Creating standards for liquid biopsies: the BLOODPAC experience

KEYWORDS:

• Liquid biopsy
• MRD
• bTMB
• Pre-Analytical
• collaboration
• blood profiling
• analytical validation
• Data Commons
• Cancer Research
• Cancer Moonshot

1. Introduction

Since the first Food and Drug Administration (FDA) approval in 2013, liquid biopsy-based platforms have transformed the precision management of patients with advanced cancer [1]. Liquid biopsy holds a demonstrated role in precision medicine that historically focused on targeted therapy selection. Yet, continued innovation is expected to drive growing utility for liquid biopsy-based tests in other areas of clinical need, including minimal (or molecular) residual disease monitoring and early-stage cancer screening.

As with any novel medical technology, the clinical potential of liquid biopsy cannot be realized without acceptance by stakeholders within the biomedical and healthcare ecosystem. This creates an urgent need to establish best practices for test development and validation and to support shared standards that lessen the burden on regulators, clinicians, patients, and payers. This framework could only be generated through an exceptional degree of collaboration among stakeholders and industry experts in this highly competitive field.

In 2016, when then-U.S. Vice President Joe Biden launched the Cancer Moonshot, the call-to-action catalyzed a collective effort to overcome hurdles in the development, validation, and clinical adoption of liquid biopsy for the benefit of patients [2]. When Blood Profiling Atlas in Cancer (BLOODPAC, also denoted as ‘BloodPAC’) formed in late 2016, it was with a clear understanding of the challenge: without a common ‘yardstick’ to guide the development and evaluation of these tests, the clinical benefits for patients would be slow to materialize.

A competitive marketplace fuels innovation. Yet, with a novel technology like liquid biopsy, competition must be grounded in broad understanding, trust, and a shared vision for standards of excellence [3]. At its inception, BLOODPAC members recognized that no single entity could establish these essential elements for a healthy competitive space. This understanding took root and, since 2016, the consortium has grown to include over 60 collaborators – diagnostic developers, pharmaceutical companies, academic institutions, nonprofit organizations, private payers, standards-setting organizations, and federal agencies – all working within ten different working groups [4].

Other industry collaborations exist to establish best practices, like Friends of Cancer Research, Quality Assurance Initiative in Pathology, and the Clinical and Laboratory Standards Institute [5–7]. BLOODPAC fills a void where guidelines do not exist. The consortium is working to address the unmet need by providing guidance for the industry, collaborating with government and other regulatory agencies, and leveraging expertise through the organization’s diverse membership.

2. BLOODPAC’s standards work to date

In the development of diagnostic technologies, the need for standards is cross-cutting. As such, BLOODPAC prioritized the work needed to generate agreement in multiple areas and has achieved ambitious and distinct milestones in a short five years. Taken together, the successes driven by BLOODPAC have generated analytical validation standards and frameworks that, with broad adoption and use, will streamline the efforts of test developers and help the FDA effectively communicate with companies and review their technologies.

2.1. Minimum technical data elements

The diversity of liquid biopsy tests is evident in the varying analytes detected or the methods used to yield clinically meaningful insights. Creating room for innovative and varied approaches to assay development has helped foster breakthroughs in these technologies. However, these different approaches make ‘apples to apples’ comparisons of clinical and diagnostic data challenging and create barriers to data-sharing efforts.

To address this challenge, BLOODPAC has worked to establish Minimum Technical Data Elements (MTDEs), reflecting factors that influence the performance of a liquid biopsy test in the laboratory that may affect the final result, for different areas of test validation. In 2020, BLOODPAC addressed pre-analytical variables by setting forth 11 MTDEs, like blood collection tube type, sample composition, time to fractionation, to enable consistent data collection and comparison between investigators, studies, and institutions [8].

These MTDEs have lent to the success of the BLOODPAC Data Commons, a vital piece of infrastructure that helps inform and scientifically validate the consortium’s frameworks. The effort to align on required data elements has yielded tangible impact. The Data Commons currently contains over 70 studies and projects spanning nearly 4,500 cases, 33,000 files, and a total of 33 terabytes of data [9].

BLOODPAC working groups are currently working to develop other analytical and clinical variables, as well as developing a standard vocabulary for other variables. Through our extensive collaboration, BLOODPAC members recognize that, in some cases, the greatest challenge in alignment are not differences in content or scientific approach, but rather differences in terminology and associated definitions. For example, when defining limits of detection for new assays, there may not yet be consensus on how it should be defined or whether existing definitions (for example, the CLSI Harmonized Database) are applicable [10]. This work will help drive a shared understanding in multi-stakeholder discussions.

2.2. Analytical validation protocols

Analytical validation demonstrates that a test meets design requirements or a specified level of performance. Existing evaluation guidelines, such as those developed by the Clinical and Laboratory Standards Institute, do not address the unique challenges encountered when evaluating liquid biopsy tests.

BLOODPAC has stepped in to fill this gap in the liquid biopsy field. Instead of individual companies communicating with regulators to understand how the safety and efficacy of a test might be evaluated, BLOODPAC has streamlined this discussion to help bring these products to patients faster.

