A New Algorithm Combining Donor Derived Cell-Free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology

P. F. Halloran¹, J. Reeve¹, K. S. Madill-Thomsen¹, N. Kaur², E. Ahmed², N. Al Haj Baddar², Z. Demko², N. Liang², R. K. Swenerton², B. G. Zimmermann², P. Van Hummelen², A. Prewett², H. Tabriziani², P. Gauthier², P. R. Billings²

¹Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada, ²Natera, Inc., Austin, TX

Meeting: 2022 American Transplant Congress

Abstract number: 1056

Keywords: Kidney transplantation, Rejection

Topic: Clinical Science » Kidney » 44 - Kidney Acute Antibody Mediated Rejection

Session Information

Session Name: Kidney Acute Antibody Mediated Rejection

Session Type: Poster Abstract

Date: Sunday, June 5, 2022

Session Time: 7:00pm-8:00pm

Presentation Time: 7:00pm-8:00pm

Location: Hynes Halls C & D

*Purpose: Donor derived cell-free DNA (dd-cfDNA) has been shown to be associated with allograft rejection, both histological and molecular (JASN, in press). Clinically available dd-cfDNA tests report dd-cfDNA fraction, but recent studies indicate that dd-cfDNA quantity may have a stronger association with rejection. In this study, we validate a novel algorithm incorporating both dd-cfDNA fraction and quantity, using the Molecular Microscope Diagnostic (MMDx) biopsy classification system as truth.

*Methods: The first 426 sequential indication biopsy-matched plasma samples (367 after exclusions) were analyzed from the patients enrolled in the Trifecta study from 27 European and US sites. Plasma dd-cfDNA was measured using the Prospera^TM test (Natera, Inc., San Carlos, CA). The first 149 samples (by collection time) were used to select a dd-cfDNA quantity cut-off. We defined a two-threshold algorithm, which considered samples as “at-risk for rejection” if they were above either the previously validated 1% dd-cfDNA cut-off or the dd-cfDNA quantity cut-off. The next 218 samples were used to validate the algorithm using MMDx biopsy results as truth. AUC was calculated using two independent statistical methods based on a continuous model.

*Results: A dd-cfDNA quantity cut-off of 78 cp/mL was selected using the training set. In the validation set, the performance of dd-cfDNA was improved using the two-threshold algorithm (83.1% sensitivity, and 81.0% specificity) compared to the 1% dd-cfDNA fraction cut-off alone (80.3% sensitivity, 83.0% specificity) using MMDx as a comparator. The two-threshold algorithm gave sensitivities for detection of ABMR, TCMR and mixed rejection in the test set of 81% (43/53), 100% (8/8) and 80% (8/10), respectively. AUC of 0.88 was calculated for the combination of dd-cfDNA fraction and quantity using MMDx as comparator, by both statistical methods.

*Conclusions: This study showed strong correlation between dd-cfDNA and molecular rejection. These findings also validate the ability of the novel two-threshold algorithm, which incorporates both dd-cfDNA fraction and quantity, to detect active rejection. The use of the two variables showed improved performance over the previously validated 1% dd-cfDNA cut-off.

To cite this abstract in AMA style:

Halloran PF, Reeve J, Madill-Thomsen KS, Kaur N, Ahmed E, Baddar NAlHaj, Demko Z, Liang N, Swenerton RK, Zimmermann BG, Hummelen PVan, Prewett A, Tabriziani H, Gauthier P, Billings PR. A New Algorithm Combining Donor Derived Cell-Free DNA Fraction and Quantity to Detect Kidney Transplant Rejection Using Molecular Diagnoses and Histology [abstract]. Am J Transplant. 2022; 22 (suppl 3). https://atcmeetingabstracts.com/abstract/a-new-algorithm-combining-donor-derived-cell-free-dna-fraction-and-quantity-to-detect-kidney-transplant-rejection-using-molecular-diagnoses-and-histology/. Accessed May 17, 2025.

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