|Subject: Cell-free DNA Testing to Aid in the Monitoring of Kidney Transplants for Rejection|
|Document #: LAB.00038||Publish Date: 07/06/2022|
|Status: Reviewed||Last Review Date: 05/12/2022|
This document addresses the use of cell-free DNA (cfDNA) as a method of detecting kidney transplant recipients at risk for transplant rejection. cfDNA-based tests for detection of kidney transplant rejection may use blood or urine samples and include, but may not be limited to, QiSant™ (NephroSant, Inc., Brisbane, CA), AlloSure® (CareDX, Inc., San Francisco, CA), Transplant Rejection Allograft Check (TRAC®) (Viracor, Lee's Summit, MO) and Prospera™ Organ Transplant Rejection Assessment Test (Natera, Inc., San Carlos, CA). This document does not address the use of organ biopsy or serum creatinine monitoring to detect kidney transplant rejection.
Note: Please see the following related document for additional information:
Investigational and Not Medically Necessary:
Cell-free DNA testing is considered investigational and not medically necessary as a non-invasive method of determining the risk of rejection in kidney transplant recipients.
Following a renal transplant, monitoring the health of the allograft is crucial for detecting evidence of rejection as early as possible. Early detection of rejection enables individualized adjustments to immunosuppressive therapy whereby decreasing the likelihood of transplant failure. The most widely accepted method for surveillance of renal allograft rejection is achieved by monitoring serum creatinine levels. Confirmatory diagnosis is made by histologic analysis of the allograft via needle biopsy, the current gold standard for diagnosis. While serum creatinine allows estimation of the glomerular filtration rate (GFR) in routine monitoring, it is not specific or sensitive for transplant rejection. Use of a biopsy for more frequent, routine monitoring is not ideal due to the invasiveness of the procedure. Measurement of donor-derived cell-free DNA (dd-cfDNA) in the blood and urine has been proposed as a noninvasive testing method that may be more specific than serum creatinine monitoring while enabling more frequent monitoring of allograft injury than biopsy permits.
In 2018, Sigdel and colleagues published results of a single center, retrospective study in which the Prospera cfDNA test kit was used to analyze 300 plasma samples from 193 unique renal transplant recipients (217 of which were biopsy-matched [38 with active rejection, 72 borderline rejection, 82 stable allografts, and 25 with other graft injuries]). The median dd-cfDNA levels were significantly higher in samples with biopsy-proven active rejection (2.3%) relative to borderline rejection (0.6%), other injuries (0.7%), and stable allografts (0.4%) (p<0.0001; all comparisons). The Prospera assay discriminated active from non-rejection status with a sensitivity of 88.7% (95% confidence interval [CI], 77.7 to 99.8%) and specificity of 72.6% (95% CI, 65.4 to 79.8%). At 6 months post transplantation, of the13 recipients with biopsy-confirmed rejection, 12 (92%) were dually identified by cfDNA testing. Study authors conclude that use of Prospera in the clinical setting is feasible. Further investigation is warranted in the setting of a prospective, randomized clinical trial. Currently, the manufacturer is conducting two prospective multi-center clinical trials with estimated study completion dates in 2027 (NCT04091984; estimated enrollment of 3000) and 2028 (NCT03984747; estimated enrollment of 500).
In 2021, Qazi and colleagues conducted a retrospective analysis of 1347 bloods samples collected from 879 adult kidney transplant recipients with the aim of assessing the clinical utility of Prospera as a part of routine clinical care. Biopsy data collected simultaneous to dd-cfDNA results was also analyzed and the rate of rejection was then calculated. The dd-cfDNA testing classified 25.2% (340/1347) of samples as high-risk. Follow-up data was available for 32.1% (109/340) of the high-risk results, including samples from 28 individuals with biopsy results. A 64% (18/28) rate of active rejection was determined in biopsy result-matched samples. Given the high rate of loss to follow-up and resulting limited sample size, further study is warranted to better characterize the utility of Prospera in routine clinical practice (Qazi, 2021).
