October 21, 2011

Clinical Genomicist Workstation

The advent of genome-wide profiling technologies and their routine use in basic science and translational research is now promoting their application in the clinical setting.  However, there are several potent informatics barriers that must be overcome before clinical sequencing can become routine.  Good Laboratory Practice-based quality assurance metrics must be established to guarantee the accuracy required to make medical decisions.  Genetic variants identified by sequencing must be systematically annotated and interpreted so that a clinical genomicist can decide which are medically actionable.  Software applications and technologies are required to facilitate reporting of genomic results and to transmit these data to the electronic health record (EHR). To address these issues, we have developed the Clinical Genomicist Workstation (CGW), which provides a 'soup-to-nuts' solution for processing clinical sequencing orders through:

  • Integration with Computerized Physician Order Entry (CPOE) and Laboratory Information Management Systems (LIMS).
  • Facilitation of complex and customized informatics analyses for individual groups of genes in the context of specific clinical indications.
  • Availability of powerful, secure, web-based interfaces to review identified variants in the context of available genomic annotation sources such as dbSNP, 1000 genomes, and Catalogue of Somatic Mutations in Cancer (COSMIC).
  • Automated drafting of the genetic report using a sophisticated rules engine that inserts appropriate, human curated clinical interpretations both within the context of the patient's disease (e.g. breast adenocarcinoma vs lung adenocarcinoma) and by considering the set of variants found (e.g. a variant in Gene X found in isolation may have a different interpretation than when found in concert with a variant in Gene Y).
  • Reporting of final results to EHR systems through standard messaging interfaces.

To obtain more information about the CGW: