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Posted 11 March 2016
This article discusses fundamentals of precision medicine, providing an update on how recent regulations and technology trends are contributing to the advancement of patient-centered healthcare.
As the field of Precision Medicine (PM) continues to escalate on the trajectory from hypothesis-driven conception to customary clinical best practice, there are facets impacting not only commercial product developers, but also select general public subgroups in dire need of individualized medical intervention. Retracing back to the Classical and Hellenistic periods between the 5th century BC and the 2nd century AD, it is evident the concepts of PM and personalized medicine were initially created by the learned Greek physicians of the Hippocratic Corpus.1 The scholars of this era hypothesized clear gender and age-defined generational distinctions in the treatment of health conditions. This was further influenced by individual habits and the environment.2 Cumulatively, these ideologies have evolved into the key technology of modern day medicine constituting Pharmacogenomics (PGx) and ultimately encompassing individualized differences at the genomic level and the relationship to a drug response. Now, consider the highly dynamic, accelerating, technologically complex personalized medicine sector in the 21st century. The basic premise of personalized medicine is defined in layman's terms as "Providing the right treatment to the right patient, at the right dose at the right time."3 The difference between the terms "personalized medicine" and "precision medicine" is subtle and was previously used interchangeably. "Precision Medicine (PM) comprises specifically customized diagnostic and therapeutic strategies targeting a patient subpopulation with susceptibility to a distinct disease condition based on the individualized discrepancies of select criteria, including genomic profiles, environmental influences, lifestyle habits and family history. Whereas, personalized medicine, specifically refers to the individualized treatment regimen tailored for the benefit of a single patient.4
It is well-known genetic variability is often a significant contributor to serious disease conditions, and an in-depth dissection, and identification of this feature would enable multifaceted benefits. These findings could culminate in the prediction of an individualistic treatment specifically targeting the potential molecular instigator of the condition and the ability to inculcate preventative mechanisms to inhibit the possible emergence or alleviate the progression of the health condition. Delineated below are examples of treatments to meet these objectives.
The personalized medicine industry has evolved into a lucrative enterprise with the global market forecasted through 2022 at nearly $2.5 billion at a Compound Annual Growth Rate (CAGR) of 11.8%. The global companion diagnostics market is predicted to reach $5.6 billion by 2019 at a CAGR of 18.1%.5, 6 Potential areas of medical emphasis include HIV drug resistant infection, oncology personalized therapy, schizophrenia antipsychotics, antidepressant therapy, antihypertensive therapy and neurological disorder personalized treatments. The incorporation of genotyping as standard clinical practice is predicted to occur in 2020.7
The fostering and acceleration of PM research endeavors in the US is bolstered by the creation of a visionary, new enterprise by the White House, called the PM Initiative8 in partnership with several organizations, including the National Institutes of Health (NIH) in January 2012.9
A additional commitment by the White House in support of advancements of all regulated products was evidenced in January 2014 by the launch of the open FDA digital strategy initiative enabling easy access of FDA public data via a digitized Application Programming Interface (API) to foster innovation, technological advancements and provide safety information (recalls, adverse events) to the interested public, and developers in the public and private industrial sectors.10
A 2010 study conducted by the Tufts Center for the Study of Drug Development (CSDD) reported 42% of all drugs and 73% of oncology drug development, as well as 20% of approved drugs were categorized as personalized medicines. The R&D investments in personalized medicine have approximately doubled during the past five years, with a 30% increment forecasted during the next three years. Approximately 69% of drug development during the ensuing five years is predicted to be driven by personalized medicine.11
Pharmacogenomics information (61%) was included in the package-inserts of more than 120 FDA approved drugs with indications for the treatment of cancer, cardiovascular, infectious and psychiatric diseases (Figure 1).12
Figure 2 depicts the integrative approach of comprehensive information flows from the patient's genome, the ensuing transcription, protein and metabolic products culminating in viable clinical applications.13 This figure systematically shows the typical data evaluation pathway with bioinformatics algorithms applied in genomics, transcriptomics and epigenomics sequencing technologies to analyze the detection of genomic mutations, genetic variants, differential gene expression, fusion transcripts, DNA methylations, transcription binding factors, etc. This figure also integrates protein expression information into appropriate genes and metabolic/functional networks, which ultimately facilitates mapping the framework for an individualized and personalized treatment strategy.
