Proposed Local Coverage Determination (LCD)

MolDX: Molecular Testing for Solid Organ Allograft Rejection


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MolDX: Molecular Testing for Solid Organ Allograft Rejection
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Issue Description

This LCD outlines limited coverage for this service with specific details under Coverage Indications, Limitations and/or Medical Necessity.

CMS National Coverage Policy

Title XVIII of the Social Security Act (SSA), §1862(a)(1)(A) allows coverage and payment for only those services that are considered to be reasonable and necessary

42 CFR §410.32(a) Diagnostic x-ray tests, diagnostic laboratory tests, and other diagnostic tests: Conditions

CMS Internet-Only Manuals, Pub. 100-02, Medicare Beneficiary Policy Manual, Chapter 15, §80 Requirements for Diagnostic X-Ray, Diagnostic Laboratory, and Other Diagnostic Tests, §80.1.1 Certification Changes

Coverage Guidance

Coverage Indications, Limitations, and/or Medical Necessity


For purposes of this policy the following definitions are used:

  • Surveillance (Protocol) – patient is asymptomatic; no clinical signs or symptoms of organ injury/rejection.
  • For-Cause – patient has clinical signs or symptoms of organ injury/rejection.
  • AR – Acute Rejection
  • ACR – Acute Cellular Rejection
  • AMR – Antibody-Mediated Rejection
  • AV – Analytical Validity
  • CV – Clinical Validity
  • OPTN - Organ Procurement and Transplantation Network
  • GEP – Gene Expression Profiling
  • dd cfDNA – Donor-Derived Cell-Free DNA

This Medicare contractor will provide limited coverage for molecular diagnostic tests used in the evaluation and management of patients who have undergone solid organ transplantation. These tests can inform decision making along with standard clinical assessments in their evaluation of organ injury for active rejection (AR). These tests may be ordered by qualified physicians considering the diagnosis of AR, helping to rule in or out this condition when assessing the need for or results of a diagnostic biopsy. They should be considered along with other clinical evaluations and results and may be particularly useful in patients with significant contraindications to invasive procedures.

Molecular diagnostic tests that assess a transplanted allograft for rejection status are covered when ALL of the following criteria are met:

  • The test must provide information about at least one of the two following clinical status determinations:
    • AR status
    • Cellular or Antibody-mediated rejection (ACR or AMR) status
  • The intended use of the test must be to inform clinical decision making as per the following:
    • To assist in the evaluation of adequacy of immunosuppression, wherein a non-invasive or minimally invasive test can be used in lieu of a tissue biopsy in a patient for whom information from a tissue biopsy would be used to make a management decision regarding immunosuppression, OR
    • As a rule-out test for AR in validated populations of patients with clinical suspicion of rejection with a non-invasive or minimally invasive test to make a clinical decision regarding obtaining a biopsy, OR
    • For further evaluation of allograft status for the probability of allograft rejection after a physician-assessed pretest, OR
    • To assess rejection status in patients that have received a biopsy, but the biopsy results are inconclusive or limited by insufficient material.

Therefore, molecular diagnostic tests are not covered if the results will not inform clinical decision making (for example if the patient has undergone a recent biopsy with a definitive diagnosis or has a planned upcoming biopsy that will be performed regardless of the result of the molecular test). Similarly, if a molecular test is performed as a result of findings from a pre-test, this suggests that the molecular test is informed by and performed after the results of the pre-test are known; as such, the molecular tests should be performed after the relevant pre-test(s).

  • IF the molecular diagnostic test is performed in-lieu of a surveillance (protocol) biopsy, the testing frequency must be no more frequent than the OPTN center-specific surveillance biopsy schedule.
  • The test demonstrates analytical validity (AV), including an analytical and clinical validation for any given measured analytes, and has demonstrated equivalence or superiority for sensitivity or specificity (depending on intended use) of detecting allograft rejection to other already-accepted tests for the same intended use measuring the same or directly comparable analytes.
  • Clinical validity (CV) of any analytes (or expression profiles) measured must be established through a study published in the peer-reviewed literature for the intended use of the test in the intended population. The degree of validity must be similar or superior to established and covered tests (see associated coverage Articles). If conducted with concordance to tissue histologic evaluation the most current Banff Classification for renal allografts or other accepted criteria (if existing) for other organs must be used.
  • The test is being used in a patient who is part of the population in which the test was analytically validated and has demonstrated CV.
  • For a given patient encounter, only one molecular test for assessing allograft status may be performed.
  • For minimally or non-invasive tests, the benefit to risk profile of the molecular test is considered by the ordering clinician to be more favorable than the benefit to risk profile of a tissue biopsy, or a tissue biopsy cannot be obtained. For example, this may be the case if a biopsy is considered medically contraindicated in a patient.
  • The test successfully completes a Molecular Diagnostic Services Program (MolDX®) Technical Assessment that will ensure that AV, CV, and clinical utility criteria set in this policy are met to establish the test as Reasonable and Necessary.

