title: Clinical genomics information management software linking cancer genome sequence and clinical decisions.
abstract: Using sequencing information to guide clinical decision-making requires coordination of a diverse set of people and activities. In clinical genomics, the process typically includes sample acquisition, template preparation, genome data generation, analysis to identify and confirm variant alleles, interpretation of clinical significance, and reporting to clinicians. We describe a software application developed within a clinical genomics study, to support this entire process. The software application tracks patients, samples, genomic results, decisions and reports across the cohort, monitors progress and sends reminders, and works alongside an electronic data capture system for the trial's clinical and genomic data. It incorporates systems to read, store, analyze and consolidate sequencing results from multiple technologies, and provides a curated knowledge base of tumor mutation frequency (from the COSMIC database) annotated with clinical significance and drug sensitivity to generate reports for clinicians. By supporting the entire process, the application provides deep support for clinical decision making, enabling the generation of relevant guidance in reports for verification by an expert panel prior to forwarding to the treating physician.
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario, Canada. stuart@morungos.com
authors.forename: Stuart
authors.initials: S
authors.lastname: Watt
authors.forename: Wei
authors.initials: W
authors.lastname: Jiao
authors.forename: Andrew M K
authors.initials: AM
authors.lastname: Brown
authors.forename: Teresa
authors.initials: T
authors.lastname: Petrocelli
authors.forename: Ben
authors.initials: B
authors.lastname: Tran
authors.forename: Tong
authors.initials: T
authors.lastname: Zhang
authors.forename: John D
authors.initials: JD
authors.lastname: McPherson
authors.forename: Suzanne
authors.initials: S
authors.lastname: Kamel-Reid
authors.forename: Philippe L
authors.initials: PL
authors.lastname: Bedard
authors.forename: Nicole
authors.initials: N
authors.lastname: Onetto
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Hudson
authors.forename: Janet
authors.initials: J
authors.lastname: Dancey
authors.forename: Lillian L
authors.initials: LL
authors.lastname: Siu
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.forename: Vincent
authors.initials: V
authors.lastname: Ferretti
mesh_terms: D014644:Genetic Variation; D005826:Genetics, Medical / Q000379:methods*; D015894:Genome, Human; D023281:Genomics / Q000191:economics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019451:Information Management; D009369:Neoplasms / Q000235:genetics*; D057285:Precision Medicine; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software
keywords: Cancer genome sequencing; Clinical genomics; Decision support; Electronic data capture; Knowledge base; Web-based application