Clinical diagnostics in PM is represented by the rapid, convenient testing of a patient's genetic polymorphism and/or genetic mutation. In addition to conventional in vitro diagnostics, this technology also is extended to Point of Care (POC) testing and portable medical devices.
Next Generation Sequencing (NGS) technologies play an integral role in enabling the expeditious sequencing of large genomic segments or even the entire genome of a single individual in clinical diagnostics. However, this valuable technology is not without critics. For example, there is skepticism regarding any potential overarching benefits of this technology beyond its specific purpose. Due to a limited portfolio of available therapies for certain indications, the bonus of additional elicited NGS information could be inconsequential. Furthermore, NGS does not autonomously provide all the required information to definitively address a clinical need and may necessitate additional non-genomic testing for a more conclusive diagnostic assessment.14
In April 2015, FDA released a guidance document delineating a voluntary program, entitled the Expedited Access Pathway (EAP) facilitating the efficient navigation of a regulatory strategy for medical devices incorporating advanced genomic technologies and addressing complex unmet dire clinical needs.15
Dr. Katherine Donigan at FDA's Office of In Vitro Diagnostic Device Evaluation and Safety (OIVD) reported on the agency's efforts with fostering PM at the annual Regulatory Affairs Professionals Society (RAPS) Convergence in October 2015. To date, 23 companion diagnostics are cleared or approved, 147 drugs targeting 50 disease biomarkers, including cystic fibrosis, cancer, psychiatric disorders, infectious diseases, cholesterol, etc., are approved, more than 60 human nucleic acid based tests are cleared or approved and since 2005, more than 24 guidance documents have been issued.16, 17, 18
A noteworthy PM collaboration occurred between Myriad Genetics, Inc. (a prominent molecular diagnostics company) and AstraZeneca. Initiated by AstraZeneca in 2009, the partnership culminated in a successful priority approval in December 2014 of the first oral prescription medication, Lynparza (olaparib) for advanced ovarian cancer patients with BRCA mutations. The BRAC Analysis Companion Diagnostic developed by Myriad was used to select eligible patients for the drug therapy. Due to the priority review categorization of the drug, the timeline for development of the diagnostic was compressed from years to months. According to Jolette Franco, Myriad's director of regulatory affairs, "Myriad worked very hard to submit a complete application, and to the highest standard, all development, validation and submission requirements in less than a years' time. Myriad/AstraZeneca and CDER/CDRH collaborated extremely well together to achieve this unprecedented accomplishment."