Based on earlier data published by Grskovic (2016), Bloom and colleagues (2017) prospectively collected 107 blood specimens from 102 kidney transplant recipients at regular intervals (months 1, 2, 3, 4, 6, 9, and 12) and at the time of clinically indicated biopsies (based on creatinine levels). Donor-derived plasma cfDNA levels were measured using the AlloSure assay and then correlated with biopsy-confirmed allograft rejection status. Using a diagnostic cutoff of 1.0% dd-cfDNA (< 1% reflects the absence of active rejection), the positive and negative predictive values for active rejection were 61% and 84%, respectively. The AlloSure successfully discriminated between biopsy specimens confirming any type of rejection (T cell-mediated rejection or antibody-mediated rejection) and controls, p<0.001 (area under the curve [AUC], 0.74; 95% CI, 0.61 to 0.86). The AUC for specifically discriminating antibody-mediated rejection from allografts without antibody-mediated rejection was slightly higher at 0.87 (95% CI, 0.75 to 0.97); positive and negative predictive values were 44% and 96%, respectively. In this relatively small prospective cohort, AlloSure’s performance as a non-invasive test for detection of allograft injury is promising. Further investigation in the setting of a large, randomized trial is warranted to establish whether use of AlloSure materially improves net health outcomes compared to established alternatives, such as monitoring serum creatinine levels.
Bu and colleagues (2022) published results from 1092 kidney transplant recipients across seven transplant centers who had been monitored with AlloSure dd-cfDNA as a component of their usual standard of care post-transplant. Study investigators sought to define the association of dd-cfDNA with histologic evidence of allograft rejection. Data was collected prospectively from 2016 to 2020 and then retrospectively examined for this study’s objectives. Allosure testing was performed at regular intervals according to each center’s standard of care and the resulting dd-cfDNA levels were used as part of surveillance testing as well as a diagnostic tool to detect graft failure. The association between allograft rejection status and dd-cfDNA levels was assessed using 219 biopsies (n=203) with biopsy-paired dd-cfDNA results. Among the 219 biopsies, 110 were for-cause biopsies and the remaining 109 were surveillance biopsies performed under center-specific clinical protocols; 113 biopsies (68 for-cause and 45 surveillance; n=101) were classified as acute rejection biopsies. Elevation of dd-cfDNA (defined as 0.5% or more) was significantly correlated with clinical and subclinical allograft rejection and a nearly three-fold increase in risk for development of de novo donor specific antibodies (hazard ratio [HR]=2.71); 91 days (inter quartile range of 30-125 days) ahead of donor specific antibody identification. Persistently elevated dd-cfDNA (more than one Allosure result above the 0.5% threshold) predicted over a 25% decline in the estimated GFR over 3 years (HR=1.97). All surveillance biopsies showing rejection had significantly higher dd-cfDNA than non-rejection biopsies (p<0.001). The study authors conclude that “… persistently low dd-cfDNA levels may accurately identify allograft quiescence, or absence of injury, paving the way for personalization of immunosuppression trials.” Yet, questions remain regarding how clinical treatment strategies would be altered by Allosure results and if forgoing the more in-depth biopsy may ultimately impair clinical decision-making. Further research is warranted in the setting of a randomized trial to determine if management of transplant recipients using Allosure materially improves clinically meaningful, long-term outcomes such as graft survival rate relative to the current standard of care (i.e., serum creatine monitoring, serial biopsies, etc.).
CareDx, the manufacture of AlloSure, is currently conducting two prospective clinical trials with estimated completion in 2025 (NCT03326076; estimated target enrollment of 5000) and 2026 (NCT04601155; estimated target enrollment of 3500).
Based on the foundational work by Watson (2019) and Yang (2020), Nolan and colleagues (2020) published validation study results of a urine-based cfDNA test known as the NephroSant QiSant Assay, comprised of six urinary DNA, protein, and metabolic biomarkers known as the Q-score. The study involved 223 kidney transplant recipient urine samples collected from 215 pediatric and adult recipients with kidney biopsy matched samples. Out of the 223 samples, acute rejection was detected in 71 samples, while 152 remained stable allografts. Additional urine samples were collected for up to 4 years post-transplant. The NephroSant Assay was able to detect acute rejection in pediatric transplant recipients with an Area Under the Curve of 100% (95% CI, 1.00 to 1.00; p<0.0001) and 99.8% in adult transplant recipients (95% CI, 0.995 to 1.00; p<0.0001). Study limitations include the cross-sectional, single-arm study design. Although initial study of NephroSant’s performance in detecting allograft rejection is promising, it has not been proven to materially improve the net health outcome or be as beneficial as established alternatives (e.g., monitoring serum creatinine levels). Additional study in the setting of a randomized controlled trial is warranted to establish improvement in net health outcomes.
