The drug diagnostic co-development concept paper

The Labyrinth of Product Development and Regulatory Approvals in Liquid Biopsy Diagnostics

The evolution of chemistries and instrument platforms for next‐generation sequencing has led to sequencing of genomic variants in both tumor biopsies as well as in circulating tumor cells (CTCs) and cell‐free DNA liquid biopsies. The transition of these analytical platforms into clinical ones has led to challenges in product development as well as regulatory strategies for the approval of diagnostic products with these platforms. Regulatory strategies for liquid biopsy diagnostics depend on a framework that has been developed over the past few years by the US Food and Drug Administration (FDA). This framework includes both guidances that cover enrichment biomarkers and companion diagnostics, as well as regulatory approval precedents, which can be used to design regulatory strategies for new liquid biopsy diagnostic products. However, the regulatory paths for these liquid biopsy diagnostics can also be tortuous, as is the example of CTC—platform liquid biopsies. The ultimate success of regulatory pathways of liquid biopsy diagnostics has been driven by the incremental value of FDA approval for Clinical Laboratory Improvement Amendment (CLIA)‐developed tests and by the inherent complexity of these diagnostics, which are practical barriers for the widespread replication of these tests throughout CLIA laboratories. The framework for FDA approval of sequence information from these liquid biopsies has been focused on single‐site approvals of diagnostics where sequencing information is considered at different diagnostic risk levels, ranging from novel or follow‐on companion diagnostics to variant calls in genomic targets considered independently valuable for therapeutic decision making.

Exclusive Drug Labeling Rights as a New Incentive for Contribution to a Communal Biomarker Resource

Biomarkers are an important tool in modern drug development. The FDA has posited that increased use of biomarkers in clinical trials can accelerate pharmaceutical industry productivity, ushering new drugs to market. Accordingly, the FDA has created two pathways for evaluation of biomarker utility. Biomarkers incorporated into clinical trials, the traditional pathway, are effectively private to a therapeutic sponsor and to the scope of the trial. By contrast, in Biomarker Qualification ("BQ"), the second pathway, a biomarker is certified as a publicly available tool. The FDA has hoped that academic, non-profit, and industry stakeholders would work together in consortia to qualify biomarkers, cumulatively generating a common resource of broad utility. In practice, utilization of Biomarker Qualification has been paltry. Incentives for BQ that align with the interests of industry resource holders are necessary to fuel increased utilization of biomarkers in clinical trials and create the communal biomarker toolkit envisioned by the FDA. A blanket extension of exclusivity for any drug successfully paired with a companion biomarker would diminish public access to medicine by encouraging spurious biomarkers and correspondingly narrowed clinical trials. As a measured alternative, an exclusive right to include a qualified companion biomarker on an FDA drug label would balance public access externalities. This exclusivity would waylay label approval, and thus marketability, of later drugs relying on the qualified biomarker for clinical safety or efficacy. Accordingly, sponsors would find no incentive to portage an ineffective or unnecessary biomarker through clinical trials, as there would be no benefit to securing exclusive rights in a tool others saw no value in using.

Variability in Platelet-Derived Growth Factor Receptor Alpha Antibody Specificity May Impact Clinical Utility of Immunohistochemistry Assays

Aberrant regulation of the receptor tyrosine kinase platelet-derived growth factor alpha (PDGFRα) is implicated in several types of cancer. Inhibition of the PDGFRα pathway may be a beneficial therapy, and detection of PDGFRα in tumor biopsies may lead to insights about which patients respond to therapy. Exploratory or clinical biomarker use of PDGFRα IHC has been frequently reported, often with polyclonal antibody sc-338. An sc-338-based assay was systematically compared with anti-PDGFRα rabbit monoclonal antibody D13C6 using immunoblot profiling and IHC in formalin-fixed and paraffin-embedded human tumor cell lines. Application of sc-338 to blots of whole cell lysates showed multiple bands including some of unknown origin, whereas application of D13C6 resulted in a prominent band at the expected molecular mass of PDGFRα. The IHC assay using D13C6 showed appropriate staining in cell lines, whereas the assay using sc-338 suggested nonspecific detection of proteins. An optimized IHC assay using D13C6 showed a range of staining in the tumor stromal compartment in lung and ovarian carcinomas. These observations suggest that use of clone sc-338 produced unreliable results and should not be used for an IHC research grade assay. In addition, this precludes its use as a potential antibody for a clinical diagnostic tool.

