Electronic common technical document submission with analysis using R.

BACKGROUND: In clinical trial development, it is a critical step to submit applications, amendments, supplements, and reports on medicinal products to regulatory agencies. The electronic common technical document is the standard format to enable worldwide regulatory submission. There is a growing trend of using R for clinical trial analysis and reporting as part of regulatory submissions, where R functions, analysis scripts, analysis results, and all proprietary code dependencies are required to be included. One unmet and significant gap is the lack of tools, guidance, and publicly available examples to prepare submission R programs following the electronic common technical document specification. METHODS: We introduce a simple and sufficient R package, pkglite, to convert analysis scripts and associated proprietary dependency R packages into a compact, text-based file, which makes the submission document self-contained, easy to restore, transfer, review, and submit following the electronic common technical document specification and regulatory guidelines (e.g. the study data technical conformance guide from the US Food and Drug Administration). The pkglite R package is published on Comprehensive R Archive Network and developed on GitHub. RESULTS: As a tool, pkglite can pack and unpack multiple R packages with their dependencies to facilitate the reproduction and make it an off-the-shelf tool for both sponsors and reviewers. As a grammar, pkglite provides an explicit trace of the packing scope using the concept of file specifications. As a standard, pkglite offers an open file format to represent and exchange R packages as a text file. We use a mock-up example to demonstrate the workflow of using pkglite to prepare submission programs following the electronic common technical document specification. CONCLUSION: pkglite and the proposed workflow enable the sponsor to submit well-organized R scripts following the electronic common technical document specification. The workflow has been used in the first publicly available R-based submission to the US Food and Drug Administration by the R Consortium R submission working group (https://www.r-consortium.org/blog/2022/03/16/update-successful-r-based-test-package-submitted-to-fda).

Development of a Prospective Real-World Data Clinical Registry of Children and Adolescents With Migraine.

OBJECTIVE: To develop a multicenter, multistakeholder, prospective clinical registry of children and adolescents with migraine to support the collection of real-world data of sufficient quality to support regulatory submissions and provide site-based infrastructure support for future clinical trials. BACKGROUND: As new migraine treatments come to market, pediatric efficacy and safety trials of these agents are needed. A clinical registry is an ideal regulatory strategy to provide both real-world data and site infrastructure to execute these trials. DESIGN: Multicenter, multistakeholder, prospective real-world data clinical registry of children and adolescents, 4-17 years of age, diagnosed with migraine with or without aura. Participants will be followed for up to 12 months at 3-month intervals, with interval recording of clinical data at study sites and self-reported data via mobile health application, as well as biobanking. We developed electronic case report forms that incorporated routinely collected clinical data with National Institute of Neurological Disorders and Stroke Headache Common Data Elements (Version 2.0). All data are captured in a 21 CFR Part 11 - compliant electronic data capture system - augmented by a real-time, web-based, and customizable data visualization platform. We engaged vendors to provide ancillary biobanking, patient data entry, and data visualization services. RESULTS: We used an iterative and highly collaborative multistakeholder approach to design and implement a streamlined registry protocol with input from all participating US sites. At each design and implementation step, we received input from therapeutic area experts, the US Food and Drug Administration (FDA), the National Institutes of Health, patient and parent advocates, health technology partners, drug developers, and site-based clinical investigators. The registry is governed by a multistakeholder steering committee with representation from sites, industry partners, patient advocates, and a member from the FDA (non-voting with respect to steering committee matters). The multistakeholder and site-driven approach to registry design and execution was highly efficient and resulted in the first patient enrolled within 6 months of concept development. CONCLUSIONS: By ensuring regulatory compliant implementation of the registry, we created both a source of real-world data and a multisite platform for the conduct of future clinical trials that can be submitted to regulatory authorities to support inclusion of pediatric data in approved drug labeling. A highly collaborative approach with broad stakeholder engagement at all stages of the registry development was a key to our operational success.

PBPK model reporting template for chemical risk assessment applications.