Other cfDNA Assays
Gielis and colleagues (2020) published a non-manufacturer sponsored study of 107 kidney transplant recipients. Plasma samples were collected prospectively up to 3 months post-transplantation. Increases of the dd-cfDNA% above a threshold value of 0.88% were significantly associated with the occurrence of episodes of acute rejection (p=0.017), acute tubular necrosis (p=0.011) and acute pyelonephritis (p=0.032). Although increases in cfDNA were associated with graft injury, authors conclude that the testing method was not specific to rejection and failed to outperform the diagnostic capacity of serum creatinine levels in the detection of acute rejection.
Three systematic reviews have investigated the use of cfDNA in monitoring allograft health after kidney transplantation (Knight, 2019; Wijtvliet, 2020; Xiao, 2021). While all the reviews conclude that cfDNA is a promising biomarker, perhaps most promisingly in the setting of antibody-mediated rejection (Xiao, 2021), “future studies will need to define how it can be used in routine clinical practice and determine clinical benefit with routine prospective monitoring” (Knight, 2019).
Currently, there is no guidance from specialty medical societies addressing the clinical utility of cfDNA in monitoring kidney allografts for rejection.
The published peer-reviewed medical literature has not established cfDNA testing for detection of kidney allograft rejection as a proven method that materially improves net health outcomes nor has any benefit been established beyond currently available alternatives (e.g., serum creatinine testing).
In 2021, approximately 37 million Americans reportedly had chronic kidney disease (CKD), with nearly 118,000 requiring initiation of treatment for kidney failure, also known as end stage renal disease (ESRD) (CDC, 2021). There was a steady rise in the rate of ESRD from 1980 to 2011, since then, the incident rate of ESRD has started to decline. As of December 2021, the Organ Procurement and Transplantation Network (OPTN) reported that there were about 90,000 Americans on the wait-list for kidney transplantation with approximately 23,000 kidney transplants performed in 2021 (OPTN, 2021). The total number of living kidney transplant recipients with a functioning graft is projected to surpass 250,000 in the next few years. The 1-, 3-, and 5-year survival rates for individuals receiving primary kidney transplants between 2008 and 2015 were 97.1%, 92.9% and 86.3%, respectively.
A kidney transplant involves the surgical removal of a diseased kidney and replacement with a healthy kidney from a deceased or living donor. Monitoring the health of the transplant is vital to the survival of both the transplant and the transplant recipient. The most widely accepted method for the surveillance of an allograft for rejection is monitoring of serum creatinine with confirmatory diagnosis achieved by histologic analysis of the allograft via needle biopsy, the current gold standard. Immunosuppressive drug therapy is adjusted according to transplant monitoring with the end-goal of preserving the allograft’s function, hence delaying or preventing graft rejection (National Institute of Diabetes and Digestive and Kidney Diseases [NIDDK], 2018).
Allograft: The transplant of an organ or tissue from one individual to another of the same species with a different genotype; for example, a transplant from one person to another, but not an identical twin.
Chronic renal disease: The permanent loss of kidney function.
End stage renal disease: Persistent decline in renal function as documented by falling creatinine clearance in an individual diagnosed with a renal disease whose natural history is progression to renal impairment requiring renal replacement (dialysis or transplant).
Glomerular filtration rate (GFR): A test used to check how well the kidneys are functioning by estimating how much blood passes through the glomeruli each minute.
Glomeruli: A cluster of nerve endings, spores, or small blood vessels, in particular a cluster of capillaries around the end of a kidney tubule, where waste products are filtered from the blood.
Nephropathy: Refers to damage or disease of the kidney.
The following codes for treatments and procedures applicable to this document are included below for informational purposes. Inclusion or exclusion of a procedure, diagnosis or device code(s) does not constitute or imply member coverage or provider reimbursement policy. Please refer to the member's contract benefits in effect at the time of service to determine coverage or non-coverage of these services as it applies to an individual member.
When services are Investigational and Not Medically Necessary:
For the following procedure codes, or when the code describes a procedure indicated in the Position Statement section as investigational and not medically necessary.
Transplantation medicine, quantification of donor-derived cell-free DNA using whole genome next-generation sequencing, plasma, reported as percentage of donor-derived cell-free DNA in the total cell-free DNA
Unlisted molecular pathology procedure [when specified as a dd-cfDNA test for kidney transplant rejection risk]
Unlisted multianalyte assay with algorithmic analysis [when specified as a dd-cfDNA test for kidney transplant rejection risk]
Complications of kidney transplant
Encounter for aftercare following kidney transplant
Kidney transplant status
Peer Reviewed Publications:
Government Agency, Medical Society, and Other Authoritative Publications:
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