Commercial enzyme-linked immunosorbent assay versuspolymerase chain reaction for the diagnosis of chronic Chagas disease: a systematic review and meta-analysis

Chronic Chagas disease diagnosis relies on laboratory tests due to its clinical characteristics. The aim of this research was to review commercial enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) diagnostic test performance. Performance of commercial ELISA or PCR for the diagnosis of chronic Chagas disease were systematically searched in PubMed, Scopus, Embase, ISI Web, and LILACS through the bibliography from 1980-2014 and by contact with the manufacturers. The risk of bias was assessed with QUADAS-2. Heterogeneity was estimated with the I2 statistic. Accuracies provided by the manufacturers usually overestimate the accuracy provided by academia. The risk of bias is high in most tests and in most QUADAS dimensions. Heterogeneity is high in either sensitivity, specificity, or both. The evidence regarding commercial ELISA and ELISA-rec sensitivity and specificity indicates that there is overestimation. The current recommendation to use two simultaneous serological tests can be supported by the risk of bias analysis and the amount of heterogeneity but not by the observed accuracies. The usefulness of PCR tests are debatable and health care providers should not order them on a routine basis. PCR may be used in selected cases due to its potential to detect seronegative subjects.

Integration of proteomics, bioinformatics, and systems biology in traumatic brain injury biomarker discovery

Traumatic brain injury (TBI) is a major medical crisis without any FDA-approved pharmacological therapies that have been demonstrated to improve functional outcomes. It has been argued that discovery of disease-relevant biomarkers might help to guide successful clinical trials for TBI. Major advances in mass spectrometry (MS) have revolutionized the field of proteomic biomarker discovery and facilitated the identification of several candidate markers that are being further evaluated for their efficacy as TBI biomarkers. However, several hurdles have to be overcome even during the discovery phase which is only the first step in the long process of biomarker development. The high-throughput nature of MS-based proteomic experiments generates a massive amount of mass spectral data presenting great challenges in downstream interpretation. Currently, different bioinformatics platforms are available for functional analysis and data mining of MS-generated proteomic data. These tools provide a way to convert data sets to biologically interpretable results and functional outcomes. A strategy that has promise in advancing biomarker development involves the triad of proteomics, bioinformatics, and systems biology. In this review, a brief overview of how bioinformatics and systems biology tools analyze, transform, and interpret complex MS datasets into biologically relevant results is discussed. In addition, challenges and limitations of proteomics, bioinformatics, and systems biology in TBI biomarker discovery are presented. A brief survey of researches that utilized these three overlapping disciplines in TBI biomarker discovery is also presented. Finally, examples of TBI biomarkers and their applications are discussed.

Benefit–risk management in the age of personalized healthcare

The ongoing developments in personalized healthcare are opening new possibilities for the optimization of the benefit–risk profiles of drugs based on the stratification of patients. Beyond this straightforward application of pharmacogenomics to the optimization of benefit–risk profiles, other approaches, such as metabolomics and systems pharmacology, may contribute to an improved use of medicines in a personalized healthcare setting. These will, however, require fundamental adaptations or new developments in various areas and by all stakeholders, including the pharmaceutical and diagnostics industries, regulators, physicians and patients. Ultimately, personalized healthcare should enable patients to take personal decisions on treatment options based on their preferred benefit–risk profiles of therapeutics.

Development and regulatory strategies for drug and diagnostic co-development

At the 5th FDA-Drug Industry Association (DIA) Workshop on 'Pharmacogenomics in Drug Development and Regulatory Decision Making', track four focused on the current thinking and issues in the co-development of therapeutic drugs or biologics, and their companion diagnostic products. Identification and validation of genomic and other biomarkers are becoming important components of drug-development strategies, and recent successes show the power of personalized approaches to change the benefit-risk paradigm for new drugs.

Systems biology and theranostic approach to drug discovery and development to treat traumatic brain injury

Traumatic brain injury is a significant disease affecting 1.4 to 2 million patients every year in the USA. Currently, there are no FDA-approved therapeutic remedies to treat TBI despite the fact that there have been over 200 clinical drug trials, all which have failed. These drugs used the traditional single drug-to-target approach of drug discovery and development. An alternative based upon the advances in genomics, proteomics, bioinformatic tools, and systems biology software has enabled us to use a Systems Biology-based approach to drug discovery and development for TBI. It focuses on disease-relevant converging pathways as potential therapeutic intervention points and is accompanied by downstream biomarkers that allow for the tracking of drug targeting and appears to correlate with disease mitigation. When realized, one is able to envision that a companion diagnostic will be codeveloped along the therapeutic compound. This "theranostic" approach is perfectly positioned to align with the emerging trend toward "personalized medicine".

