Precision Oncology Core Data Model to Support Clinical Genomics Decision Making.

PURPOSE: Precision oncology mandates developing standardized common data models (CDMs) to facilitate analyses and enable clinical decision making. Expert-opinion-based precision oncology initiatives are epitomized in Molecular Tumor Boards (MTBs), which process large volumes of clinical-genomic data to match genotypes with molecularly guided therapies. METHODS: We used the Johns Hopkins University MTB as a use case and developed a precision oncology core data model (Precision-DM) to capture key clinical-genomic data elements. We leveraged existing CDMs, building upon the Minimal Common Oncology Data Elements model (mCODE). Our model was defined as a set of profiles with multiple data elements, focusing on next-generation sequencing and variant annotations. Most elements were mapped to terminologies or code sets and the Fast Healthcare Interoperability Resources (FHIR). We subsequently compared our Precision-DM with existing CDMs, including the National Cancer Institute's Genomic Data Commons (NCI GDC), mCODE, OSIRIS, the clinical Genome Data Model (cGDM), and the genomic CDM (gCDM). RESULTS: Precision-DM contained 16 profiles and 355 data elements. 39% of the elements derived values from selected terminologies or code sets, and 61% were mapped to FHIR. Although we used most elements contained in mCODE, we significantly expanded the profiles to include genomic annotations, resulting in a partial overlap of 50.7% between our core model and mCODE. Limited overlap was noted between Precision-DM and OSIRIS (33.2%), NCI GDC (21.4%), cGDM (9.3%), and gCDM (7.9%). Precision-DM covered most of the mCODE elements (87.7%), with less coverage for OSIRIS (35.8%), NCI GDC (11%), cGDM (26%) and gCDM (33.3%). CONCLUSION: Precision-DM supports clinical-genomic data standardization to support the MTB use case and may allow for harmonized data pulls across health care systems, academic institutions, and community medical centers.

Overcoming Major Barriers to Build Efficient Decision Support Systems in Pharmacovigilance.

Many decision support methods and systems in pharmacovigilance are built without explicitly addressing specific challenges that jeopardize their eventual success. We describe two sets of challenges and appropriate strategies to address them. The first are data-related challenges, which include using extensive multi-source data of poor quality, incomplete information integration, and inefficient data visualization. The second are user-related challenges, which encompass users' overall expectations and their engagement in developing automated solutions. Pharmacovigilance decision support systems will need to rely on advanced methods, such as natural language processing and validated mathematical models, to resolve data-related issues and provide properly contextualized data. However, sophisticated approaches will not provide a complete solution if end-users do not actively participate in their development, which will ensure tools that efficiently complement existing processes without creating unnecessary resistance. Our group has already tackled these issues and applied the proposed strategies in multiple projects.

Feature engineering and machine learning for causality assessment in pharmacovigilance: Lessons learned from application to the FDA Adverse Event Reporting System.

BACKGROUND: Our objective was to support the automated classification of Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) reports for their usefulness in assessing the possibility of a causal relationship between a drug product and an adverse event. METHOD: We used a data set of 326 redacted FAERS reports that was previously annotated using a modified version of the World Health Organization-Uppsala Monitoring Centre criteria for drug causality assessment by a group of SEs at the FDA and supported a similar study on the classification of reports using supervised machine learning and text engineering methods. We explored many potential features, including the incorporation of natural language processing on report text and information from external data sources, for supervised learning and developed models for predicting the classification status of reports. We then evaluated the models on a larger data set of previously unseen reports. RESULTS: The best-performing models achieved recall and F1 scores on both data sets above 0.80 for the identification of assessable reports (i.e. those containing enough information to make an informed causality assessment) and above 0.75 for the identification of reports meeting at least a Possible causality threshold. CONCLUSIONS: Causal inference from FAERS reports depends on many components with complex logical relationships that are yet to be made fully computable. Efforts focused on readily addressable tasks, such as quickly eliminating unassessable reports, fit naturally in SE's thought processes to provide real enhancements for FDA workflows.

Information Visualization Platform for Postmarket Surveillance Decision Support.

INTRODUCTION: The US FDA receives more than 2 million postmarket reports each year. Safety Evaluators (SEs) review these reports, as well as external information, to identify potential safety signals. With the increasing number of reports and the size of external information, more efficient solutions for data integration and decision making are needed. OBJECTIVES: The aim of this study was to develop an interactive decision support application for drug safety surveillance that integrates and visualizes information from postmarket reports, product labels, and biomedical literature. METHODS: We conducted multiple meetings with a group of seven SEs at the FDA to collect the requirements for the Information Visualization Platform (InfoViP). Using infographic design principles, we implemented the InfoViP prototype version as a modern web application using the integrated information collected from the FDA Adverse Event Reporting System, the DailyMed repository, and PubMed. The same group of SEs evaluated the InfoViP prototype functionalities using a simple evaluation form and provided input for potential enhancements. RESULTS: The SEs described their workflows and overall expectations around the automation of time-consuming tasks, including the access to the visualization of external information. We developed a set of wireframes, shared them with the SEs, and finalized the InfoViP design. The InfoViP prototype architecture relied on a javascript and a python-based framework, as well as an existing tool for the processing of free-text information in all sources. This natural language processing tool supported multiple functionalities, especially the construction of time plots for individual postmarket reports and groups of reports. Overall, we received positive comments from the SEs during the InfoViP prototype evaluation and addressed their suggestions in the final version. CONCLUSIONS: The InfoViP system uses context-driven interactive visualizations and informatics tools to assist FDA SEs in synthesizing data from multiple sources for their case series analyses.