S&T Excellence

Challenge

"The aim of the CliniMARK network is
to establish a ‘Best Biomarker Practice’ community to significantly increase
the number of biomarkers with reproducibly demonstrated feasibility."

Description of the Challenge (Main Aim)

Thousands of circulating proteins and metabolites have been shown to be hallmarks of emerging diseases, response to treatments, or a patients’ prognosis. The identification of these biomarkers holds a great promise for significant improvement of personalized medicine based on simple blood tests. For instance, diagnosis and prognosis with biomarkers (carcinoembryonic antigen (CEA)) has significantly improved patient survival in colorectal cancer patients.
Unfortunately, despite significant investments in biomarker discovery studies, only ~150 out of thousands of identified biomarkers have currently been regulatory accepted implemented in clinical practice. This is mainly caused by an incoherent pipeline from biomarker research to market introduction. A lack of accurately validated protein biomarkers - The process from discovery of a biomarker to clinical implementation consists of 3 phases (Figure 1 below): (1) Research: discovery studies to identify potential biomarkers for a given indication,
(2) Development: determining the feasibility of the biomarker through analytical development and validation of a prototype biomarker test, and validation in clinical studies, (3) Market: further development and extensive validation of a clinical-grade biomarker assay fulfilling diagnostic and regulatory criteria towards clinical use of the biomarker. Significant hurdles lie within the transitions of phase 1 to 2 and phase 2 to 3, yielding two large biomarker innovation gaps .

Figure 1

The number of biomarkers in the phases 1-3
of the pipeline from biomarker discovery to clinical use.
"Therefore, the CliniMARK network will focus on the analytical and clinical validation
of biomarkers to improve the transition of biomarkers from the Research to the Market phase."
Improving the pipeline from biomarker Research to Market - The large biomarker innovation gaps are caused by two main problem. First, due to lack of standardisation and harmonisation, biomarker data can hardly be reproduced. Efforts to combine and standardize approaches in biobanks and databases at the (inter)national level exist (e.g. the EATRIS, BBMRI, and ELIXIR initiatives), but mostly aim at establishing larger databases and more analytical capacity by standardizing data collection, while as of yet not standardizing study designs with regard to reporting on meta- and rawdata acquisition, description of data analysis protocols and statistical methods. As a result, when a biomarker reaches phase 3, different research groups have studied the biomarker using different detection, calibration, and validation methods, using poorly described data analysis protocols, study designs established ad hoc and different statistical methods [1].
This results in different outcomes on measured biomarker levels in 80% of the cases [1]. In addition, only about 20% of published data is available according to the FAIR data principles (Findable, Accessible, Interoperable, Reusable), leading to a total percentage of reproducible and reliable biomarker studies of 4% [2]. Thus, in the vast majority of cases, clinical diagnostic laboratories and companies need to repeat the studies already performed in order to acquire reliable data before investing significant amounts of money into the development of a clinical-grade diagnostic assay. Second, the different phases in biomarker development are not well connected. Guidelines exist on biosample isolation and storage [3], analytical assay validation in general [4, 5], specific technologies as clinical mass spectrometry [6] and next generation sequencing [7], and for data stewardship [2]. In addition, development of clinical-grade assays is guided by FDA regulations such as the ICH E16.
However, there has been no combination of existing guidelines into one comprehensive agnostic guideline on biomarker discovery, validation and development to streamline and connect the different phases, that takes considerations for market approval into account from the start. As a result, when a biomarker reaches phase 3, companies cannot rely on available data and are forced to repeat most of the work from phases 1-2 to fill in the gaps and regain confidence in the specific biomarker. Phase 3, guided by FDA and EMA regulations, itself is receiving significant interest at the global level, and new guidelines on regulatory requirements will be generated during the WRIB (Workshop on Recent Issues in Bioanalysis) meeting in Orlando in April 2016.
"To maximize the efficiency of transitioning biomarkers from phase 1 to 3
and provide companies with convincing biomarker for development in phase 3,European guidelines to standardize biomarker research and connect the separate phases must be developed."
In addition, with scientific journals dictating what is published and what is not, thereby driving the activities
of scientists, adherence to existing guidelines is low. For scientists, no direct incentive exist to adhere to best
practices and/or whitepapers and even the journals publishing these guidelines do not adhere to them.
"For new guidelines to be effective, new strategies to improve
adherence to guidelines are essential and their acceptance must be measurable."

