Molecular Diagnostics with Clinical Utility: Their Promise in Advancing Precision Medicine in Cancer

Howard I. Scher
Memorial Sloan Kettering Cancer Center

Caroline C. Sigman
CCS Associates

Gary J. Kelloff
Head
National Cancer Institute

David R. Parkinson
ESSA Pharma

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iomarker development is focused on a context of use represented by the unmet need for a more informed diagnostic or therapeutic decision at a particular point in the course of a disease. Once need is determined, a test is developed and standardized to measure and report the information required.

However, developing tests with rigorously validated clinical utility can be challenging from an evidence generation perspective, as well as in attaining consensus among patients, physicians, researchers, regulators, and third -party payers regarding what defines utility in a specific context. The result is high failure rates, higher costs, and limited deployment of potentially beneficial tests for the patients who need them.

Analytical validation is the demonstration that the test is accurate, specific, reproducible, and robust over the specified range of concentrations at which the target molecule(s) will be analyzed.

Clinical validation is the evidence generated through a sequence of trials linking the test result to a clinical outcome that includes understanding the variability of the target molecule(s) in patients in the associated clinical setting.

Clinical utility cannot be established for a molecular diagnostic until it has been shown to be analytically and clinically validated. Simply defined, clinical utility is the demonstration that using the test result to guide patient management improves outcomes or the benefit-to-harm ratio compared with not using the test. Other factors may contribute to clinical utility, such as minimal invasiveness (incurs little or no patient harm), cost-effectiveness (provides the same or better benefit than other tests and requires fewer resources), or wide or easy availability (more likely to be used to make management decisions).

The primary hurdle is attaining analytical and clinical validity, i.e., assuring that a test measures what it is intended to measure, detects what is measured at levels expected to be meaningful, is reproducible and repeatable, is adequately reported, and usable in clinical settings. High levels of evidence are required, but tissue and blood with associated clinical outcomes against which to validate tests are scarce. Further, standards against which to conduct tests and analyze test data are lacking. Therefore, the aggregation of results from different laboratories to build evidence for a single test or to compare tests is difficult. What is needed are test control materials, protocols for collecting blood and tissue for use in the tests, and protocols for evaluating the results.

Another constraint is the rapid pace at which relevant technologies (e.g., multiplex immunochemistry, genomic sequencing, single-cell analysis, and multi-parameter imaging) are evolving. It is entirely possible that tests will be obsolete before they are validated. A third issue is cost vs. benefit. New tests are often accompanied by expensive new technology, and in the eyes of payers – even with strong scientific rationale as background – a new test may not provide enough information relevant to clinical decision making to warrant extra costs.

A final challenge is access. For example, large academic research centers may have certified clinical and pathology laboratories with facilities and expertise to develop and run complex tests. Such capabilities are not widely available outside such centers, limiting the applicability of some newer, sophisticated technologies in the whole research community.

Great Progress Has Been Made

The most dramatic progress has been made in the development of molecular diagnostics based on genomic or proteogenomic profiles. These include tests for single or a small number of alterations (such as mutations in the epidermal growth factor receptor [EGFR]) and molecular signatures based on a specific panel of alterations or broad genome/proteome screens.

Typically, molecular diagnostics for other than blood-based cancers have been derived in tissue. However, tissue biopsies are invasive and, because only small amounts of tissue are available, are often limited to establishing a cancer diagnosis based on analysis of the primary tumor. Hence, research on and development of molecular diagnostics in more abundant liquid sources (blood, urine) is increasing rapidly. These liquid biopsies are usually safer for patients than tissue biopsies and can be repeated over time, allowing monitoring of patients during treatment.

An example is a test for androgen receptor splice variant 7 (AR-V7) mutations in patients with metastatic prostate cancer. These mutations confer resistance to antiandrogen therapy and their presence suggests that alternative therapies should be used. Recently, a blood-based assay for AR-V7 mutations in circulating tumor cells (CTCs) has been developed and is now available commercially. Another example is the first FDA-approved liquid biopsy, which detects cancer-related mutations in EGFR DNA circulating in plasma from patients with non-small cell lung cancer and predicts sensitivity of the patients’ tumors to treatment with EGFR inhibitors.

Of course, this science is still at an early stage and questions remain relating to how well the results of liquid tests reflect what is happening in the tumors. Many large academic research centers, such as the Memorial Sloan Kettering Cancer Center and MD Anderson Cancer Center, have precision medicine programs with detailed plans for profiling patients using molecular diagnostics and designing treatment and monitoring based on these profiles.

These programs require ongoing research to develop strategies for reconciling such differences. Also, although there are few clinical settings in which this is possible, high definition imaging and single-cell analysis are being carried out to compare tumor tissue and CTCs. One such clinical setting is metastatic colorectal cancer where cells from metastases in the liver can be compared with CTCs concurrent at the time of surgery to remove the metastases.

Perhaps the most exciting developments in molecular diagnostics for cancer over the past two decades are genomic profiling tests using deep sequencing techniques (so called next generation sequencing or NGS) to characterize tumors. These profiles, now primarily based on tissue but moving to liquid biopsy, provide source data for design of multiple biomarker tests, involving one or several molecular alterations or for characterizing overall mutational burden.