Physiologically-based pharmacokinetic (PBPK) modeling analysis does not stand on its own for regulatory purposes but is a robust tool to support drug/chemical safety assessment. While the development of PBPK models have grown steadily since their emergence, only a handful of models have been accepted to support regulatory purposes due to obstacles such as the lack of a standardized template for reporting PBPK analysis. Here, we expand the existing guidances designed for pharmaceutical applications by recommending additional elements that are relevant to environmental chemicals. This harmonized reporting template can be adopted and customized by public health agencies receiving PBPK model submission, and it can also serve as general guidance for submitting PBPK-related studies for publication in journals or other modeling sharing purposes. The current effort represents one of several ongoing collaborations among the PBPK modeling and risk assessment communities to promote, when appropriate, incorporating PBPK modeling to characterize the influence of pharmacokinetics on safety decisions made by regulatory agencies.

A standard-driven approach for electronic submission to pharmaceutical regulatory authorities.

OBJECTIVE: Using standards is not only useful for data interchange during the process of a clinical trial, but also useful for analyzing data in a review process. Any step, which speeds up approval of new drugs, may benefit patients. As a result, adopting standards for regulatory submission becomes mandatory in some countries. However, preparing standard-compliant documents, such as annotated case report form (aCRF), needs a great deal of knowledge and experience. The process is complex and labor-intensive. Therefore, there is a need to use information technology to facilitate this process. MATERIALS AND METHODS: Instead of standardizing data after the completion of a clinical trial, this study proposed a standard-driven approach. This approach was achieved by implementing a computer-assisted "standard-driven pipeline (SDP)" in an existing clinical data management system. SDP used CDISC standards to drive all processes of a clinical trial, such as the design, data acquisition, tabulation, etc. RESULTS: A completed phase I/II trial was used to prove the concept and to evaluate the effects of this approach. By using the CDISC-compliant question library, aCRFs were generated automatically when the eCRFs were completed. For comparison purpose, the data collection process was simulated and the collected data was transformed by the SDP. This new approach reduced the missing data fields from sixty-two to eight and the controlled term mismatch field reduced from eight to zero during data tabulation. CONCLUSION: This standard-driven approach accelerated CRF annotation and assured data tabulation integrity. The benefits of this approach include an improvement in the use of standards during the clinical trial and a reduction in missing and unexpected data during tabulation. The standard-driven approach is an advanced design idea that can be used for future clinical information system development.

Designs of clinical swallowability assessments of solid oral dosage forms in regulatory submissions.

The swallowability of solid oral dosage forms (SODFs) is crucial for medication safety and adherence. Both regulatory agencies and sponsors are concerned with bringing swallowable SODFs to patients. However, no best practices are available for assessing swallowability. Therefore, we conducted a comparative analysis of clinical swallowability assessments (CSAs) for SODFs in regulatory submissions to identify current study design practices. CSAs were identified from a "swallowability" keyword search of a Food and Drug Administration database. Notable design trends among the 17 CSAs were not assessing swallowability as a primary endpoint (76 %); enrolling pediatric patients (76 %); administering assessments post-screening (76 %); and utilizing questionnaires (100 %). A design trend with near equal frequency (∼50 %) was single- or multiple-doses of product administration. Study subjects were the primary questionnaire respondents (82 %), usually using a Likert scale (92 %, 12/13). CSAs generally dichotomized the responses for analysis (65 %) without pre-specified threshold values (59 %). Overall, while study designs exhibited trends, methodology variations may impact swallowability measurements affecting the interpretation of results. Thus, developing robust and valid assessment tools for swallowability is imperative to produce clinically relevant data and inform regulatory decision-making. Collaboration between regulatory agencies and sponsors is warranted to create best practices and ensure high quality swallowability data.

Developing and Validating a Model of Humeral Stem Primary Stability, Intended for In Silico Clinical Trials.

In silico clinical trials (ISCT) can contribute to demonstrating a device's performance via credible computational models applied on virtual cohorts. Our purpose was to establish the credibility of a model for assessing the risk of humeral stem loosening in total shoulder arthroplasty, based on a twofold validation scheme involving both benchtop and clinical validation activities, for ISCT applications. A finite element model computing bone-implant micromotion (benchtop model) was quantitatively compared to a bone foam micromotion test (benchtop comparator) to ensure that the physics of the system was captured correctly. The model was expanded to a population-based approach (clinical model) and qualitatively evaluated based on its ability to replicate findings from a published clinical study (clinical comparator), namely that grit-blasted stems are at a significantly higher risk of loosening than porous-coated stems, to ensure that clinical performance of the stem can be predicted appropriately. Model form sensitivities pertaining to surgical variation and implant design were evaluated. The model replicated benchtop micromotion measurements (52.1 ± 4.3 µm), without a significant impact of the press-fit ("Press-fit": 54.0 ± 8.5 µm, "No press-fit": 56.0 ± 12.0 µm). Applied to a virtual population, the grit-blasted stems (227 ± 78µm) experienced significantly larger micromotions than porous-coated stems (162 ± 69µm), in accordance with the findings of the clinical comparator. This work provides a concrete example for evaluating the credibility of an ISCT study. By validating the modeling approach against both benchtop and clinical data, model credibility is established for an ISCT application aiming to enrich clinical data in a regulatory submission.