Covered tests with AV that is significantly below similar services may have coverage rescinded.

Summary of Evidence

Allograft solid-organ transplantation has become a standard of care in patients with end-stage organ disease. In some patients, these treatments, along with other advances in care, have transformed fatal disease into treatable and preventable disease.1-3 Transplant patients are placed on immunosuppressant drug therapy and are routinely monitored for indicators of rejection to prolong the survival of the donor allograft. Serologic and laboratory markers aid in monitoring graft function and in the early detection of AR which may occur as ACR or AMR.9 Transplant recipients may also undergo (a) surveillance biopsies to detect histologic changes that precede functional allograft decline and/or (b) for-cause biopsies when clinically indicated. With early intervention, these changes may still be amenable to treatment. The cost for managing a failed allograft may be 500% more than a patient with a functioning transplant.4 Early detection of AR has led to significant improvement in allograft survival in the first 12 months posttransplantation.5 

The importance of graft rejection and immunosuppression was discovered early on following the development of transplantation, a challenge that started to be overcome with the availability of immunosuppressants, though with the current standard-of-care for managing solid organ transplant patients, rejection remains a common problem with a high frequency of graft failure at 5 and 10 years.4,6-8 

Graft assessment is also used clinically to assist in the management of immunosuppression; the clinical value it brings is that it allows modification of immunosuppressive therapy so as to maximize graft longevity, which is a focus of post-transplant care. Histology has traditionally been used, often in conjunction with serologic and other laboratory markers as a common graft assessment tool.8,10-15 While histology is considered the gold standard of diagnosis at this point in time, this requires a biopsy, which is invasive and may be associated with significant risks, complications and access to care barriers.

Molecular diagnostic methods have emerged in an attempt to address limitations in current diagnostics including the measurement of donor-derived cell-free deoxyribonucleic acid (hereon cfDNA) and gene expression profile (GEP) assays, which have been developed in a number of organ allografts including kidney, heart, liver, and lung.16-24 The principle underlying cfDNA assays to assess rejection is that the transplantation of a new organ involves transplantation of new genetic material, and genetic material is shed into the bloodstream as part of rejection.25 The fraction of cfDNA in the blood-stream may serve as a marker of rejection.18-21 While this is a straightforward principle, DNA concentration in the bloodstream is quite small, and therefore tests relying on cfDNA require advanced technological methods that can accurately capture and quantify the presence of cfDNA specific to the allograft.18,21,25 GEP tests tend to quantify expression of numerous genes in the allograft recipient and use these data in algorithms developed with sophisticated modeling or machine learning to determine whether rejection is occurring.22,24,26 These tests can not only provide information about graft status in a minimally-invasive manner, but they can be sensitive enough to be able to detect AR before it is evident histologically or by other clinical and laboratory indicators.25

However, these molecular tests have different strengths and weaknesses and can be leveraged for different populations. For example, some GEP tests have high negative predictive value for the likelihood of AR, but may be limited in their ability as a positive predictor for ACR or even detecting AMR, which may still be useful in a stable patient at low risk for rejection.27 Other tests may have higher sensitivity or positive predictive value, suitable for higher-risk patients.18,21

While these technologies are newer, large and multicenter studies have supported their use in renal and heart transplantation as minimally and non-invasive methods to assess allograft status, modify immunosuppression regimens, and avoid unnecessary biopsies.18,19,23,28-29 Evidence continues to develop for other transplant allograft organs and other analytes.16,17,30-33 Additionally, there is evidence that while some cfDNA and GEP tests may have different intended uses, combining both may further improve graft rejection determination in certain circumstances.34

Contractor Advisory Committee (CAC) Summary

Kidney and Liver Allograft CAC

On November 16, 2022, Noridian and Palmetto jointly facilitated a CAC to discuss molecular testing for the diagnosis of acute rejection in kidney or liver transplant recipients where GEP, dd cfDNA, and multiomic tests were discussed. The subject matter experts (SMEs) expressed a high degree of certainty that there is sufficient evidence to support the use of molecular tests like dd cfDNA in kidney allograft patients.

