Results of a recent analytical validation study from Natera Inc, San Carlos, Calif, have demonstrated the superior performance of the company’s donor-derived cell-free DNA (dd-cfDNA) test for detecting active rejection in kidney transplant recipients.1 The study showed superior assay precision, with a coefficient of variation up to five times better than previously published studies.
Natera’s analytical validation study was based on an analysis of 1,064 replicate samples from both related and nonrelated donor-recipient pairs. The study measured key properties of the assay, including lower limit of detection, linearity, and precision.
In repeatability and reproducibility studies, the assay’s precision was shown to be particularly strong, with a coefficient of variation up to five times better than that of a competitive dd-cfDNA assay (1.85% versus 9.2% within run; 1.99% versus 4.5% across runs).
Natera’s organ transplant rejection assay is designed to detect active allograft rejection in patients who have undergone renal transplantation. The assay works by measuring the fraction of dd-cfDNA in the recipient’s blood, which can spike relative to background recipient cfDNA when the transplanted organ is injured due to immune rejection.
The assay leverages Natera’s core single-nucleotide polymorphism (SNP) -based massively multiplexed PCR (mmPCR) technology to more accurately measure dd-cfDNA levels without the need for donor genotyping. It has been clinically and analytically validated for test performance independent of donor type, rejection type, and clinical presentation.
Previously published analytical studies using other dd-cfDNA assays did not include related donor-recipient cases, such as parents or siblings, which is notable given the technical challenge of differentiating DNA patterns from close relatives. To achieve high accuracy in such cases, Natera leveraged its experience using SNP-based methods to analyze fetal DNA in maternal blood.
“We believe the excellent analytical performance can be attributed to the test’s underlying core technology, based on Natera’s unique SNP-based mmPCR method, which has been a key differentiator in the analysis of cell-free DNA in the prenatal setting, in oncology, and now in organ transplantation,” says Allison Ryan, PhD, Natera’s vice president of data science. “We achieved high precision by targeting more than 13,000 SNPs selected to be informative regardless of ethnicity, optimizing the DNA extraction and library preparation to maximize performance, and developing a unique bioinformatics method that is highly accurate, even in more challenging related donor-recipient cases.”
Paul Billings, MD, Natera.
The analytical performance of Natera’s dd-cfDNA assay underpins its clinical performance in detecting active allograft rejection. In its recently published clinical validation study, Natera reported higher sensitivity (89% versus 59%) and higher area under the curve (0.87 versus 0.74) than the competing dd-cfDNA assay. In that study, Natera also outperformed the competing assay in detecting T-cell mediated rejection, which represents approximately one-third of all allograft rejection diagnoses. In addition, it was the first assay to report high accuracy in detecting subclinical rejection, which occurs in 20% to 25% of patients within the first 2 years after transplantation, and is considered a major driver of graft failure.
“The growing body of evidence from our analytical and clinical validation studies supports our belief that Natera’s noninvasive test will be a valuable tool for the management of kidney transplant recipients,” says Paul Billings, MD, PhD, Natera’s chief medical officer and senior vice president for medical affairs. “Our ultimate goal is to help physicians detect rejection earlier, so that patients’ immunosuppression levels can be optimized before irreversible organ damage occurs.”
There are more than 190,000 people living with a kidney transplant in the United States and roughly 20,000 new kidney transplant surgeries are performed each year. It is estimated that 20% to 30% of organ transplants fail within 5 years, and approximately 50% fail within 10 years. Current tools for diagnosing organ transplant rejection are either invasive biopsies or inaccurate, based on serum creatinine, creating a strong unmet need for better diagnostic tools to improve patient management and outcomes.
Reference
- Altu? Y, Liang N, Ram R, et al. Analytical validation of a single-nucleotide polymorphism-based donor-derived cell-free DNA assay for detecting rejection in kidney transplant patients. Transplantation. Online first, February 19, 2019; doi: 10.1097/tp.0000000000002665,
