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Natera Adds Clinical Utility Evidence for Cell-Free DNA in Allograft Health


NEW YORK – Over the course of three studies, Natera and its academic collaborators have presented evidence for the clinical utility of Natera's Prospera assay and of monitoring allograft health through donor-derived cell-free DNA (dd-cfDNA) in general.

The studies evaluated the use of Prospera in monitoring allograft health in heart, lung, and kidney transplants, respectively, with the kidney study specifically assessing the correlation between cfDNA and organ health in the context of COVID-19.

Assessing organ health via dd-cfDNA works because cfDNA in general is a marker of cell death and dd-cfDNA comes specifically from a donor organ.

"Because the donor is genetically distinct from the recipient, it's technically possible to very accurately quantify how much cell-free DNA in the blood is of donor origin versus recipient origin," said Phil Gauthier, Natera's lead senior medical director for organ health.

While Natera is not planning any specific action based on these studies, they collectively reinforce the use of dd-cfDNA as a less invasive diagnostic tool.

"I think the most powerful evidence that we give to doctors is a publication that's been peer reviewed," said Bernie Tobin, Natera's general manager of organ health.

Although the company doesn't expect dd-cfDNA to become a sole means of predicting graft rejection, David Ross, Natera's medical director for lung transplantation, thinks that it "should be able to obviate the need for a significant number of surveillance biopsies."

In a prospective clinical validation study of the use of dd-cfDNA in surveilling lung transplant health, published in Transplantation Direct, Ross and his colleagues found that dd-cfDNA accurately detected several forms of allograft injury, including acute rejection, chronic lung allograft dysfunction, and infection among 103 lung transplant patients.

Similarly, a study of 223 heart transplant patients published in the Journal of the Heart and Lung Association showed that elevated dd-cfDNA fractions, as well as elevated absolute quantities of dd-cfDNA, accurately predicted acute rejection in that context.

In a post hoc analysis of this study, Natera found that absolute quantification of dd-cfDNA further improved the performance of Prospera's measurements.

Because of this, Natera now reports absolute dd-cfDNA quantity along with the percentage of dd-cfDNA, Gauthier said. This study, he added, provides "one of the first sets of evidence that suggested that that was a better approach, which could result in an improvement in test performance."

Gauthier led the third of the recent slate of studies, published in Transplantation Proceedings, which investigated the association between total cfDNA and SARS-CoV-2 infections in kidney transplant patients.

Infection by SARS-CoV-2 can cause kidney damage on its own and the danger is compounded in kidney transplant recipients, who are already immunocompromised and at risk for multiple comorbidities. Immunosuppressive treatments can help attenuate severe cases of COVID-19 by mitigating the cytokine storm and ensuing kidney damage, but physicians need to know which patients are at high versus low risk of graft rejection to best prescribe them.

Gauthier and his colleagues retrospectively analyzed 29 kidney transplant recipients hospitalized with COVID-19 and found that the higher overall cfDNA fractions caused by infection could mask the dd-cfDNA fraction, limiting physicians' ability to accurately identify rejection. As this study was preliminary in nature, the authors pointed out that future studies would be needed to better characterize the relationship between total cfDNA and dd-cfDNA in cases of infection.

Gauthier expressed optimism that such future studies would validate this relationship, saying that "in the near future, we'll be able to use cell-free DNA to more accurately dose immune suppression."

Nonetheless, Tobin suggested that dd-cfDNA will likely remain one tool of many in a physician's kit.

"I think it's difficult to imagine a standalone biomarker that is going to totally replace the value of biopsy unless and until you do studies that prove that biopsy is no longer necessary or needed," he said.

Natera is currently planning to launch a multicenter, randomized and controlled trial to investigate the non-inferiority of dd-cfDNA compared to lung biopsies in conducting graft surveillance.

This trial, Ross said, can help determine "whether we can eliminate biopsies in a surveillance mode for a lot of lung transplant patients."

Other companies also look to use dd-cfDNA to limit the more invasive biopsies.

CareDx, another leader in the organ transplant field, recently initiated its own clinical study to assess the clinical value of the company's post-transplant liver surveillance LiverCare product, as compared to standard-of-care protocols.

That study, called Molecular Assessment and Profiling of Liver Transplant Recipients (MAPLE), takes place at Mount Sinai Hospital in New York City and aims to enroll 1,500 liver transplant recipients.

The LiverCare package consists of AlloSure Liver, AlloMap Liver, HistoMap Liver, AlloHeme Liver, and AlloID. Together this suite of tools assesses a broad array of genomic and metagenomic signals of allograft health.

In concordance with Natera, CareDx expects broader acceptance of dd-cfDNA as an allograft surveillance tool in the near future.

Via email, the company pointed out that the International Society for Heart and Lung Transplantation has already included AlloMap Heart in their guidelines.

"With this in mind," a spokesman wrote, "we do believe that continuing to publish real-world data with a focus on outcomes is key to supporting guidelines."

CareDx noted that the tissue biopsies that currently serve as the standards for clinical validation are prone to variation by individual pathologists and sampling errors, whereas dd-cfDNA measurements would likely be more reproducible.

Even if a particular biopsy test is validated to a single center's reporting standards, CareDx stated, "it may not translate to real-world use."

Because of this, Natera has sought to validate Prospera against a more accurate standard. The firm recently published the results from its Trifecta study, which compared plasma levels of dd-cfDNA to the molecular phenotypes of kidney transplant biopsies obtained via the microarray-based Molecular Microscope Diagnostic System.

"This technique involves looking at gene transcripts in tissue and it's considered to be more accurate than conventional histology," Gauthier said.

Natera found that in its study, dd-cfDNA correlated better to the molecular microscope than to conventional histology.

Ross also pointed out that the technology that enables dd-cfDNA detection also enables the detection of other types of circulating DNA that can also provide information on a transplant recipient's health.

"There is a plethora of cell-free DNA which comes from bacteria, fungi, and viruses circulating in all of us," he said, adding that detecting these may both identify occult infections and add to our general understanding of graft injury.

Although Natera wouldn't comment on specific projects related to nonhuman cfDNA in its pipeline, Tobin said that the firm is actively looking into "a number of things."

"We're excited about what the science is allowing us to do," Tobin said. "We're trying to extend graft survival for patients and we really believe that what we're bringing to market is aiding in that. But we also know there's a lot of work left to do, and we're excited about the things that are left to be done as well."