polymorphisms, the present method extends to other known CNV polymorphisms such as those described by Conrad et al. (2010) supra and McCarroll et al. (2008) supra.

Aspects contemplated herein are further described by the following non-limiting Examples.

Example 1 Development of a CNV-Deletion Genotyping Panel to Distinguish Recipient from Donor Plasma DNA

A panel of CNV deletions is selected which is expected to have approximate null frequencies of 40-50% in the general population. This is done by in silico analysis of public data (Conrad et al. (2010) supra; McCarroll et al. (2008) supra). These CNV regions are polymorphic and have no intrinsic clinical significance. CNV selection and frequency calculations are performed as follows: The HapMap data set includes trio-data for each CNV. For frequency calculations, only singleton and parental samples are included. CNVs with only 0, 1 and 2 copy genotypes are selected for analysis (i.e. CNVs of more than 2 copy and Chromosomes X and Y CNVs are excluded). For each selected CNV, frequencies of 0, 1 and 2 copy genotypes are calculated. CNVs in the form of CNDs overlapping with segmental duplications were excluded. CNVs with 0.4-0.5 null copy frequency and less than 3 kb in size were selected from Table 2. The list in Table 2 should be read in conjunction with, and includes, other known CNVs such as those defined in Conrad et al. (2010) supra; McCarroll et al. (2008) supra. An example is the CNVs listed in Table 3.

