Improving diagnostic performance of kidney allograft rejection with a model combining relative fraction and absolute copies of donor-derived cell-free DNA - results from five independent cohorts

IntroductionDonor-derived cell-free DNA (dd-cfDNA) is a standard-of-care biomarker in kidney transplantation, reported as percentage of total cfDNA or copies/mL. We hypothesized that combining both metrics into a continuous composite score would reduce false classifications thus improving the accuracy of rejection diagnosis. MethodsWe analyzed 443 dd-cfDNA measurements in 383 individual patients from five independent kidney transplant cohorts with both percentage and copies/mL. A random discovery set of 31 biopsy-proven rejection and 29 non-rejection cases was used to derive a continuous composite score (CM-Score) integrating dd-cfDNA (%) and copies/mL. Fixed thresholds from the discovery group were validated in 75 rejections and 279 non-rejections for diagnostic performance and compared to twelve published cohorts. ResultsThe CM-Score outperformed dd-cfDNA percentage and cp/mL alone. At the predefined threshold (at 25% prevalence), the CM-Score retained a high NPV of 91% (89-93%), while significantly improving PPV to 80% (78-83%; P<0.002), compared to the published values (weighted average NPV: 88%; 89-90%; PPV: 51% 50-53%, N=6,861). In addition, a decision curve analysis yielded a significantly higher net benefit for the CM-Score (P<0.003; prevalence 10-25% at threshold 15-50%). This superior diagnostic performance of the CM-Score can broaden the applicability of dd-cfDNA to real-world transplantation populations. ConclusionsThe CM-Score is a robust and clinically meaningful tool that improves diagnostic accuracy for both ruling-out and ruling-in rejection using dd-cfDNA and establishes itself as a superior stand-alone metric with clear potential to improve decision-making in kidney transplantation. Lay Summary (Clinical)Kidney transplant failure remains a major concern, and early detection of injury is crucial to prevent long-term damage. A less invasive alternative to a biopsy is a simple blood test that measures tiny fragments of DNA from the transplanted kidney, called donor-derived cell-free DNA (dd-cfDNA). These results can be reported either as a percentage of total DNA or as the number of DNA copies in the blood. We examined whether combining both measurements could improve the detection of rejection. Using data from five transplant cohorts, we developed a combined measure (CM-score) and validated it in 279 samples without rejection and 75 with rejection. At an assumed rejection rate of 25%, it correctly identified rejection with a positive predictive value of 80% and ruled it out with a negative predictive value of 91%. Overall, the CM-score may help doctors diagnose rejection more accurately and make timely treatment decisions.