Delivering on the promise of personalized healthcare

Personalized healthcare (PHC) aims to deliver the right medicine, to the right patient, at the right dose and time, and has the potential to benefit everyone in the healthcare system. Delivering the promise of PHC depends on overcoming key challenges (e.g., identifying biomarkers or disease segmentation tools, facilitating partnerships, clinical development, regulatory engagement and market access) in an integrated fashion. Despite this, progress in PHC has been accelerating over the last few years and is now at a turning point. Flexibility from all those involved in PHC, including the pharmaceutical and diagnostic industries, health authorities and payers, will be required to ensure that the field comes to maturity and delivers its potential to improve patients' lives.

A perspective on challenges and issues in biomarker development and drug and biomarker codevelopment

A workshop sponsored by the National Cancer Institute and the US Food and Drug Administration addressed past lessons learned and ongoing challenges faced in biomarker development and drug and biomarker codevelopment. Participants agreed that critical decision points in the product life cycle depend on the level of understanding of the biology of the target and its interaction with the drug, the preanalytical and analytical factors affecting biomarker assay performance, and the clinical disease process. The more known about the biology and the greater the strength of association between an analytical signal and clinical result, the more efficient and less risky the development process will be. Rapid entry into clinical practice will only be achieved by using a rigorous scientific approach, including careful specimen collection and standardized and quality-controlled data collection. Early interaction with appropriate regulatory bodies will ensure studies are appropriately designed and biomarker test performance is well characterized.

Drug–diagnostic codevelopment strategies: FDA and industry dialog at the 4th FDA/DIA/PhRMA/PWG/BIO Pharmacogenomics Workshop

The 4th US FDA/Industry Workshop on Pharmacogenomics in Drug Development and Regulatory Decision Making, was held in MD, USA, on December 10–12, 2007. One of the breakout sessions of the workshop focused on the regulatory issues around codevelopment of drugs and companion diagnostics. This session used hypothetical case studies as focal points for discussion of current thought and critical issues for both industry and the FDA in this evolving field. The panel and the audience discussed the evolution of the FDA’s thinking on the regulatory path for companion diagnostics since the release of the April 2005 draft Drug Test Codevelopment Concept Paper and the issues faced by industry in attempting codevelopment efforts. This session provided an opportunity to allow an exchange of ideas between the FDA and industry and to identify critical issues that need further discussion in this important and evolving field.

Beyond receptor expression levels: the relevance of target accessibility in ligand-directed pharmacodelivery systems

For development of a new ligand-directed pharmacology, it is critical to measure delivery of targeted drug ligands via molecular imaging or diagnostic readouts (termed theranostics). Combinatorial peptide libraries serve as unbiased functional screens that can identify specific peptides targeting cell-surface receptors accessible to the circulation. As candidate drug leads, such peptides provide motifs likely to modify ligand-receptor interactions and downstream signal transduction pathways. This strategy is synergistic with genomic and proteomic approaches and has yielded insights into the specialized nature of the target tissue microenvironment. However, for this vision to be realized, one must look, as recent literature suggests, beyond receptor levels and critically analyze ligand accessibility as a key determinant in pharmacodelivery systems.

From pharmacogenomics to translational biomarkers

There is a need for new biomarkers to enable faster detection of adverse events due to drugs and disease processes. One would prefer biomarkers that are useful in multiple species (i.e., translational or bridging biomarkers) so that it would be possible to directly link responses between species and follow such injury in both preclinical and clinical settings. This chapter will explore some of the issues surrounding the use of pharmacogenomics to identify and qualify such biomarkers, and examples will be provided.

From the bench to the clinic and back again: translational biomarker discovery using in silico mining of pharmacogenomic data

To improve drug efficacy and safety and advance medical intervention in diseases, new biomarkers are urgently needed. Pharmacogenomics can provide a tool to discover and begin to qualify biomarkers useful for these indications and is readily applicable to multiple species. One can begin and end with genes or focus on tissue-derived expression analysis of those genes that encode secreted proteins to discover potential biomarkers that can be monitored in body fluids. The paper will discuss issues surrounding such investigations, show examples of translational biomarkers and end with a summary of the US FDA’s work in this field over the last 6 years.