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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Clinical exome sequencing reports: current informatics practice and future opportunities.

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Journal of the American Medical Informatics Association : JAMIA
|May 24, 2017
PubMed
Summary

Clinical whole exome sequencing (WES) reports lack standardized data elements, hindering data integration and research. Structuring these reports is crucial for advancing personalized medicine and improving patient care.

Keywords:
Common data elementsHealth Level-7 Fast Healthcare Interoperability Resourcesclinical WESelectronic health recordsexome reportstructured vocabulary

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Area of Science:

  • Genomics
  • Bioinformatics
  • Clinical Genetics

Background:

  • Clinical whole exome sequencing (WES) adoption is increasing, improving diagnostics for complex genetic conditions.
  • Current informatics practices for WES data are underdeveloped, lacking standardized vocabularies and data formats.
  • Genetic testing results are often shared as PDFs, complicating secondary analysis and data extraction.

Purpose of the Study:

  • To assess and identify common data elements in clinical whole exome sequencing reports.
  • To evaluate the completeness of mandatory elements according to practice guidelines.
  • To identify additional elements that could aid report interpretation and data integration.

Main Methods:

  • Review of a sample of clinical exome reports from CLIA-certified laboratories.
  • Assessment of data elements present in reports.
  • Comparison of report content against existing practice guidelines.

Main Results:

  • Significant variability and lack of common data elements identified in clinical WES reports.
  • Certain mandatory elements are missing from some reports.
  • Elements like patient consent, though not always present, are important for interpretation.

Conclusions:

  • Standardizing clinical WES reports is essential for data integration into electronic health records.
  • Structured genetic reports will facilitate retrospective research on WES clinical utility.
  • Improved data integration supports personalized medicine and enhanced patient outcomes.