Dr. John Friedewald, MD, FAST, is a transplant nephrologist and a Professor of Medicine and Surgery at Northwestern University‘s Feinberg School of Medicine. He also serves as the Medical Director of Kidney Transplantation at Northwestern Medicine .

Dr. Friedewald closely oversees research and development efforts related to transplant medicine, including studies on the use of molecular biomarkers for optimizing post-transplant treatment. His work in this area has provided clinical support for TRAC ID’s ability to integrate viral surveillance and donor-derived cell-free DNA (dd-cfDNA) to better manage transplant patients through personalized precision medicine.

In December 2024, Dr. Friedewald spoke about TRAC ID in a Eurofins Transplant Genomics Webinar. This article summarizes the information presented during that event.

Post-Transplant Monitoring: The Need for Precision Biomarkers

While post-transplant care has improved greatly over the decades, current care remains hampered by the limitations of traditional monitoring techniques, particularly in balancing patient immunosuppression and effectively detecting subclinical rejection. Clinical teams working with kidney transplant patients are challenged by:

The risks of over-immunosuppression. Too much immunosuppression can lead to infections and cancer. Common infections in transplant patients in the first year include adenovirus, BK polyomavirus, cytomegalovirus, and Epstein Barr virus. The first 12 months of treatment often involve an immunosuppression balancing act to ward off latent infections, relapses, and opportunistic infections while protecting graft health. Even beyond the 1-year mark, opportunistic viruses remain a consideration.
The risks of under-immunosuppression. On the other hand, too little immunosuppression can lead to rejection, which can increase the risk of graft failure and patient death.
Detecting subclinical rejection in a timely manner. Traditionally, graft health was monitored via surveillance biopsies. The invasive and expensive nature of biopsy monitoring often meant rejection was discovered too late, creating a significant barrier to optimal patient outcomes.

TruGraf and TRAC Pioneered in Answer to These Challenges

Transplant Genomics pioneered TruGraf and TRAC as molecular biomarkers to better understand graft health and the risks of subclinical rejection in kidney transplant patients.

TruGraf uses gene expression profiling, measuring a patient’s immune state and comparing it to benchmarks to understand whether the patient is more likely “TX” (immune system quiescence) or “non-TX” (subclinical rejection). TRAC is a dd-cfDNA quantification that uses whole genome sequencing. It returns a measurement that demonstrates the likelihood of ongoing graft injury, typically from antibody-mediated injury. These biomarkers can help clinicians understand overall graft health and identify trends toward subclinical rejection via non-invasive monitoring methods.

TRAC ID: Integrating Gene Expression and dd-cfDNA

TRAC ID adds another level of information to post-transplant monitoring by combining viral identification and quantification and dd-cfDNA analysis. This creates a more comprehensive picture of immune activity and organ health, allowing clinical teams to make proactive decisions about immunosuppression and other treatments.

Dr. Friedewald explains the whole genome sequencing process, noting that plasma is collected and nucleic acids within the sample are isolated and optimized for cfDNA. A library prep sequence is performed, and then, a whole genome sequence is completed. From that, human sequences are isolated, allowing teams to understand what percentage of the human cfDNA is donor-derived versus recipient-derived.

The percentage of dd-cfDNA is critical to the TRAC test for rejection. The threshold is 0.7% — less than that indicates low risk of rejection on the TRAC assay.

How dd-cfDNA Viral Insight Supports Tailored Post-Transplant Care

Dr. Friedewald notes that the microbial sequences created as part of the whole genome sequencing were being ignored — being thrown out, as it were. His research team went back and looked at the microbial sequences to learn more about the value of this metagenomic viral detection.

The team looked at a clinical trial that involved 2,000 samples from 256 patients. The samples were taken over the 2 years post-transplant. Dr. Friedewald noted that the microbial information from the trial demonstrated the expected presence of common pathogenic viruses. The team wanted to find a non-pathogenic virus — one that is not known to cause human disease but that would respond to immunosuppression in the same way that pathogenic viruses did.

Based on prior research and the findings from this study, that virus appears to be torque teno virus (TTV). TTV is especially prevalent — Dr. Friedewald said that it can be present in around 90% of post-transplant patients. It’s also an accurate indication of the level of immunosuppression. In the clinical trial population, the trends in TTV closely followed the traditional curve of immune therapy in the 2 years following a transplant.

With these insights, the team wondered: Could cfDNA viral detection occur prior to reported clinical infection, making it a helpful tool in better managing immunosuppression and supporting customized treatment approaches? The answer appears to be yes.

For BKV, CMV, and EBV, the cfDNA viral detection was 100% accurate on the day clinical infection was reported. It was 91.6% accurate between 1 and 10 days before a reported infection and around 50% accurate 11 to 30 days before a reported infection.

The value of the metagenomic viral detection data was too much to be ignored any longer. This information was added to the TRAC assay, creating TRAC ID.

The Complementary Role of TruGraf and TRAC ID

Dr. Friedewald continues to champion a comprehensive approach to post-transplant monitoring and discussed the complementary role of TruGraf and TRAC ID for this purpose. He noted that previously, TruGraf and TRAC enhanced the ability of clinical post-transplant teams to identify and proactively treat patients in acute and subclinical rejection. However, that’s only around a fourth of post-transplant patients.