TABLE 2 Copy Number Variant Polymorphisms Size 0 Copy 1 Copy 2 Copy CNP ID Chr Start (hg18) End (hg 18) (bp) frequency frequency frequency CNVR358.1 chr1 150,822,234 150,856,715 34481 0.393 0.459 0.148 CNVR217.1 chr1 72,538,870 72,584,557 45687 0.393 0.459 0.148 CNVR483.1 chr1 205,359,125 205,359,831 706 0.459 0.426 0.115 CNVR451_full chr1 192,716,897 192,721,360 4463 0.459 0.418 0.107 CNVR376.1 chr1 157,134,152 157,136,674 2522 0.508 0.418 0.074 CNVR381.1 chr1 157,915,386 157,916,253 867 0.582 0.344 0.049 88 chr1 110,025,907 110,044,476 18569 0.583 0.350 0.067 CNVR431.1 chr1 185,731,458 185,733,106 1648 0.598 0.320 0.041 262 chr2 97,507,179 97,528,142 20963 0.367 0.450 0.167 CNVR1138.2 chr2 219,761,436 219,762,572 1136 0.385 0.410 0.180 CNVR1138.3 chr2 219,760,351 219,762,572 2221 0.385 0.418 0.164 CNVR966.1 chr2 126,159,644 126,168,438 8794 0.393 0.418 0.164 CNVR1037.1 chr2 159,668,040 159,669,209 1169 0.492 0.418 0.066 CNVR952.1 chr2 121,513,996 121,515,257 1261 0.516 0.352 0.098 CNVR801_full chr2 54,419,132 54,420,976 1844 0.574 0.361 0.041 CNVR842.1 chr2 76,627,234 76,628,943 1709 0.582 0.320 0.074 CNVR1041_full chr2 162,039,479 162,042,198 2719 0.672 0.270 0.033 CNVR1058.1 chr2 176,973,956 176,980,168 6212 0.672 0.254 0.049 CNVR894.2 chr2 101,419,843 101,420,750 907 0.680 0.180 0.008 CNVR1648.2 chr3 180,032,900 180,033,574 674 0.352 0.492 0.156 CNVR1438_full chr3 80,144,512 80,147,226 2714 0.377 0.484 0.139 CNVR1576.1 chr3 147,867,879 147,873,031 5152 0.426 0.459 0.115 CNVR1419.1 chr3 68,822,189 68,830,557 8368 0.426 0.393 0.180 CNVR1685.1 chr3 194,358,041 194,368,093 10052 0.443 0.443 0.115 CNVR1610.1 chr3 164,247,638 164,251,756 4118 0.508 0.426 0.066 CNVR1341.1 chr3 32,077,088 32,082,966 5878 0.516 0.361 0.107 CNVR1464.1 chr3 100,381,786 100,385,095 3309 0.656 0.295 0.041 CNVR2196.1 chr4 182,293,552 182,294,187 635 0.352 0.443 0.148 CNVR1894.1 chr4 39,701,722 39,702,524 802 0.361 0.516 0.123 CNVR2221_full chr4 187,330,507 187,348,434 17927 0.361 0.492 0.123 CNVR1937.1 chr4 61,621,762 61,624,843 3081 0.369 0.525 0.107 CNVR1935_full chr4 61,012,725 61,017,305 4580 0.492 0.434 0.074 CNVR1819.6 chr4 9,783,252 9,843,664 60412 0.508 0.410 0.082 CNVR2172_full chr4 173,661,594 173,670,645 9051 0.525 0.434 0.016 CNVR2168_full chr4 172,610,978 172,616,208 5230 0.557 0.361 0.025 726 chr4 173,661,522 173,665,218 3696 0.567 0.350 0.067 CNVR2613_full chr5 135,143,151 135,148,760 5609 0.377 0.484 0.139 CNVR2535_full chr5 98,373,056 98,375,260 2204 0.402 0.410 0.189 CNVR2344_full chr5 10,326,006 10,327,951 1945 0.467 0.385 0.115 CNVR2469.1 chr5 57,359,283 57,369,499 10216 0.615 0.361 0.025 CNVR2304.1 chr5 1,977,604 1,978,111 507 0.672 0.328 0.000 896 chr5 177,160,157 177,165,211 5054 0.683 0.300 0.017 CNVR2939.3 chr6 65,405,092 65,405,828 736 0.369 0.426 0.139 CNVR2939.2 chr6 65,401,412 65,406,139 4727 0.369 0.475 0.156 CNVR2799.1 chr6 18,510,099 18,510,860 761 0.393 0.426 0.148 CNVR3004.1 chr6 95,250,114 95,251,113 999 0.393 0.459 0.123 CNVR2906.1 chr6 54,036,723 54,042,793 6070 0.451 0.475 0.066 CNVR2972_full chr6 77,154,212 77,160,412 6200 0.459 0.443 0.090 CNVR2859_full chr6 35,734,415 35,737,723 3308 0.467 0.443 0.082 933 chr6 32,539,530 32,681,749 142219 0.550 0.383 0.067 CNVR3009.1 chr6 100,141,275 100,141,994 719 0.623 0.377 0.000 CNVR3472_full chr7 81,279,416 81,280,521 1105 0.377 0.467 0.156 CNVR3319.1 chr7 24,004,755 24,006,584 1829 0.434 0.344 0.139 CNVR3495.1 chr7 93,379,735 93,380,461 726 0.443 0.410 0.148 1103 chr7 70,058,925 70,064,077 5152 0.450 0.483 0.067 CNVR3451.1 chr7 73,467,042 73,469,172 2130 0.549 0.328 0.123 CNVR3609.1 chr7 147,704,059 147,707,263 3204 0.656 0.311 0.033 CNVR3753_full chr8 4,110,308 4,112,335 2027 0.426 0.426 0.131 CNVR3935.1 chr8 75,525,410 75,529,549 4139 0.451 0.369 0.172 CNVR4014.1 chr8 112,363,260 112,365,469 2209 0.500 0.410 0.082 CNVR3831.1 chr8 25,122,647 25,126,577 3930 0.598 0.328 0.049 CNVR3689.1 chr8 584,449 589,454 5005 0.689 0.262 0.041 CNVR4250.1 chr9 36,352,611 36,353,818 1207 0.369 0.508 0.115 CNVR4331.1 chr9 70,927,946 70,933,190 5244 0.443 0.467 0.082 CNVR4374.1 chr9 88,344,772 88,345,596 824 0.557 0.361 0.074 CNVR4203.1 chr9 17,900,038 17,901,633 1595 0.598 0.352 0.025 CNVR4332.1 chr9 71,085,050 71,086,301 1251 0.631 0.328 0.025 CNVR4841.1 chr10 89,265,522 89,266,538 1016 0.377 0.459 0.156 CNVR4665.1 chr10 27,039,121 27,041,860 2739 0.377 0.410 0.213 CNVR4886.1 chr10 108,020,303 108,022,518 2215 0.410 0.418 0.172 CNVR4596.1 chr10 4,698,559 4,700,493 1934 0.607 0.311 0.082 CNVR4906.1 chr10 122,216,913 122,218,702 1789 0.664 0.270 0.057 1730 chr11 54,458,221 54,514,519 56298 0.433 0.367 0.100 CNVR5122.1 chr11 28,963,726 28,969,302 5576 0.434 0.434 0.115 CNVR5294.1 chr11 103,772,866 103,778,468 5602 0.475 0.369 0.148 CNVR5429.1 chr12 9,524,006 9,626,453 102447 0.393 0.402 0.139 CNVR5853_full chr13 38,831,627 38,833,387 1760 0.385 0.451 0.148 CNVR5923.1 chr13 71,743,783 71,744,892 1109 0.402 0.533 0.041 CNVR5850.1 chr13 37,955,318 37,958,191 2873 0.426 0.434 0.139 CNVR5871.1 chr13 49,967,347 49,973,131 5784 0.590 0.361 0.033 CNVR6133.1 chr14 39,679,595 39,687,469 7874 0.352 0.475 0.156 CNVR6211.1 chr14 81,568,879 81,573,106 4227 0.385 0.377 0.189 CNVR6084.1 chr14 21,951,540 21,952,070 530 0.451 0.418 0.107 CNVR6074_full chr14 19,621,390 19,625,018 3628 0.582 0.344 0.057 CNVR6357.1 chr15 37,531,690 37,532,136 446 0.508 0.410 0.066 CNVR6540.1 chr15 97,392,250 97,392,985 735 0.508 0.426 0.057 CNVR6670.1 chr16 22,955,370 22,957,061 1691 0.377 0.525 0.074 CNVR6676.1 chr16 25,247,611 25,250,595 2984 0.443 0.459 0.074 CNVR6782.1 chr16 75,096,634 75,101,530 4896 0.443 0.443 0.098 CNVR7144.1 chr17 53,042,845 53,044,836 1991 0.410 0.434 0.148 CNVR7096.1 chr17 36,675,163 36,685,731 10568 0.484 0.402 0.107 CNVR7301.1 chr18 33,560,073 33,560,645 572 0.418 0.451 0.123 CNVR7344.1 chr18 53,097,735 53,099,702 1967 0.508 0.393 0.082 CNVR7543.1 chr19 12,555,939 12,559,475 3536 0.475 0.402 0.057 CNVR7581_full chr19 22,932,698 22,934,767 2069 0.648 0.270 0.025 2434 chr19 58,210,563 58,244,245 33682 0.683 0.233 0.067 2454 chr20 1,509,580 1,541,893 32313 0.483 0.467 0.050 CNVR7808.1 chr20 21,234,267 21,236,529 2262 0.516 0.418 0.066 CNVR7849.1 chr20 41,705,581 41,707,310 1729 0.664 0.311 0.008 CNVR7796_full chr20 15,657,506 15,660,363 2857 0.672 0.279 0.033 2559 chr22 22,613,016 22,670,785 57769 0.383 0.467 0.150 CNVR8147.1 chr22 33,975,445 33,976,472 1027 0.451 0.426 0.115 CNVR8114.4 chr22 22,604,143 22,607,619 3476 0.451 0.434 0.107 CNVR8154.1 chr22 35,473,303 35,476,957 3654 0.566 0.352 0.074

