MMDx-Kidney Diagnostic System Extension

Calibrating circulating donor-derived cell-free DNA against molecular biopsy assessments.

Investigators: Philip F Halloran, Jeff Reeve, Soroush Shojai, Sita Gourishankar and the MMDx-Kidney Study Group ( NCT04239703)

Biopsies both for indications and by protocol play an important role in managing organ transplants, but histology assessment has high interobserver disagreement ("noise") and cannot assess recent tissue injury. To improve precision and accuracy of biopsy assessment, the Alberta Transplant Applied Genomics Centre of the University of Alberta ATAGC) has developed a new biopsy assessment system: the Molecular Microscope® Diagnostic System (MMDx), which measures global gene expression in the biopsy and uses ensembles of machine learning derived algorithms to diagnose rejection and injury. However, the decision to biopsy is often difficult for the clinician, and new tools for predicting abnormalities in the organ transplant are needed.

A new blood-based test may guide decisions to biopsy: donor-derived cell-free DNA (DD-cfDNA). The donor kidney cells release DD-cfDNA during rejection and injury episodes. The Natera DD-cfDNA test is based on massively multiplexed PCR that targets 13,392 single nucleotide polymorphisms. Targeted sequences are then quantified by Next Generation Sequencing (mmPCR-NGS).

The ATAGC cfDNA-MMDx study ("Trifecta") will compare DD-cfDNA, DSA, and MMDx results in prospectively collected clinically indicated kidney transplant biopsies and accompanying blood samples from participating American and European centers. DD-cfDNA (Prospera® test; Natera Inc.) levels will be calibrated against the MMDx biopsy diagnoses of T cell-mediated rejection (TCMR), antibody-mediated rejection (ABMR, and its stages), and acute and chronic injury. The Trifecta study also includes donor-specific antibody (DSA) assessment by One Lambda.

The DD-cfDNA will be calibrated for its ability to predict the MMDx phenotypes in the biopsy. The major trial objectives are 1.) to calibrate DD-cfDNA readings against the MMDx assessments of TCMR, ABMR, and injury; 2.) to optimize and quantify donor DNA measurements; 3.) to develop new treatment algorithms that incorporate both rejection mechanisms is kidney and release of donor DNA.

We believe that calibrating the Prospera® DD-cfDNA test and One Lambda HLA typing results against MMDx will improve transplant patient care but also generate novel insights into clinical scenarios. In addition, DD-cfDNA testing plus MMDx may reduce unnecessary indication biopsies, and make the biopsies that are performed much more useful, and the management decisions more effective. More accurate diagnoses will lead to increasingly personalized treatment, superior endpoints for clinical trials of new agents, and prolonged graft survival.

MMDx-Kidney Diagnostic System Extension Publications:

  1. Halloran PF, Reeve J, Madill-Thomsen KS, Demko Z, Prewett A, Billings P, et al. The Trifecta Study: Comparing Plasma Levels of Donor-derived Cell-Free DNA with the Molecular Phenotype of Kidney Transplant Biopsies. J Am Soc Nephrol. 2022;33(2):387-400.
  2. Halloran PF, Reeve J, Madill-Thomsen KS, Demko Z, Prewett A, Gauthier P, et al. Antibody-mediated rejection without detectable donor-specific antibody releases donor-derived cell-free DNA: results from the Trifecta study. Transplantation. 2022;3 Oct 2022:10.1097/TP.0000000000004324.
  3. Halloran PF, Reeve J, Madill-Thomsen KS, Kaur N, Ahmed E, Cantos C, et al. Combining Donor-derived Cell-free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology as Confirmation. Transplantation. 2022;106(12):2435-42.