The impact of PM is palpable with the recent approvals of complementary and companion diagnostics aligned with advanced non-squamous Small Cell Lung Cancer (NSCLC) therapy. Both diagnostic tests described below from the same manufacturer, Dako, target the same PD-L1 tumor types; yet differ by validation for detectable levels of PD-L1 tumor proportion scores. FDA approved the complementary diagnostic, PD-L1 IHC 28-8 pharmDx in conjunction with an expanded indication for a breakthrough therapy for all NSCLC patients, OPDIVO (nivolumab; Bristol-Meyers Squib) on 9 October 2015. This test was validated based on the PD-L1 score evident with approximately 50% of tumor cells gauging the survival benefits of the overall patient population with elevated PD-L1 expression and thereby enabling customized treatment regiments. On 2 October 2015, a companion diagnostic, PD-L1 IHC 22C3 pharmDx test was accepted with KEYTRUBA (pembrolizumab; Merck) for advanced NSCLC patients. This test was designed to monitor drug efficacy based on detection of PD-L1 expression levels in approximately 10% of tumor cells.19
Notable are the first FDA cleared medical devices for NGS in the PM arena for the comprehensive testing of cystic fibrosis in 2013 were manufactured by Illumina. On 19 November 2013, the NGS platform comprising the MiSeqDx System and the MiSeqDx Universal Kit 1.0 of sequencing reagents for use with the instrument secured de novo classification for the targeted sequencing of human genomic DNA from peripheral whole blood samples. On the same date, 510(k) clearance for the MiSeqDx instrument was obtained for two In Vitro Diagnostic (IVDs) tests, the MiSeqDx Cystic Fibrosis 139-Variant Assay and the MiSeqDx Cystic Fibrosis Clinical Sequencing Assay intended for the detection of the cystic fibrosis transmembrane conductance regulator gene mutations and variants. These multifaceted genomic cystic fibrosis targeted tests are intended to screen populations of adult carriers, as a confirmatory test in newborns and children, and for the diagnosis of suspect individuals with the disease. On 19 February 2015, FDA permitted marketing authorization for the first Direct To Consumer (DTC) genetic test, 23andMe PGS Bloom Syndrome Carrier Test to screen healthy autosomal recessive carriers for gene variants of this inheritable disorder. Furthermore, in an attempt to promote innovation and foster client support, FDA has indicated the intent to formulate a regulatory pathway with genetic carrier screening tests with analogous purposes by being categorized as Class II and exempt from premarket review. In direct context to the approval of the first 23andMe test, the agency seems to agree consumers could have access to personal genetic information from specific FDA accepted diagnostic tests, without intervention from a practicing clinician as quoted by Dr. Alberto Gutierrez, Director, OIVD, "The FDA believes that in many circumstances, it is not necessary for consumers to go through a licensed practitioner to have direct access to their personal genetic information. Today's authorization and accompanying classification, along with FDA's intent to exempt these devices from premarket review, supports innovation and ultimately benefit consumers. These tests have the potential to provide people with information about possible mutations in their genes that could be passed on to their children."20
Regulations for PM have not been fully established to meet the developmental requirements of the rapidly evolving and complex technologies. The entire premise of regulatory oversight is to ensure product safety and effectiveness determined by analytical, process and clinical validation studies. The convoluted charge for creation and instituting regulations and policy implementation resides with the CDRH, CBER, CDER and Office of Special Medical Programs (OSMP). In lieu of directly applicable finalized guidance documents, FDA has identified several issued guidance documents to enable clarification of the appropriate regulatory strategy, expected performance/characterization requirements, coordination of milestone reviews with the different agencies, key deliverables and defining timeliness to enable a smooth application process.21
Regulations applicable for diagnostic instruments and assays intended to be used in PM must meet the primary performance criteria mandated for accurate, reproducible and reliable clinical data. The magnanimity of this endeavor can be underscored because the present conventional clinical tests focus on the detection of typically a single medical condition or a few closely interrelated conditions. NGS has the capability of identifying three billion base pairs of DNA in the human genome typically with about three million genetic variants in an individual, unlike other genetic technologies, e.g., PCR where the focus is on targeted regions of genomic interest. In addition, it is alleged the accuracy of this data could be error prone due to technicalities during sample preparation, instrument malfunctions, etc., rendering glitches with the design of reliable validation protocols.22
New guidelines are mandated for the effective use of NGS in clinical applications. At present, based on the successful marketing authorization of the first NGS, MiSeqDx System, the agency intends to incorporate a comparable approach to determine analytical performance by focusing on representative subsets of variant types with new NGS test submissions. The inference is the evaluation of varied configurations of specific genomic sequences enriched for analytically challenging and clinically relevant markers is adequate to unequivocally ascertain analytical validity acceptance criteria required for the entire platform. Additional approaches for establishing unique analytical performance metrics of previously cleared or approved NGS tests is under consideration. In addition, the agency is investigating the development of best practice computational and technical metrics and measurements to establish QA/QC standards, and also evaluate analytical performance.23