TABLE 3 Copy Number Deletion Polymorphisms 0 Copy 1 Copy 2 Copy CNV CND ID CNP id chr start hg18 end hg18 SIZE bp frequency frequency frequency Info CND_01 CNVR376.1 chr1 157,134,152 157,136,674 2,522 0.508 0.418 0.074 agenic CND_02 CNVR7344.1 chr18 53,097,735 53,099,702 1,967 0.508 0.393 0.082 agenic CND_03 CNVR4014.1 chr8 112,363,260 112,365,469 2,209 0.500 0.410 0.082 agenic CND_04 CNVR6084.1 chr14 21,951,540 21,952,070 530 0.451 0.418 0.107 Intronic CND_05 CNVR6676.1 chr16 25,247,611 25,250,595 2,984 0.443 0.459 0.074 agenic CND_06 CNVR3319.1 chr7 24,004,755 24,006,584 1,829 0.434 0.344 0.139 agenic CND_07 CNVR5850.1 chr13 37,955,318 37,958,191 2,873 0.426 0.434 0.139 agenic CND_08 CNVR3753_full chr8 4,110,308 4,112,335 2,027 0.426 0.426 0.131 Intronic CND_09 CNVR7301.1 chr18 33,560,073 33,560,645 572 0.418 0.451 0.123 agenic CND_10 CNVR4886.1 chr10 108,020,303 108,022,518 2,215 0.410 0.418 0.172 agenic

