The Trials and Tribulations of a) developing and b)
commercializing a non-invasive biomarker for subAR
a) Development
The TruGraf® Blood Gene Expression Test (Transplant Genomics, Inc,
Mansfield, MA) is a microarray-based assay that analyzes gene expression
profiles (GEP) in the peripheral blood. Our initial strategy was to
develop a “rule in”’ test, whereby a positive test would be highly
predictive of a positive biopsy (subAR). We used a locked support vector
machine (SVM) based classifier with a bootstrap to prevent over-fitting
of the discovery set for internal validation as the bio-informatics
approach (20). We found two interesting observations: first, at
different thresholds, we traded PPV for NPV to the point that a “rule
in” test was not possible using this approach. We then switched to
Random Forest (RF) as the bio-informatics approach (21) and used a
different threshold, but again it was evident that the intended use of
the biomarker would need to change. Because the performance metrics were
better with RF, we proceeded to use RF but picked thresholds more
favorable for a ”rule out” test (21). The product was a GEP classifier
that associates with either a normal protocol kidney biopsy (Transplant
eXcellence– TX) or the absence of a normal biopsy (not-TX) in patients
with stable renal function. All aspects of discovery and external
validation of the TruGraf test were performed on blood samples paired
with biopsies from prevalent cohorts. For the purpose of validation, the
model derived from pre-selected bio-informatics and the threshold used
to test performance on the discovery cohort were locked. These data led
us to use this approach for external validation in an early access
program (EAP) for patients (22). The external clinical validation from
seven EAP transplant centers defined the key clinical performance
parameters for this assay, as summarized in Table 1 and Figure 1. In
this study, the high negative predictive value (NPV) of TruGraf was
demonstrated in clinical use, making it a strong rule-out test. Over
90% of stable patients who received a TX results were confirmed to have
an immune quiescent phenotype, meaning that a physician can have a high
degree of confidence that a patient who tests as TX does not harbor
silent subclinical rejection. Importantly this study also found that up
to 65% of surveillance biopsies could be avoided in the cohort tested.
Unpublished data involving analysis of an additional 129
biopsy-confirmed blood samples provided by Northwestern University
(originally used for the CTOT-08 study) revealed identical performance
metrics for TruGraf (NPV of 90%). A fourth publication described the
impact of TruGraf results on physician decision making for clinical
decisions (23). This study highlighted the high degree of confidence
physicians place in the ability of TruGraf to provide valuable, added
information that could lead to avoidance of unnecessary surveillance
biopsies as summarized in Table 2.
As a result of these experiences, we changed the proposed COU from
replacing surveillance biopsies for detecting subAR, to reducing the
number of necessary biopsies in stable patients which should lead to
many less invasive procedures (Table 1) as well as significantly less
negative or unnecessary biopsies. The COU proposed in the recent
approval from CMS states that “The TruGraf test is intended for use in
kidney transplant recipients with stable renal function as an
alternative to surveillance biopsies in facilities that utilize
surveillance biopsies”. While primarily used to rule out subAR, it is
expected that both centers that perform or do not perform surveillance
biopsies can use the test to assess the need for a surveillance biopsy
in stable patients (24).
Figure 2 illustrates a proposed approach for implementation of TruGraf
into clinical care for kidney transplant recipients. For patients with
stable renal function, a TruGraf result of “TX” identifies those who
have a high likelihood of immune quiescence and a low likelihood of
histologically defined rejection at the borderline level or higher. A
result of “Not-TX” identifies those in whom silent rejection cannot be
confidently ruled out, and thus carry a higher risk of immune activation
and borderline or higher rejection. Patients with a “Not-TX” result
might benefit from further evaluation and possibly a change in therapy.
Early identification of these patients potentially allows better
allocation of physician resources, and potential reversal of the process
before permanent damage to the donated kidney occurs.
b) Pathway to Commercialization of TruGraf
Developed in 2011, the Molecular Diagnostic Services (MolDX) program is
run by Palmetto GBA, a Centers for Medicare and Medicaid Services (CMS)
Medicare administrative contractor. It performs the following functions:
- Facilitates detailed and unique identification through registration of
molecular diagnostics tests to facilitate claims processing and to
track utilization.
- Establishes clinical utility expectations. Completes technical
assessments of published test data to determine clinical utility and
coverage.
CMS approved reimbursement for commercial TruGraf testing on November
25, 2019.