In November 2015, FDA conducted a public workshop, "Standards Based Approach to Analytical Performance Evaluation of Next Generation Sequencing In Vitro Diagnostic Tests" with the purpose of establishing optimal analytical standards for regulating NGS IVDs. The emphasis was on the incorporation of established design and validation principles generating results to support the indications for use and also to permit flexibility with validation parameters customized to meet individualized performance requirements of highly specialized detection targets.24, 25 Prio to this, in an effort to facilitate discussion, FDA issued a whitepaper on the preliminary approaches to NGS test standardization entitled "Developing Analytical Standards for NGS Testing."26
Designed clinical trials during drug development which use NGS technology in their development strategy must meet the agency's regulations for analytical and process validation, clinical validation and clinical utility. Analytical and process validation must meet pre-determined acceptance criteria for parameters of accuracy, specificity, precision, sensitivity and robustness. Clinical validity must inculcate the merits of accurate disease identification, clinical sensitivity, clinical specificity and predictive values, and clinical utility must substantiate the benefits of this medical intervention in healthcare.27 These regulatory considerations would mandate the selection of the appropriate population subset where the predictions of positive and negative drug interventions are most precisely revealed in susceptible and afflicted patients in comparison to the control group. Validated sequencing methodologies and updated informatics software are critical in a clinical setting. Some investigators surmise in circumstances when the sequencing data has not been verified with a gold standard or analytically validated, it would not be deemed suitable for efficiently conducted clinical trials. Informatics software handling a vast plethora of information flow must be current with updates to release pertinent information to oncologists in a timely manner.28 However, in situations where a gold standard (predicate) does not exist, FDA has stated novel medical devices at low or medium risk or high risk breakthrough devices for treatment of unmet medical needs with no alternative therapies may be considered for the revamped de novo regulatory pathway.29 In order to minimize the burden of selecting the clinical valid patient population, FDA has promoted an enrichment strategy. This process includes the prospective utilization of key selection criteria consolidating a cohesive test population with limited comprehensive heterogeneity (genomic and environmental) with the targeted disease conditions that could unequivocally verify the beneficial effects or failure of the investigational drugs.30
Adaptive clinical trial paradigms with latitude to prospectively modify study design and/or postulations based on evident patient responses during the course of the investigational drug trial also are integrated in individualized clinical trials.31
Regulatory strategies followed by the biopharmaceutical industries in the development of companion diagnostics are contingent on the indication and product type. Designing the regulatory path most desirable is either a least burdensome approach or the 510(k) route where the development time is protracted. The current inference is a major segment of NGS diagnostic tests will be used as Laboratory Developed Tests (LDT) in a clinical laboratory setting. An example is evident with tests targeting the BRAF gene, an oncogene which expresses the serine/threonine- B-Raf protein kinase enzyme, a key protein in the BRAF/MAPK regulatory pathway and essential for normal cell growth and differentiation prior to birth.32 This gene is implicated in many cancers, particularly melanoma, and also inherited disorders in the mutated form. About 45% of diagnostic tests detecting BRAF gene mutations are being utilized as LDTs despite Premarket Approval (PMA) of the Roche and GSK tests described below.33 For drug/diagnostic combination products, the strategy will need to be defined based on whether the drug product has or has not secured agency approval. For example, in 2011, Roche obtained PMA approval for the companion diagnostic, the Cobas 4800 BRAF V600 Mutation Test targeting the BRAF gene for the drug Zelboraf (vermurafenib)indicated for thetreatment of the potentially lethal form of skin cancer, metastatic or unresectable melanoma, caused by mutations in the BRAF V600E gene due to the requirement of more stringent performance criteria. In 2013, two of GSK's single melanoma drugs, Tafinlar® (dabrafenib) (BRAF inhibitor) and Mekinist (trametinib) (MEK inhibitor) both of which target tumor cells expressing the BRAF V600E or V600K gene mutations were approved with the ThxID BRAF companion diagnostic, a real time PCR test on the Applied Biosystems 7500 Fast Dx to determine if the melanoma cells carried the V600E or V600K BRAF gene mutation. FDA has expressed consternation especially with certain high risk, complex LDTs, validated in compliance with minimal CLIA requirements without assurance the agency's rigorous performance expectations mandated for IVDs are met. A genomic LDT of concern mentioned is MiraDx's PreOvar KRAS-Variant Ovarian Cancer Screening Test for the detection of women at elevated risk for ovarian cancer. It was determined the correlation between the KRAS-variant and cancer risk and therapeutic response was not validated and compounded further by inaccurate data analysis.34
Despite the astounding progress with technological breakthroughs, escalating resource allocation and continual investments in PM, this field is still adversely impacted by broad challenges. The same broad list of concerns and challenges exist for all sectors, including physicians, healthcare institutions, biopharmaceutical industries, regulatory agencies and insurance companies involved with PM. Scientific discovery and clinical R&D precedes the list of challenges, followed by appropriate regulatory guidelines, suitable reimbursement standards and lastly education of healthcare professionals directly involved with PM to generate accurate interpretations and prognostic assessments of clinical data.
