Standards for clinical grade genomic databases

Sophia L. Yohe, Alexis B. Carter, John D. Pfeifer, James M. Crawford, Allison Cushman-Vokoun, Samuel Caughron, Debra G.B. Leonard

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Context.-Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. Objectives.-To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. Design.-Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. Results.-Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. Conclusion.-These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.

Original languageEnglish (US)
Pages (from-to)1400-1412
Number of pages13
JournalArchives of Pathology and Laboratory Medicine
Volume139
Issue number11
DOIs
StatePublished - Nov 2015

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Medical Laboratory Technology

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    Yohe, S. L., Carter, A. B., Pfeifer, J. D., Crawford, J. M., Cushman-Vokoun, A., Caughron, S., & Leonard, D. G. B. (2015). Standards for clinical grade genomic databases. Archives of Pathology and Laboratory Medicine, 139(11), 1400-1412. https://doi.org/10.5858/arpa.2014-0568-CP