The FDA long ago recognized the potential value of information provided by these tests but has struggled with producing guidance for establishing analytical and clinical validation of these methods. This includes establishing a workable path for regulatory approval of the methods, improvements in the base technology, and additions to the repertoire of biomarkers detected with these diagnostics.

However, much progress was made this past year. The FDA granted marketing approval to six NGS tests or test systems, published guidance on the regulatory approach that will be taken for these tests (Considerations for Design, Development, and Analytical Validation of Next Generation Sequencing (NGS)–Based In Vitro Diagnostics (IVDs) Intended to Aid in the Diagnosis of Suspected Germline Diseases) that provides recommendations for designing, developing and validating NGS-based tests, and announced their commitment to work with NGS test developers to use the least burdensome approach for reviewing their tests. A second guidance (Use of Public Human Genetic Variant Databases to Support Clinical Validity for Genetic and Genomic-Based In Vitro Diagnostics), describes an efficient approach where test developers may rely on clinical evidence from FDA-recognized public databases (such as NIH’s ClinGen) and peer-reviewed literature to support clinical evidence for their tests and help provide assurance of the accurate clinical evaluation of the genomic test results.

Briefly, as described by the FDA, the regulatory approach has three levels of requirements, based on the evidence needed for intended uses of the assays (see Table 1). The highest levels of evidence are required for companion diagnostics (Level 1), and less evidence is needed for other uses (Levels 2 and 3). After the FDA has reviewed and authorized an NGS test, developers will be able to report post-market additional molecular variants of the same type as in the original panel, and additional FDA review is not required to move tests from Level 3 up to Level 2.

Concomitantly with FDA marketing approvals of NGS tests, the Centers for Medicare & Medicaid Services (CMS) confirmed payer support for these assays by issuing a guidance recommending reimbursement for Level 1 NGS testing and reimbursement for evidence development for other NGS testing.

Table 1. Regulatory Guidance for Development of Molecular Diagnostics Based on Next Generation Sequencing (NGS).

LEVEL 1 (Highest Rigor) Companion Diagnostics (CDx)
These tests provide information on one or more biomarkers essential
for the safe and effective use of specific therapeutic products,
typically drugs.

For NGS tests, CDx use should be supported by analytical validation
for each biomarker comprising the test and a clinical study showing
how the test results correlate with clinical outcomes or with a
previously approved CDx.
LEVEL 2 (Lesser Rigor) Cancer Mutations with Evidence of Clinical Significance
Information from tests for these biomarkers allows physicians to
manage patients according to the body of available clinical evidence
regarding the use of the biomarkers.

These uses require demonstration of analytical validity (either on
the specific biomarker mutation(s) or on representative targets in
the NGS panel) and clinical validity (can be based on publicly
available clinical evidence, such as professional guidelines or peer-
reviewed literature).
LEVEL 3 (Least Rigor) Cancer Mutations with Potential Clinical Significance
Other mutations identified in NGS tests may not meet the criteria
for Level 1 or Level 2 but may still provide information useful to
physicians in characterizing and managing patients’ disease.

For example, these mutations may be useful in screening patients
for clinical trials. These uses are supported through analytical
validation, primarily of representative targets in the NGS panel, and
clinical or mechanistic rationales from peer-reviewed literature or
preclinical data.

Adapted from FDA Fact Sheet: CDRH’s Approach to Tumor Profiling Next Generation Tests (UCM584603).

The Future and Great Promise of Molecular Diagnostics for Precision Medicine in Cancer

Successful precision medicine for cancer depends on molecular diagnostics to provide evidence that patients with and without selected molecular biomarkers respond differently to drug therapy or other treatment. Clinical utility of these tests is becoming more important as understanding of cancer biology increases, biomarker targets for treatment and resistance become more specific and selective, and the number and complexity of molecular diagnostics increase. Several ongoing initiatives are addressing these needs for developing molecular diagnostics to support precision medicine. For example, FDA and NIH have initiated the BEST (Biomarkers, EndpointS, and other Tools) Resource for use in translational science and medical product development. The first phase of BEST is a glossary of terms related to biomarkers.

Other initiatives include public-private collaborations, such as the Blood Profiling Atlas Consortium (BloodPAC) started under Biden’s Cancer Moonshot program, which is gathering relevant protocols, other materials, and data from academic and commercial partners; and the Biomarkers Consortium of the Foundation for the NIH, which has a project for developing control materials for NGS and single biomarker diagnostics. Data sharing initiatives such as Project Data Sphere and the NCI Cancer Genomics Cloud are providing clinical and molecular data that will contribute to the validation of molecular diagnostics.

Friends of Cancer Research recently convened a forum to consider policy for research on and use of NGS testing in precision medicine that demonstrated how fruitful it is for all stakeholders—FDA, academic researchers, pharmaceutical and diagnostic companies, NCI, FDA, CMS, and patient advocates—to work collaboratively to accelerate the development of these tools.

It is up to all of us to follow the critical path for biomarker development on which there are no shortcuts, so that we can prove utility.