Clarity with clinical significance of known and newly identified genetic markers, the undesirable side-effects of gene-based therapies and design of clinical trials that will precisely pin-point genetic variants with direct correlation to a drug response are some aspects requiring resolution from a scientific perspective. Due to the vast information on variants identified by NGS tests, it would be cumbersome to evaluate the true positive or negative rates during clinical trials with each variant. It is recommended secondary, complimentary tests be developed to confirm each unique positive finding on a complementary platform.35, 36
At the policy level, the extent of regulation necessary in the development of clinical products for PM to ensure patient protection and encourage innovation continues to be a challenge.
Unfortunately, personalized medicine is not yet recourse to a vast proportion of insured, cancer patients who would benefit immensely from customized treatment. Since personalized medicine continues to be an evolving field, the extent of research, validation and confirmatory evidence required to corroborate individualized genetic tests provide the ideal panacea for deadly maladies continue to be a conundrum for insurance providers. Succinctly, the volume of cumulative proof to support the overall concept remains undefined or inadequate to justify reimbursement with many deadly cancers, such as pancreatic cancer, lung cancer and melanoma.37
FDA is championing these endeavors and has postulated future regulatory goals for NGS tests which include efficiency to enable innovation for patient protection, condensing the time between discovery and clinical use, understanding the correlation and anticipating future developments with the present status of technology and current best practices.38
Despite these many unresolved roadblocks, efforts continue to foster collaboration among academic researchers and clinicians, the biopharmaceutical industry, regulators, policy makers and insurers. These realistic objectives to build on the current advancements with PM technologies (proteomics, metabolomics, genomics, mobile health technology) and streamline the process to clinical practice to one that is unambiguous and easily comprehensible by the general public to ensure PM and individualized treatments for all patients in dire need will be attained with relative ease.
About the Author
Chitra Edwin, PhD, RAC has significant experience in product development, regulatory affairs and quality affairs of In Vitro Diagnostics (IVD), medical devices and biologics (vaccines), infectious diseases, oncology and cardiology. Dr. Edwin is an adjunct associate professor of pharmaceutical sciences, College of Pharmacy, University of Cincinnati. She obtained her PhD from the University of Minnesota and post-doctoral training at the Harvard Medical School and the Dana Farber Cancer Institute. She was a Biopharmaceutical Review Board member of Opus Institutional Review Board (IRB). She is also an entrepreneur and co-founder of non-profit organizations on science and international business. She can be contacted at firstname.lastname@example.org.
Sincere gratitude to Alfred Pan and Jolette Franco for their valuable time and effort invested with discussions, reviewing this article and for offering insightful suggestions.
Cite as: Edwin, C. "Precision Medicine: Technology, Regulations and Challenges." Regulatory Focus. March 2016. Regulatory Affairs Professionals Society.
Tags: Precision medicine, Precision medicine initiative, PMI, Next generation sequencing
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