Dataset Information

Integrating cancer genomic data into electronic health records.

ABSTRACT: The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10-15 years. At the same time, new technologies and the electronic health record (EHR) in particular have permeated the oncology clinic. Initially designed as billing and clinical documentation systems, EHR systems have not anticipated the complexity and variety of genomic information that needs to be reviewed, interpreted, and acted upon on a daily basis. Improved integration of cancer genomic data with EHR systems will help guide clinician decision making, support secondary uses, and ultimately improve patient care within oncology clinics. Some of the key factors relating to the challenge of integrating cancer genomic data into EHRs include: the bioinformatics pipelines that translate raw genomic data into meaningful, actionable results; the role of human curation in the interpretation of variant calls; and the need for consistent standards with regard to genomic and clinical data. Several emerging paradigms for integration are discussed in this review, including: non-standardized efforts between individual institutions and genomic testing laboratories; "middleware" products that portray genomic information, albeit outside of the clinical workflow; and application programming interfaces that have the potential to work within clinical workflow. The critical need for clinical-genomic knowledge bases, which can be independent or integrated into the aforementioned solutions, is also discussed.

SUBMITTER: Warner JL

PROVIDER: S-EPMC5081968 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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Integrating cancer genomic data into electronic health records.

Warner Jeremy L JL Jain Sandeep K SK Levy Mia A MA

Genome medicine 20161026 1

The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10-15 years. At the same time, new technologies and the electronic health record (EHR) in particular have permeated the oncology clinic. Initially designed as billing and clinical documentation systems, EHR systems have not anticipated the complexity and variety of genomic information that needs to be reviewed, interpreted, and acted upon on a daily basis. Improved integration of ...[more]

PMID: 27784327

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Project description:Temporal variability in health-care processes or protocols is intrinsic to medicine. Such variability can potentially introduce dataset shifts, a data quality issue when reusing electronic health records (EHRs) for secondary purposes. Temporal data-set shifts can present as trends, as well as abrupt or seasonal changes in the statistical distributions of data over time. The latter are particularly complicated to address in multimodal and highly coded data. These changes, if not delineated, can harm population and data-driven research, such as machine learning. Given that biomedical research repositories are increasingly being populated with large sets of historical data from EHRs, there is a need for specific software methods to help delineate temporal data-set shifts to ensure reliable data reuse. EHRtemporalVariability is an open-source R package and Shiny app designed to explore and identify temporal data-set shifts. EHRtemporalVariability estimates the statistical distributions of coded and numerical data over time; projects their temporal evolution through non-parametric information geometric temporal plots; and enables the exploration of changes in variables through data temporal heat maps. We demonstrate the capability of EHRtemporalVariability to delineate data-set shifts in three impact case studies, one of which is available for reproducibility. EHRtemporalVariability enables the exploration and identification of data-set shifts, contributing to the broad examination and repurposing of large, longitudinal data sets. Our goal is to help ensure reliable data reuse for a wide range of biomedical data users. EHRtemporalVariability is designed for technical users who are programmatically utilizing the R package, as well as users who are not familiar with programming via the Shiny user interface.Availability: https://github.com/hms-dbmi/EHRtemporalVariability/Reproducible vignette: https://cran.r-project.org/web/packages/EHRtemporalVariability/vignettes/EHRtemporalVariability.htmlOnline demo: http://ehrtemporalvariability.upv.es/.

Dataset Information

Integrating cancer genomic data into electronic health records.

Publications

Integrating cancer genomic data into electronic health records.

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