Relevance and timeliness

Protein and metabolite biomarkers have been used for diagnosis and prognosis for decades. With the exponential progress in development of high-throughput and comprehensive detection techniques like mass spectrometry, next generation sequencing, imaging, and multi-plex immunoassays, biomarkers hold great promise for personalized medicine. As a result, biomarker research has received significant attention worldwide. This is exemplified by recent initiatives for extensive public and private funding, such as the biomarker focused HORIZON2020 calls
(and specifically the PHC12 calls in 2014 and 2015; € 110 million [8] and SME instrument calls in 2017; € 45 million [9]), president Obama’s precision medicine initiative ($215 million) [10]), IMI 2 program (€ 3.2 billion) and national programs such as CTMM (Netherlands, € 321 million). In addition, regulatory and other authorities recognize the need to regulate and standardize biomarker development, as explained in several meetings and reports by the FDA [11], the European Science Foundation [12], and the Organisation for Economic Co-operation and Development [13].
Efforts are also being made to connect biobanks and laboratories throughout Europe (BBMRI, EATRIS), and to coordinate biomarker validation studies for specific diseases (e.g. Alzheimer’s association ‘Global Biomarker Standardization Consortium’ [14]). Despite these efforts, only few newly developed diagnostic and prognostic biomarker assays enter the clinic. The significant investments to increase the number of studies on biomarkers and to connect existing biobanking infrastructures, are unfortunately not matched by similar efforts in standardization.

Specific Objectives

Objectives 1 and 2

Best Biomarker Practice Guidelines to (1) select and validate biomarker detection tests and
(2) select and design studies to for clinical biomarker feasibility studies – To increase the number of clinically used biomarkers, CliniMARK will, in collaboration with biomarker initiatives throughout Europe,
improve the quality and reproducibility of clinical biomarker feasibility studies, rather than further increasing the number of biomarker discovery studies.
CliniMARK aims to achieve this goal by creating Best Biomarker
Practice (BBP) Guidelines, which will provide guidance for:
  • 1. Discovery of biomarkers,
  • 2. Classification of biomarkers according to their characteristics, anticipated clinical use, and their phase of development,
  • 3. Selection, development and validation of appropriate research-grade biomarker detection tests,
  • 4. Selection of appropriately designed studies and biological samples to reliably and reproducibly determine the feasibility of biomarkers clinically,
  • 5. Selection and reporting on appropriate clinical database structure and vocabularies, biomarker data storage, data analysis protocols, privacy concerns, ethical issues, and statistical methods, and
  • 6. Connection of the separate phases by keeping the eventual goal of market introduction in mind.

Objective 3

Implementation of the CliniMARK approach: Demonstrator project in Chronic Obstructive Pulmonary Disease (COPD)
To demonstrate the value of the generated BBP guidelines, COPD will be chosen as a demonstrator project. The CliniMARK network will gather and classify all known COPD biomarkers and select the appropriate research-grade detection tests.
Furthermore, the CliniMARK network will design technical validation studies, and design clinical multi-centre feasibility studies.