Development and validation of qPCR methods for nucleic acid biomarkers as a drug development tool: points to consider.

Nucleic acid (NA) biomarkers play critical roles in drug development. However, the global regulatory guidelines for assessing quantification methods specific to NA biomarkers are limited. The validation of analytical methods is crucial for the use of biomarkers in clinical and post-marketing evaluations of drug efficacy and adverse reactions. Given that quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR) methods are the gold standards for the quantification of NA biomarkers, the Biomarker Analytical Method Validation Study Group in Japan has discussed considerations and made recommendations for the development and validation of qPCR- and RT-qPCR-based analytical methods for endogenous NA biomarkers as drug development tools. This white paper aims to contribute to the global harmonization of NA biomarker assay validation.

Compliance and regulatory considerations for the implementation of the multi-attribute-method by mass spectrometry in a quality control laboratory.

Multi-attribute methods employing mass spectrometry are applied throughout the biopharmaceutical industry for product and process characterization purposes but are not yet widely accepted as a method for batch release and stability testing under the good manufacturing practice (GMP) regime, due to limited experience and level of comfort with the technical, compliance and regulatory aspects of its implementation at quality control (QC) laboratories. This article is the second part of a two-tiered publication aiming at providing guidance for implementation of the multi-attribute method by peptide mapping liquid chromatography mass spectrometry (MAM) in a QC laboratory. The first part [1] focuses on technical considerations, while this second part provides considerations related to GMP compliance and regulatory aspects. This publication has been prepared by a group of industry experts representing 14 globally acting major biotechnology companies under the umbrella of the European Federation of Pharmaceutical Industries and Associations (EFPIA) Manufacturing & Quality Expert Group (MQEG).

Communicating regulatory high-throughput sequencing data using BioCompute Objects.

This project demonstrates the use of the IEEE 2791-2020 Standard (BioCompute Objects [BCO]) to enable the complete and concise communication of results from next generation sequencing (NGS) analysis. One arm of a clinical trial was replicated using synthetically generated data made to resemble real biological data and then two independent analyses were performed. The first simulated a pharmaceutical regulatory submission to the US Food and Drug Administration (FDA) including analysis of results and a BCO. The second simulated an FDA review that included an independent analysis of the submitted data. Of the 118 simulated patient samples generated, 117 (99.15%) were in agreement in the two analyses. This process exemplifies how a template BCO (tBCO), including a verification kit, facilitates transparency and reproducibility, thereby reinforcing confidence in the regulatory submission process.

Use of Clinical Data Interchange Standards Consortium (CDISC) Standards for Real-world Data: Expert Perspectives From a Qualitative Delphi Survey.