Working in collaboration with the FDA, BLOODPAC achieved a critical milestone when we published a set of recommended generic analytical validation protocols to help test developers address the challenges in evaluating Next-Generation Sequencing-Based ctDNA Assays [11]. These challenges include the limited amount of blood that can be drawn; the low frequency of tumor-derived DNA molecules in the blood, relative to the amount of nontumor-derived cell-free DNA; the extremely high level of sensitivity and specificity needed to detect ctDNA; the potential for false negatives in detecting these rare molecules; and the increased need for contrived samples to attain sufficient ctDNA for analytical validation. For example, the required types and numbers of samples evaluated in analytical validation studies is always reviewed on a case-by-case basis depending on the assay. Yet without guidance, it may still be unclear if a study such as an accuracy study should require tens or hundreds of samples. Our previously mentioned publication recommended ‘10 to 20 positive samples for each type of variant included in the assay’s Level 1 claims.’ Developers must still justify if this guideline is appropriate, yet its availability allows them to design their studies quickly and with confidence.

BLOODPAC has devoted specific efforts to create standards for contrived materials that can demonstrate functional equivalence with native ctDNA. Through a collaboration among 10 independent laboratories, the group is conducting an analytical study to increase the quality and consistency of ctDNA analysis through inter-laboratory testing of well-recognized analytical tools and reference materials. The working group is currently developing a report to share the results of this analytical study.

2.3. Looking ahead: creating standards for MRD & bTMB

BLOODPAC has been working to address standards for analytical validation in three areas: 1) multimarker tests or multivariate index assays, tests that incorporate multiple markers into a composite score, 2) MRD tests, and 3) blood tumor mutational burden (bTMB) tests [12]. The latter two tests associate a pattern of biological signals with treatable disease states. Even more than liquid biopsies reporting on the status of a set of individual somatic mutations, MRD and bTMB combine multiple mutations or markers to assess these disease states. Even if the clinical indications being tested are similar, these tests are inherently difficult because each developer may use different biomarkers, combine them in different ways and use different analytical methods.

Discussions are ongoing with working groups and FDA to align on two key areas. First, the group is working to determine how performance goals may be defined for tests measuring multiple markers to assess one disease state. Second, group members are working to assess how studies evaluating individual markers can be leveraged to characterize the performance of tests that utilize multiple markers or a composite score of those markers.

3. Standards that meet the needs of stakeholders

As the community of innovative diagnostics developers, pharmaceutical companies, academic researchers, nonprofits, government agencies, and other stakeholders work to bring a wider scope of utility to liquid biopsy in patient care, the route to success has been well-charted by BLOODPAC’s efforts over the last 5 years. Fostering collaboration has been essential in setting analytical validation standards needed to expand on the power of liquid biopsy to inform treatment selection and bring growing promise to patient care in monitoring for disease recurrence and for early-stage cancer screening.

In some ways, BLOODPAC’s diverse collaboration mirrors how the practice of medicine has evolved. As scientific advances drive deeper understanding of the complexities of disease, multidisciplinary approaches have become critical. Similarly, in diagnostics, it is no longer possible for small groups to have expertise in all the clinical, analytical, and economic aspects of developing liquid biopsies. By serving as the ‘connective tissue’ among stakeholders who might not otherwise have a cooperative space to collaborate, experts can serve their respective organization missions, while amplifying their own impact within a culture of shared ideas, fresh perspectives, and critical thinking.

Each of BLOODPAC’s members have made deep investments of time and expertise to develop standards because broadly accepted standards benefit all stakeholders within the ecosystem of innovation. At its core, a standard is an example or precedent that others have found acceptable to repeat themselves or upon which to rely when utilizing liquid biopsy-based assessments to drive therapeutic decision-making. Who better to provide these examples than the subject matter experts that develop competing tests and the physicians that use these tests to support their patients? Our goal is to ultimately improve healthcare, whether that be through encouraging consistent use or validation of a test or increasing access and understanding of the test. For both assay developers and FDA, industry-wide standards support faster, more efficient regulatory review, and greater receptivity by clinicians and payers. For clinicians, the use of common standards for the analytical validations and regulatory review of liquid biopsy provides an additional piece of evidence that can help them feel comfortable that tests are ready for clinical use and will benefit their patients. For payers, FDA-informed standards offer confidence when deciding whether a test is appropriate for reimbursement. For patients, multistakeholder collaboration driven by a common goal – better care and outcomes – offers greater assurance on the benefit of new technologies in their lives.

As BLOODPAC continues to chart its course for the next 5 years, we will work to develop analytical validation protocols for the development and use of control materials for MRD, bTMB, and potentially envision the needed framework for home-based collection of samples. The successes generated by BLOODPAC in its first 5 years demonstrate that these next endeavors will serve as essential steppingstones in realizing the benefits of liquid biopsy in improving patient care and outcomes.

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewers Disclosure

Peer reviewers on this manuscript have no relevant financial relationships or otherwise to disclose.

Correction Statement

This article has been republished with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This paper was not funded.