The other three-quarters of patients are typically considered stable and healthy — but viruses and other issues impact that patient population, too. Dr. Friedewald points out that TRAC ID provides clinically valuable information that helps identify issues, even in seemingly stable transplant patients, to better guide immunosuppression therapies.

The result is a multi-prong approach to monitoring:

TruGraf helps identify subclinical acute cellular rejection.
TRAC ID helps detect both antibody-mediated rejection and graft injury along with a potential host of viral infections.

Leveraging Whole Genome Sequencing for Viral Detection and a More Inclusive Medical Decision Tree

To demonstrate how this additional clinical information impacts decision-making in post-transplant care, Dr. Friedewald gives some hypotheticals:

TruGraf and TRAC are both negative. This indicates no sign of organ injury or subclinical rejection, so teams would assess immunosuppression status for possible over-immunosuppression and continue with treatment and monitoring.
TruGraf is positive, and TRAC is negative. This indicates no sign of significant organ injury but the potential for subclinical immune activation, so the team may want to repeat tests, increase immunosuppression, or get a biopsy.
TruGraf is negative, and TRAC is positive. This indicates the potential subclinical antibody-mediated rejection and organ injury, so teams may want to repeat tests, increase immunosuppression, check for anti-donor antibodies, or get a biopsy.
Both tests are positive. This indicates a high likelihood of organ rejection, so teams may want to order a for-cause biopsy.

The ID panel, Dr. Friedewald says, can help teams make even more proactive clinical care and decisions. He notes that category 1 above — TruGraf and TRAC are both negative — usually accounts for more than half of patients. Adding in the TTV viral load and information about other viruses provides information to help teams make decisions about whether someone is over-immunosuppressed no matter what category they fall into. Dr. Friedewald presented a medical decision tree based on the new information in the TRAC ID test:

dd-cfDNA is greater than or equal to 0.7% with high levels of TTV. This could indicate immunosuppression issues, and teams should run further tests to understand viral loads. That may include a biopsy to rule out allograft injury.
dd-cfDNA is greater than or equal to 0.7% with the presence of a pathogen like BKV. Teams should test to confirm the pathogen and treat the virus by making changes to immunosuppression or using direct acting antiviral therapy. They might also want to do a biopsy to rule out allograft injury due to the high TRAC result.
dd-cfDNA is greater than or equal to 0.7% and viral pathogen is negative. Teams should presume under-immunosuppression and potential alloimmune-mediated injury and respond accordingly.
dd-cfDNA less than 0.7% and viral pathogen is negative. This indicates the potential for under-immunosuppression, and teams should monitor dd-cfDNA trends.
dd-cfDNA less than 0.7% with the presence of a pathogen like BKV. The patient is potentially being over-immunosuppressed. Teams should confirm the pathogen with qPCR and treat any viral infection.
dd-cfDNA less than 0.7% with high levels of TTV. The patient is potentially being over-immunosuppressed, so teams may want to consider titration.

Clinical Validation of TRAC ID

Dr. Friedewald presented data that demonstrated how patient trends aligned with information from multiple biomarkers. He showed the trends related to a single patient for 2 years post-transplant. The patient had three biopsies during that time: a normal biopsy around 3 months, a biopsy that indicated rejection at around 15 months, and a normal biopsy around the 2-year mark.

Overlaying data about the patient’s TruGraf, TRAC, and TTV numbers over the biopsy findings on a graph created a visual story of exactly what happened with the patient:

TRAC scores started high due to post-transplant inflammation and other factors but dropped quickly. TTV figures rose, indicating a high amount of immunosuppression, and around the time of the first normal biopsy, the patient had instances of BKV and CMV.
After that, TTV numbers dropped substantially while TRAC and TruGraf results rose. The story in the graph is this: Without the TTV information Dr. Friedewald had later, the team likely overdid immunosuppression in the beginning and then overreacted to the BKV and CMV, dropping immunosuppression too low.
Eventually, the too-low level of immunosuppression led to subclinical rejection. TRAC results around the same time as the irregular biopsy indicated 1% dd-cfDNA.
After that second biopsy, the team got a handle on immunosuppression, and the data leveled out.

This data verified TRAC ID’s ability to detect alloimmune-mediated rejection even earlier than biopsy. As TTV dropped quickly, dd-cfDNA began to trend upward. Those results tell the story of under-immunosuppression and ongoing allograft injury.

Personalized Precision Medicine With TRAC ID

Combining TRAC ID and TruGraf provides support for precision medicine in post-transplant situations.

Future Innovations in Transplant Genomics

Ongoing innovation in molecular biomarkers will continue to drive tailored care and optimized clinical decision-making post-transplant. TRAC ID’s success could lead to ongoing innovations in transplant care, as this approach has potential for adoption across other organ transplant processes.

Transforming Transplant Monitoring

TRAC ID sets new standards in post-transplant monitoring by providing added clinical value. Its ability to detect subclinical rejection, monitor graft injury, and identify viral infections allows post-transplant care teams to be more proactive and provide a more personalized level of care.

Transplant Genomics aims to improve transplant outcomes for recipients through non-invasive treatment options. Learn more today.