Heart and Lung Allograft CAC

On November 17, 2022, Noridian and Palmetto jointly facilitated a CAC to discuss molecular testing for the diagnosis of acute rejection in heart or lung transplant recipients where GEP and dd cfDNA tests were discussed. The SMEs were unanimous that the evidence is sufficient to support the use of GEP and/or dd cfDNA for surveillance of acute organ injury to help replace an unnecessary biopsy. However, they also agreed that there is a lack of data to support the routine use of molecular combination testing. Moreover, they did not endorse the use of molecular diagnostic tests in lieu of biopsy in patients with a very high clinical and laboratory suspicion for acute rejection and who can also safely tolerate a biopsy. All SMEs agreed that these tests do not discern the etiology of organ injury, indicating that they had a high degree of confidence in the detection of allograft injury, but additional clinical testing was necessary to discern the cause.

Documents associated with the CAC meetings can be found here:

Contractor Advisory Committee (CAC) - JE Part B - Noridian (

Analysis of Evidence (Rationale for Determination)

Numerous prior Medicare coverage decisions have considered the evidence in the hierarchical framework of Fryback and Thornbury35 where Level 2 addresses diagnostic accuracy, sensitivity, and specificity of the test; Level 3 focuses on whether the information produces change in the physician's diagnostic thinking; Level 4 concerns the effect on the patient management plan and Level 5 measures the effect of the diagnostic information on patient outcomes. To apply this same hierarchical framework to analyze an in vitro diagnostic test, we utilized the ACCE Model Process for Evaluating Genetic Tests.35 The practical value of a diagnostic test can only be assessed by taking into account subsequent health outcomes. When a proven, well established association or pathway is available, intermediate health outcomes may also be considered. For example, if a particular diagnostic test result can be shown to change patient management and other evidence has demonstrated that those patient management changes improve health outcomes, then those separate sources of evidence may be sufficient to demonstrate positive health outcomes from the diagnostic test.

Graft assessment is a well-accepted part of solid organ transplant management. Evidence clearly shows that patients are living with functioning organs transplanted from immunologically and genetic distinct individuals using current transplant management techniques, which may demonstrate significant heterogeneity among centers or even among individual physicians. For example, the CAC SMEs acknowledged that only approximately 18% of transplant centers perform routine surveillance biopsies in kidney transplant patients, because the evidence on the benefit of that practice is conflicting. Similarly, some centers have moved away from performing protocol biopsies in other transplant types due to the highly invasive nature of the procedures and the high risk of complications.

It is also well accepted within the transplant community that immunosuppression management is an important component of post-transplant care to both optimize graft longevity while avoiding side effects and toxicity of immunosuppressive therapies. Graft assessment is an important decision tool used to help clinicians optimize immunosuppressive treatment. The gold standard for assessing rejection or injury has historically been and remains a biopsy in conjunction with serologic criteria. However, given the invasive nature and risks associated with a biopsy, tests that can potentially mitigate the need for a biopsy while still providing clinicians with actionable information that can be used to help optimize immunosuppressive therapy are reasonable and necessary. Additionally, ongoing studies have supported that cfDNA and GEP can accurately determine allograft status in several organ types, and that molecular characterization can both precede and enhance histologic findings. As such, these approaches, as a service type, are reasonable and necessary for graft assessment.

Non-invasive graft assessment remains an actively evolving area of medicine as does the assessment of graft rejection via histology. As such, this contractor will continue to monitor the evidence, and new developments may impact this coverage decision.