Example 2 Genotyping Recipients Using Simple PCR Assays with Cell-Derived DNA

PCR reactions are designed with primers located within the 10 CNV-deletion regions provided in Table 3 (Example 1) to confirm the expected null frequencies (i.e. no PCR product) using genomic DNA from a group of 21 normal individuals. FIG. 1a shows confirmation of the predicted 40-50% frequency for CND_01, i.e. 12 out of 21 null genotypes. To confirm that the deletions are real rather than PCR failure artefacts, PCR reactions are run with flanking primers. The results are shown for CND_01 (FIG. 1b). These give a precise product shorter than the wild-type confirming all the null deletions detected in (a), the rest being null/wild-type heterozygotes with the exception of two (arrowed) that are wild-type homozygotes (note: the larger, wild-type product is absent as the undeleted CNV is too large to be amplified).

Example 3 Validation of the Genotyping PCRs

The identity of the internal PCR products is proven unequivocally by sequencing the corresponding, shorter flanking PCR products and mapping them back to a genome location using BLAT. In all cases, this was to the correct, unique genome locus.

An advantage of this approach is that there is no need to genotype the donor. Recipient genotype is determined using the leukocyte cell component of the same anti-coagulated blood sample from which plasma is obtained. The assay detects non-self, i.e. donor specific, CNV regions in plasma.

Example 4 CNV-Deletion Genotyping Using Plasma-Derived DNA

CNV-deletion (CND) genotyping using plasma DNA is demonstrated. Unlike cell-derived DNA, plasma DNA is degraded into short 400-600 bp fragments. FIG. 2 demonstrates completely concordant CNV-deletion genotyping for 4 individuals (3 heterozygotes/or homozygotes and 1 null) using leukocyte DNA and plasma DNA from the same blood samples, in this case for CND_02 by PCR.

Example 5 Optimization of the CNV-Detection Panel (100-150 Individuals)

In order to optimize the CNV-deletion panel for use in the local population, it is necessary to determine accurately the null frequencies in a larger set of genomic DNA samples (from approximately 100-150 individuals) taking into account differences based on ethnicity. The informativeness of the final panel is likely to be 100% for any one recipient. For very rare recipients who have no ‘null’ genotypes within the panel, alternative bespoke assays designs can be used based on ‘null’ genotypes in the donor. In clinical transplantation there is a low level of microchimaerism with donor dendritic cells, in particular. It is not anticipated that the low level of contaminating cells will interfere with establishing the donor DNA profile, as this will not be performed at high sensitivity.

Example 6 Sensitivity of CNV-Deletion Genotyping PCR Using Plasma DNA

An indication of the achievable sensitivity using simple PCR has been obtained from a ‘spiking’ experiment. A control sample which is heterozygous (i.e. 1 copy) for CND_01 loci is ‘spiked’ into a nullisomic sample at proportions of 0-100% and run in a simple PCR assay. The results in FIG. 3 show that CND_01 could be detected at proportions as low as 1% (arrowed). Furthermore, q-PCR assays are developed which have sensitivities an order of magnitude more sensitive than 1%.

