Jun 19, 2016

The Precision Medicine Knowledge Base: an online application for collaborative editing, maintenance and sharing of structured clinical-grade cancer mutations interpretations

BioRxiv : the Preprint Server for Biology
Linda HuangOlivier Elemento

Abstract

This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance and sharing of structured clinical-grade cancer mutations interpretations. PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as Human Genome Variation Society (HGVS) variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. The PMKB interpretations have been used in over 1,500 AmpliSeq tests and 750 whole exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existin...Continue Reading

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Mentioned in this Paper

EGFR
BRAF protein, human
Genome
Oncologic
Epidermal Growth Factor Receptor Activity
Neoplasms
Gene Mutation
Cancer Gene Mutation
Oncology Field
Whole Exome Sequencing

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