Objective 4

Capacity building: New channels for BBP dissemination - CliniMARK aims to develop novel strategies to improve adherence to guidelines. Implementation of BBP guidelines throughout Europe will greatly improve the biomarker research capacity. Therefore CliniMARK will disseminate the results through channels such as publication of guidelines in scientific journals, LinkedIn groups, conferences, flyers, and publication of reports.
However, these channels have proven insufficient to promote strong adherence to guidelines. One new example that will be investigated is an online platform where the expertise of all network members will be compiled and classified. Scientists who aim to study a biomarker can enter this biomarker in the online tool, classify the biomarker according to the BBP guidelines and receive an overview of which studies must be performed for each phase and of experts or existing platforms
(like the EATRIS Biomarker and BBMRI Biobanking platforms) that can provide the necessary expertise, samples and tools for each phase. In addition, the network will seek collaboration with scientific journals on biomarkers to develop a publication policy to stimulate adherence to the BBP. The relationship between the CliniMARK aim, objectives, Action challenge and the multidisciplinary Action network is represented in Figure 2 below.
Figure 2: The relation between CliniMARK aim, objectives and cost challenge

Progress beyond the state-of-the-art and Innovation Potential

Description of the state-of-the-art

State-of-the-art technologies to measure protein biomarkers include: Within CliniMARK, the focus will be on protein biomarkers using two key technologies: (1) mass spectrometry based methods like Matrix-Assisted Laser Desorption/Ionization (MALDI), Liquid Chromatography coupled to tandem mass spectrometry (LC-MS/MS) and Selective Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM)/Parallel Reaction Monitoring (PRM), (2) immuno-assay based methods include immunocyto/histochemistry, western blotting, the enzyme-linked immunosorbent assay (ELISA), multiplex assays (e.g. Luminex or affimer/aptamerbased technologies), and plasmon resonance imaging.
Continuous development of these analytical techniques improves their reliability, detection limits, and high-throughput potential. However, since in guidelines for early development no attention is payed to eventual market introduction, different research groups use methods that cannot be used in later phases (e.g. for market introduction). State-of-the-art clinical biomarker feasibility studies. Case-control studies to determine sensitivity, and specificity of biomarkers are mostly performed on human samples from biobanks. The use of biobank materials has significant issues such as low sample amounts, non-standardized sample collection, handling and storage, and lack of uniformity of concomitant clinical data.
Several efforts have been made to provide standardized guidelines on biobanking, and to extend sample cohorts by connecting existing biobanks throughout Europe (e.g. BBMRI). Only limited efforts, however, exist to standardize clinical validation study designs. As a result, the sensitivity and specificity of biomarkers are often reported based on ill-designed studies that lack critical information (e.g. health status, confounding factors like BMI or medication, health care costs, technical details on the used biomarker detection technique). This makes it very difficult to reproduce and compare biomarker validation studies.

Progress beyond the state-of-the-art

This COST Action is the first pan-European initiative to deliver guidelines for ‘Best Biomarker Practice’ that cover the design of biomarker development studies to establish clinical feasibility of the biomarker and connect the different phases in biomarker research. These will include sample handling, detection techniques, laboratory reproducibility assessments, clinical validation designs, and extensive diagnostic assay development of biomarkers. To establish the BBP, the network will focus on one disease: COPD, with the objective to define a general framework that is applicable to more technologies, disease indications, and other biomarker use. CliniMARK will rank known COPD protein biomarkers based on physico-chemical characteristics (e.g. size, charge, concentration), and evaluate all research-grade detection techniques and their shortcomings that are available for each biomarker, related to their clinical use. For each biomarker, CliniMARK will then select the most appropriate detection technique per biomarker with regards to expected analytical sensitivity and specificity, with-in run and between run reproducibility, expected optimization and analytical validation duration, and feasibility to further develop the research-grade test into a clinical-grade test.
Subsequently, CliniMARK will define the requirements for analytical validation for the selected test for each biomarker (e.g. what sample material to use, and limits for variability, and reproducibility). Furthermore, the network will compile and use existing guidelines on biobanking for biobanks in COPD. CliniMARK will classify COPD biomarker classes according to their prospective use (e.g. diagnosis, companion diagnostic, prognosis) and evaluate optimal clinical validation study designs (e.g. sensitivity, specificity, clinical impact, economic impact). For each protein biomarker, a development plan for appropriate feasibility study designs will be developed. In addition, in parallel to the specific development plans for COPD biomarkers, a BBP will be designed, based on the thorough evaluation of available biomarker measurement techniques, clinical feasibility study design and existing guidelines. This process will result in two documents: First, a standardized development plan, (outlining intended use, analytical specificiations, and clinical feasibility study design) for selected COPD biomarkers to efficiently enter into phase 3. And second, during development of the plan for specific biomarkers, all decisions and considerations for these decisions will be documented and integrated to develop a standardized BBP whitepaper on selection and analytical validation of research-grade detection techniques and clinical feasibility studies for biomarkers in general.
Furthermore, the CliniMARK network will identify current technological hurdles of detection techniques (e.g. sample preparation, sensitivity, high-throughput potential, sample preparation methods), and establish development plans to overcome these hurdles. The development plans to pass COPD biomarkers through phase 2 will subsequently be carried out by the CliniMARK network members. For each task in the development, the network member with appropriate expertise will be selected. This will result in the standardized development of 1 selected biomarker from phase 1 into phase 3. In addition, the CliniMARK network will develop a pilot online tool to establish research networks for biomarker feasibility research and development. This tool will be designed according to the BBP and be loaded with information on the CliniMARK network with regards to expertise on biomarker detection, biobanking, medical expertise, data analysis, study design, statistical analysis, and health technology. Members can subsequently enter a biomarker in this tool, provide its class and will subsequently receive a biomarker study plan according to the BBP with suggestions of CliniMARK network members that can provide the necessary expertise and data.