Example 7 Developing Quantitative PCR (q-PCR) Assays for the Donor CNVs (10 Assays)

A specific q-PCR assay is developed for each CNV region in the CNV-deletion panel for absolute quantitation of plasma CNV concentrations. This provides very sensitive detection of donor DNA sequences matching the recipient CNV-deletions. An analogous q-PCR assay for sensitive quantitation of SRY in plasma samples from female recipients with an organ transplant from a male donor (FIG. 4). This is a model system for each of the panel CNV regions. q-PCR is performed essentially as previously described (Lo et al. (1998) Am J Hum Genet 62(4):768-75). It demonstrates the feasibility of taking this approach for quantitation of low levels of donor-specific DNA sequences in recipient plasma.

As very low concentrations of DNA are assayed using q-PCR, there is a risk of contamination with DNA from other sources (operator or samples). The multiple informative CNV-deletions that are assayed for each recipient-donor pair provides a valuable indicator of any inconsistencies in individual assay results. An additional requirement is that ‘no template’ controls are included in each qPCR experiment.

Example 8 Sensitivity of qPCR Assays Using Genomic DNA

The sensitivity of the qPCR assays for measurement of a rare DNA species in a mixture of DNA was determined using ‘spiking’ experiments. For each qPCR assay in the panel, a control sample which is heterozygous (i.e. 1 copy) for the respective CND locus is ‘spiked’ into a nullisomic sample at a range (20-500) of haploid copies (i.e. genomic equivalents per reaction). The results in FIGS. 5a, b, c for CND01, CND02 and CND03 respectively show that the qPCR assays generate accurate, precise and robust measurements of the level of rare DNA in the mixture down to 20 GE per reaction.

Example 9 Detection of Donor (Non-Self) DNA in Plasma Samples from a Kidney Transplant Recipient

A blood sample is collected from a patient manifesting clinical rejection. DNA is prepared from the leukocyte and plasma fractions and PCR assays specific for each of the panel 10 CNV-deletions run. The leukocyte DNA (self) is ‘null’ for CND_02, CND_03 and CND_08 (FIG. 6). Non-self PCR products (transplant-derived) are found in the plasma DNA for CND_03 and CND_08. No plasma product is found for CND_02 as the organ donor was presumably also ‘null’ for this CNV-deletion (the probability of the occurring is 1 in 2 [50%])).

The CND_03 and CND_08 PCR products from plasma were sequenced and shown by BLAT to match exactly with the expected respective genome sequences showing them to be unique and non-self in origin.

Example 10 Clinical Studies

All recipients are first genotyped to determine genotype status for all CNV in the panel. CNV markers where the recipient is heterozygous for wild-type sequence are used to assay total plasma concentrations of self-DNA (a separate HBB qPCR assay is also used for this purpose). CNV markers where the recipient is ‘null’ and the donor is not are used to determine donor-specific plasma DNA concentrations in recipient plasma. The total recipient plasma DNA and the donor-specific plasma DNA were measured in 35 transplant recipients, including 26 stable transplant recipients, 6 transplant recipients experiencing variable clinical signs of rejection of which two showed very high-levels of circulating donor DNA (AUS_01 and ORG_01) and 3 transplant recipients experiencing other complications (ORG_03, ORG_25 and ORG_31). Measurements of plasma transplant-derived cfDNA and total plasma cfDNA for all 35 samples are shown in FIGS. 7a and 7b. In the six transplant recipients experiencing variable clinical signs of rejection, the donor-specific plasma DNA concentrations were found to vary and this appeared to correlate with the immunologic mechanism of rejection (i.e. humoral versus cellular mediated) as well as the medical category of rejection (i.e. acute versus chronic).

Example 11 Longitudinal Investigations in a Single Sample

Informative qPCR assays were run on samples taken from a transplant recipient at the following time-points: pre-transplant, weekly for 4 weeks post-transplantation, at 12 weeks and at 24 weeks. Measurements of plasma transplant-derived cfDNA and total plasma cfDNA are shown in FIGS. 8a and 8b.