Proposed Process Information

Synopsis of Changes
Changes Fields Changed
Revision for clarity of coverage criteria section and CAC session held on November 16th and 17th, 2022. There is no change in coverage from the current Policy. Only comments pertaining to the changes made for clarity will be considered. Coverage Indications, Limitations and/or Medical Necessity
Associated Information


Sources of Information


  1. USRDS Coordinating Center United States Renal Data System. 2018; USRDS. Accessed 7/19/2023.
  2. Ponikowski P, Voors AA, Anker SD, et al. 2016 ESC Guidelines for the diagnosis and treatment of acute and chronic heart failure: the task force for the diagnosis and treatment of acute and chronic heart failure of the European Society of Cardiology (ESC). Developed with the special contribution of the Heart Failure Association (HFA) of the ESC. Eur J Heart Fail. 2016;18(8):891-975.
  3. Yancy CW, Jessup M, Bozkurt B, et al. 2013 ACCF/AHA guideline for the management of heart failure: a report of the American College of Cardiology Foundation/American Heart Association Task Force on Practice Guidelines. J Am Coll Cardiol. 2013;62(16):e147-239.
  4. United States Government Accountability Office. End-Stage Renal Disease: Characteristics of Kidney Transplant Recipients, Frequency of Transplant Failures, and Cost to Medicare. In:2007.
  5. Seron D, Arns W, Chapman JR. Chronic allograft nephropathy—clinical guidance for early detection and early intervention strategies. Nephrol Dial Transplant. 2008;23(8):2467-2473.
  6. Lamb KE, Lodhi S, Meier-Kriesche HU. Long-term renal allograft survival in the United States: a critical reappraisal. Am J Transplant. 2011;11(3):450-462.
  7. Stegall MD, Gaston RS, Cosio FG, Matas A. Through a glass darkly: seeking clarity in preventing late kidney transplant failure. J Am Soc Nephrol. 2015;26(1):20-29.
  8. Stehlik J, Kobashigawa J, Hunt SA, Reichenspurner H, Kirklin JK. Honoring 50 years of clinical heart transplantation in Circulation: in-depth state-of-the-art review. Circulation. 2018;137(1):71-87.
  9. McManigle W, Pavlisko EN, Martinu T. Acute cellular and antibody-mediated allograft rejection. Semin Respir Crit Care Med. 2013;34(3):320-335.
  10. Haas M, Loupy A, Lefaucheur C, et al. The Banff 2017 kidney meeting report: revised diagnostic criteria for chronic active T cell–mediated rejection, antibody-mediated rejection, and prospects for integrative endpoints for next-generation clinical trials. Am J Transplant. 2018;18(2):293-307.
  11. Solez K, Axelsen RA, Benediktsson H, et al. International standardization of criteria for the histologic diagnosis of renal allograft rejection: the Banff working classification of kidney transplant pathology. Kidney Int. 1993;44(2):411-422.
  12. Bruneval P, Angelini A, Miller D, et al. The XIIIth Banff conference on allograft pathology: The Banff 2015 heart meeting report: improving antibody-mediated rejection diagnostics: strengths, unmet needs, and future directions. Am J Transplant. 2017;17(1):42-53.
  13. Stewart S, Winters GL, Fishbein MC, et al. Revision of the 1990 working formulation for the standardization of nomenclature in the diagnosis of heart rejection. J Heart Lung Transplant. 2005;24(11):1710-1720.
  14. Mehr MR. Heart transplantation at 50. Lancet. 2017;390(10111):E43-E45.
  15. Nankivell BJ, Alexander SI. Rejection of the kidney allograft. N Engl J Med. 2010;363(15):1451-1462.
  16. Richmond ME, Zangwill SD, Kindel SJ, et al. Donor fraction cell-free DNA and rejection in adult and pediatric heart transplantation. J Heart Lung Transplant. 2020;39(5):454-463.
  17. Levitsky J, Asrani SK, Schiano T, et al. Discovery and validation of a novel blood-based molecular biomarker of rejection following liver transplantation. Am J Transplant. 2020;20(8):2173-2183.
  18. Sigdel TK, Archila FA, Constantin T, et al. Optimizing detection of kidney transplant injury by assessment of donor-derived cell-free DNA via massively multiplex PCR. J Clin Med. 2018;8(1).
  19. Bloom RD, Bromberg JS, Poggio ED, et al. Cell-free DNA and active rejection in kidney allografts. J Am Soc Nephrol. 2017;28(7):2221-2232.