BACKGROUND: Real-world data (RWD) and real-world evidence (RWE) are playing increasingly important roles in clinical research and health care decision-making. To leverage RWD and generate reliable RWE, data should be well defined and structured in a way that is semantically interoperable and consistent across stakeholders. The adoption of data standards is one of the cornerstones supporting high-quality evidence for the development of clinical medicine and therapeutics. Clinical Data Interchange Standards Consortium (CDISC) data standards are mature, globally recognized, and heavily used by the pharmaceutical industry for regulatory submissions. The CDISC RWD Connect Initiative aims to better understand the barriers to implementing CDISC standards for RWD and to identify the tools and guidance needed to more easily implement them. OBJECTIVE: The aim of this study is to understand the barriers to implementing CDISC standards for RWD and to identify the tools and guidance that may be needed to implement CDISC standards more easily for this purpose. METHODS: We conducted a qualitative Delphi survey involving an expert advisory board with multiple key stakeholders, with 3 rounds of input and review. RESULTS: Overall, 66 experts participated in round 1, 56 in round 2, and 49 in round 3 of the Delphi survey. Their inputs were collected and analyzed, culminating in group statements. It was widely agreed that the standardization of RWD is highly necessary, and the primary focus should be on its ability to improve data sharing and the quality of RWE. The priorities for RWD standardization included electronic health records, such as data shared using Health Level 7 Fast Health care Interoperability Resources (FHIR), and the data stemming from observational studies. With different standardization efforts already underway in these areas, a gap analysis should be performed to identify the areas where synergies and efficiencies are possible and then collaborate with stakeholders to create or extend existing mappings between CDISC and other standards, controlled terminologies, and models to represent data originating across different sources. CONCLUSIONS: There are many ongoing data standardization efforts around human health data-related activities, each with different definitions, levels of granularity, and purpose. Among these, CDISC has been successful in standardizing clinical trial-based data for regulation worldwide. However, the complexity of the CDISC standards and the fact that they were developed for different purposes, combined with the lack of awareness and incentives to use a new standard and insufficient training and implementation support, are significant barriers to setting up the use of CDISC standards for RWD. The collection and dissemination of use cases, development of tools and support systems for the RWD community, and collaboration with other standards development organizations are potential steps forward. Using CDISC will help link clinical trial data and RWD and promote innovation in health data science.

Analytical method validation for biomarkers as a drug development tool: points to consider.

Biomarkers are an important drug developmental tool. Assessment of quantitative analytical methods of biomarkers is not included in any regulatory documents in Japan. Use of biomarkers in clinical evaluations and supporting the post-marketing evaluation of drug efficacy and/or adverse reactions requires assessment and full validation of analytical methods for these biomarkers. The Biomarker Analytical Method Validation Study Group is a research group in Japan comprising industry and regulatory experts. Group members discussed and prepared this 'points to consider document' covering measurements of endogenous metabolites/peptides/proteins by ligand binding assays and chromatographic methods with or without mass spectrometry. We hope this document contributes to the global harmonization of biomarker assay validation.

The use of real-world data/evidence in regulatory submissions.

The 21st Century Cures Act passed by the United States (US) Congress in December 2016 requires the US Food and Drug Administration (FDA) shall establish a program to evaluate the potential use of real-world evidence (RWE) which is generated from real-world data (RWD) to (i) support approval of new indication for a drug approved under section 505 (c) and (ii) satisfy post-approval study requirements. RWE offers the opportunities to develop robust evidence using high-quality data and sophisticated methods for producing causal-effect estimates regardless randomization is feasible. In this article, we have demonstrated that the assessment of treatment effect (RWE) based on RWD could be biased due to the potential selection and information biases of RWD. Although fit-for-purpose RWE may meet regulatory standards under certain assumptions, it is not the same as substantial evidence (current regulatory standard in support of approval of regulatory submission). In practice, it is then suggested that when there are gaps between fit-for-purpose RWE and substantial evidence, we should make efforts to fill these gaps based on a comprehensive evaluation of the treatment effect. We also review two RWE examples to show some potential use of RWE in clinical studies.

In Silico Clinical Trials in the Orthopedic Device Industry: From Fantasy to Reality?

The orthopedic device industry relies heavily on clinical evaluation to confirm the safety, performance, and clinical benefits of its implants. Limited sample size often prevents these studies from capturing the full spectrum of patient variability and real-life implant use. The device industry is accustomed to simulating benchtop tests with numerical methods and recent developments now enable virtual "in silico clinical trials" (ISCT). In this article, we describe how the advancement of computer modeling has naturally led to ISCT; outline the potential benefits of ISCT to patients, healthcare systems, manufacturers, and regulators; and identify how hurdles associated with ISCT may be overcome. In particular, we highlight a process for defining the relevant patient risks to address with ISCT, the utility of a versatile software pipeline, the necessity to ensure model credibility, and the goal of limiting regulatory uncertainty. By complementing-not replacing-traditional clinical trials with computational evidence, ISCT provides a viable technical and regulatory strategy for characterizing the full spectrum of patients, clinical conditions, and configurations that are embodied in contemporary orthopedic implant systems.

Progress in Prediction and Interpretation of Clinically Relevant Metabolic Drug-Drug Interactions: a Minireview Illustrating Recent Developments and Current Opportunities.