Those skilled in the art will appreciate that the disclosure described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the disclosure contemplates all such variations and modifications. The disclosure also enables all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations of any two or more of the steps or features or compositions or compounds.

BIBLIOGRAPHY

  • Cass et al. (2010) Kidney Health Australia 27
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  • Howard et al. (2009) Nephrology 14:123-132
  • Lee et al. (2006) Transfusion 46:1870-1878
  • Livak et al. (1995) Nature Genetics 9:341-342
  • Lo et al. (1998) Am J Hum Genet 62(4):768-75
  • McCarroll et al. (2008) Nat Genet 40(10):1166-1174
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Claims

1. A method of detecting circulatory nucleic acids from a transplanted tissue in a transplant recipient, the method comprising:

amplifying circulatory nucleic acids from a transplanted tissue in a blood sample from the transplant recipient, and
detecting amplification of a copy number deletion (CND) polymorphism from the transplanted tissue, wherein the CND polymorphism is selected from the group consisting of: chromosome 1, nucleotides 157,134,152-157,136,674, chromosome 18, nucleotides 53,097,735-53,099,702, chromosome 8, nucleotides 112,363,260-112,365,469, chromosome 14, nucleotides 21,951,540-21,952,070, chromosome 16, nucleotides 25,247,611-25,250,595, chromosome 7, nucleotides 24,004,755-24,006,584, chromosome 13, nucleotides 37,955,318-37,958,191, chromosome 8, nucleotides 4,110,308-4,112,335, chromosome 18, nucleotides 33,560,073-33,560,645, and chromosome 10, nucleotides 108,020,303-108,022,518.

2. The method of claim 1 wherein the transplanted tissue is an organ selected from the group consisting of a kidney, heart, lung, pancreatic islet, liver, intestine and skin.

3. The method of claim 1 wherein the transplanted tissue is a microtissue or stem cells.

4. The method of claim 1 wherein the transplanted tissue is a kidney.

5. The method of claim 1, wherein circulatory nucleic acids are amplified using digital PCR.

6. The method of claim 1, wherein at least 2 CND polymorphisms from the transplanted tissue are detected.

7. The method of claim 1, wherein at least 3 CND polymorphisms from the transplanted tissue are detected.

8. The method of claim 1, wherein the selected CND polymorphism is nullisomic with regard to circulatory nucleic acids that are not from the transplanted tissue.

9. A method for determining the status of a donor tissue transplanted into a recipient, said method comprising screening a sample from the recipient for the presence or absence of circulatory nucleic acids which have a copy number deletion (CND) polymorphism which indicates they are donor-derived nucleic acids wherein the presence of donor nucleic acids is indicative of cellular damage of the transplanted tissue and the absence of donor nucleic acids or a level of donor nucleic acids relative to a control is indicative of no cellular damage or cellular damage to an acceptable level.

10. The method of claim 9, wherein the tissue transplanted is a kidney.

11. A circulatory nucleic acid having a copy number deletion (CND) polymorphism, wherein the CND polymorphism is selected from the group consisting of:

chromosome 1, nucleotides 157,134,152-157,136,674,
chromosome 18, nucleotides 53,097,735-53,099,702,
chromosome 8, nucleotides 112,363,260-112,365,469,
chromosome 14, nucleotides 21,951,540-21,952,070,
chromosome 16, nucleotides 25,247,611-25,250,595,
chromosome 7, nucleotides 24,004,755-24,006,584,
chromosome 13, nucleotides 37,955,318-37,958,191,
chromosome 8, nucleotides 4,110,308-4,112,335,
chromosome 18, nucleotides 33,560,073-33,560,645, and
chromosome 10, nucleotides 108,020,303-108,022,518.
Patent History
Publication number: 20170342492
Type: Application
Filed: Aug 11, 2017
Publication Date: Nov 30, 2017
Inventors: Howard Robert Slater (Parkville), Damien Luis Bruno (Airport West), Devika Ganesamoorthy (Epping)
Application Number: 15/675,466
Classifications
International Classification: C12Q 1/68 (20060101);