Innovation in tackling the challenge

Significant investments have been made in biomarker discovery studies, clinical biomarker feasibility studies, and development of diagnostic tests to increase the amount of validated biomarkers and clinically implemented diagnostic tests.
These investments have resulted in the discovery of thousands of new potential biomarkers, but not in reproducible outcomes of clinical biomarker feasibility studies, nor in a significant increase in clinically implemented diagnostics tests. Therefore, CliniMARK will not focus on discovery or on full diagnostic development but on the intermediate analytical and clinical biomarker development phase (Figure 1 above).
CliniMARK intends to improve the quality and reproducibility of discovered biomarkers through a unique European network that will standardise and connect methods to clinically validate biomarkers.

Added value of networking

In relation to the Challenge

The main aim of CliniMARK is to develop a European network of analytical, clinical, and industrial biomarker experts that define consensus on selection and validation of biomarker detection techniques and clinical feasibility study designs.
Separated networks at the national level exist but significant efforts by these networks often lead to non-reproducible results. To develop a BBP guideline to increase the number of thoroughly validated, reliable biomarkers,
a pan-European academic-industrial network is not only valuable, but an absolute necessity [15].

In relation to existing efforts at the European and/or international level

The CliniMARK Action is complementary to existing efforts. To achieve its long term goal of increasing the number of reproducibly studied biomarkers, the developed BBP guidelines must be implemented in running projects. To achieve such implementation, CliniMARK follows a 3-phased approach. First, CliniMARK will invite members from current biomarker initiatives throughout Europe to join the CliniMARK Action from the start to help establish BBP.
Identified initiatives include ESFRI landmark infrastructures such as EATRIS, BBMRI, and ELIXIR, the FP7 projects IMPROvED, EPREDICE and DIPROMON, the Horizon 2020 PHC-12 projects, and other projects such as BIOAIR, BIOFINDER. Second, to demonstrate the value of the BBP approach, CliniMARK will implement these guidelines in running projects on COPD as a demonstrator project. COPD has been selected as multiple members of the CliniMARK network are involved in COPD biomarker projects and actual implementation of the BBP guidelines in these projects is feasible.
Third, since members of existing European biomarker initiatives have been invited to CliniMARK network at the start, the network to implement the demonstrated CliniMARK BBP approach can be directly transferred to biomarker validation projects for other medical conditions through the CliniMARK network. In addition, the CliniMARK network will establish close contacts with EMA and FDA initiatives on regulatory guidelines for biomarkers (such as the WRIB meetings and EBF (European Bioanalysis Forum) meetings).