PURPOSE OF REVIEW: This review gives a perspective on the current "state of the art" in metabolic drug-drug interaction (DDI) prediction. We highlight areas of successful prediction and illustrate progress in areas where limits in scientific knowledge or technologies prevent us from having full confidence. RECENT FINDINGS: Several examples of success are highlighted. Work done for bitopertin shows how in vitro and clinical data can be integrated to give a model-based understanding of pharmacokinetics and drug interactions. The use of interpolative predictions to derive explicit dosage recommendations for untested DDIs is discussed using the example of ibrutinib, and the use of DDI predictions in lieu of clinical studies in new drug application packages is exemplified with eliglustat and alectinib. Alectinib is also an interesting case where dose adjustment is unnecessary as the activity of a major metabolite compensates sufficiently for changes in parent drug exposure. Examples where "unusual" cytochrome P450 (CYP) and non-CYP enzymes are responsible for metabolic clearance have shown the importance of continuing to develop our repertoire of in vitro regents and techniques. The time-dependent inhibition assay using human hepatocytes suspended in full plasma allowed improved DDI predictions, illustrating the importance of continued in vitro assay development and refinement. SUMMARY: During the past 10 years, a highly mechanistic understanding has been developed in the area of CYP-mediated metabolic DDIs enabling the prediction of clinical outcome based on preclinical studies. The combination of good quality in vitro data and physiologically based pharmacokinetic modeling may now be used to evaluate DDI risk prospectively and are increasingly accepted in lieu of dedicated clinical studies.

Reporting guidelines for population pharmacokinetic analyses.

The purpose of this work was to develop a consolidated set of guiding principles for the reporting of population pharmacokinetic (PK) analyses based on input from a survey of practitioners as well as discussions between industry, consulting, and regulatory scientists. The survey found that identification of population covariate effects on drug exposure and support for dose selection (in which population PK frequently serves as preparatory analysis for exposure-response modeling) are the main areas of influence for population PK analysis. The proposed guidelines consider 2 main purposes of population PK reports: (1) to present key analysis findings and their impact on drug development decisions, and (2) as documentation of the analysis methods for the dual purpose of enabling review of the analysis and facilitating future use of the models. This work also identified 2 main audiences for the reports: (1) a technically competent group responsible for in-depth review of the data, methodology, and results; and (2) a scientifically literate but not technically adept group, whose main interest is in the implications of the analysis for the broader drug development program. We recommend a generalized question-based approach with 6 questions that need to be addressed throughout the report. We recommend 8 sections (Synopsis, Introduction, Data, Methods, Results, Discussion, Conclusions, Appendix) with suggestions for the target audience and level of detail for each section. A section providing general expectations regarding population PK reporting from a regulatory perspective is also included. We consider this an important step toward industrialization of the field of pharmacometrics such that a nontechnical audience also understands the role of pharmacometric analyses in decision making. Population PK reports were chosen as representative reports to derive these recommendations; however, the guiding principles presented here are applicable for all pharmacometric reports including pharmacokinetics/pharmacodynamics and simulation reports.

Pre-clinical Implants of the Levitronix PediVAS® Pediatric Ventricular Assist Device - Strategy for Regulatory Approval.

The PediVAS blood pump is a magnetically levitated centrifugal pump designed for pediatric bridge-to-decision or bridge-to-recovery in pediatric patients from 3-20kg in weight. In preparation for submission of an investigational device exemption (IDE) application, we completed a final six-animal series of pre-clinical studies. The studies were conducted under controlled conditions as prescribed by the recently released FDA guidance document for animal studies for cardiovascular devices. Three 30-day chronic left ventricular support studies were completed in a juvenile lamb model to demonstrate the safety and hemocompatibility of the PediVAS pump. Three additional 8-hour acute biventricular support studies were performed to demonstrate the feasibility of this approach from a hemodynamic and systems standpoint. It is estimated that 50% of pediatric patients who require left ventricular support also require right ventricular support. All studies were successfully completed without complications, device malfunctions, or adverse events. End-organ function was normal for the chronic studies. We noted small surface lesions on one kidney from each chronic study as well as the presence of ring thrombus on connectors, as expected for these types of studies in animal models. The strategy and challenges imposed by performing a controlled cardiovascular device study in a juvenile lamb model are discussed. We believe that these successful implants demonstrate safety and performance for the PediVAS device for support of an IDE application to initiate human clinical trials and provide a roadmap for other researchers.