  20. Bromberg JS, Brennan DC, Poggio E, et al. Biological variation of donor-derived cell-free DNA in renal transplant recipients: clinical implications. J App Lab Med. 2017;2(3):309-321.
  21. Grskovic M, Hiller DJ, Eubank LA, et al. Validation of a clinical-grade assay to measure donor-derived cell-free DNA in solid organ transplant recipients. J Mol Diagn. 2016;18(6):890-902.
  22. First MR, Whisenant T, Friedewald JJ, et al. Clinical utility of peripheral blood gene expression profiling of kidney transplant recipients to assess the need for surveillance biopsies in subjects with stable renal function. J Transplant Technol Res. 2017;7(3).
  23. Marsh C, Kurian SM, Rice J, et al. Application of TruGraf® v1: a novel molecular biomarker for managing kidney transplant recipients with stable renal function. Transplant Proc. 2019;51(3):722-728.
  24. Roedder S, Sigdel T, Salomonis N, et al. The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study. PLoS Med. 2014;11(11).
  25. Beck J, Oellerich M, Schulz U, et al. Donor-derived cell-free DNA is a novel universal biomarker for allograft rejection in solid organ transplantation. Transplant Proc. 2015;47(8):2400-2403.
  26. Kurian S, Velazquez E, Thompson R, et al. Orthogonal comparison of molecular signatures of kidney transplants with subclinical and clinical acute rejection: equivalent performance is agnostic to both technology and platform. Am J Transplant. 2017;17(8):2103-2116.
  27. Pham MX, Teuteberg JJ, Kfoury AG, et al. Gene-expression profiling for rejection surveillance after cardiac transplantation. N Engl J Med. 2010;362(20):1890-1900.
  28. Khush KK, Patel J, Pinney S, et al. Noninvasive detection of graft injury after heart transplant using donor-derived cell-free DNA: a prospective multicenter study. Am J Transplant. 2019;19(10):2889-2899.
  29. Pattar SKG, Steven C. Circulating nucleic acids as biomarkers for allograft injury after solid organ transplantation: current state-of-the-art. Transplant Research and Risk Management. 2019;11:17-27.
  30. Schutz E, Fischer A, Beck J, et al. Graft-derived cell-free DNA, a noninvasive early rejection and graft damage marker in liver transplantation: a prospective, observational, multicenter cohort study. PLoS Med. 2017;14(4):e1002286.
  31. Guzzi F, Cirillo L, Buti E, et al. Urinary biomarkers for diagnosis and prediction of acute kidney allograft rejection: a systematic review. Int J Mol Sci. 2020;21(18).
  32. Adam B, Afzali B, Dominy KM, et al. Multiplexed color-coded probe-based gene expression assessment for clinical molecular diagnostics in formalin-fixed paraffin-embedded human renal allograft tissue. Clin Transplant. 2016;30(3):295-305.
  33. Sigdel T, Nguyen M, Liberto J, et al. Assessment of 19 genes and validation of CRM gene panel for quantitative transcriptional analysis of molecular rejection and inflammation in archival kidney transplant biopsies. Front Med (Lausanne). 2019;6:213.
  34. Depasquale E, Hall S, Crespo-Leiro M, Kao A, Teuteberg J, Hiller D, Yee J. Combination of cell-free DNA with gene-expression profiling in the diagnosis of acute rejection. J Heart Lung Transplant. 2019;38:S387.
  35. Fryback DG, Thornbury JR. The efficacy of diagnostic imaging. Med Decis Making. 1991;11(2):88-94.
Open Meetings
Meeting DateMeeting StatesMeeting Information
09/18/2023 South Carolina


Contractor Advisory Committee (CAC) Meetings
Meeting DateMeeting StatesMeeting Information
11/16/2022 South Carolina

Multi-jurisdictional teleconference hosted by Noridian and Palmetto GBA

11/17/2022 South Carolina

Multi-jurisdictional teleconference hosted by Noridian and Palmetto GBA

Proposed LCD Posting Date
Comment Period Start Date
Comment Period End Date
Reason for Proposed LCD
  • Provider Education/Guidance
Requestor Information
This request was MAC initiated.
Contact for Comments on Proposed LCD
MolDX Policy
PO Box 100238 (JM) or PO Box 100305 (JJ)
Columbia, SC 29202

Associated Documents

Related National Coverage Documents


  • Solid Organ Allograft Rejection

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