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Context is Everything: Integrating Genomics, Epidemiological and Clinical
Data Using GenEpiO
Emma GriffithsBrinkman Lab
Simon Fraser University, Burnaby, Canada
On behalf of the GenEpiO Development TeamWill Hsiao & Damion Dooley (BC Public Health Lab),
Emma Griffiths & Fiona Brinkman (SFU)
Sept 15, 2016
Each year, one in eight Canadians (or 4 million people)
get sick with a domestically acquired food-borne illness.http://www.phac-aspc.gc.ca/efwd-emoha/efbi-emoa-eng.php
Slide courtesy of Will Hsiao
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Genomic sequences don’t mean much without contextual information.
• Must be combined with contextual information to make sense of the data… FAST!
Contextual info = Lab, Clinical, Epi Data
What is the pathogen?
Where did the exposures occur?
When were the exposures?
Who is at risk?
What virulence factors or drug resistance
determinants are present?
How severe is the disease?
Why did the contamination happen?
Bacterial Genome 1Bacterial Genome 2Bacterial Genome 3
Bacterial Genome 4Bacterial Genome 5Bacterial Genome 6Bacterial Genome 7Bacterial Genome 8Bacterial Genome 9
OUTBREAK?
Whole genome sequencing is increasingly used for diagnostics in foodborne outbreaks and surveillance.
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The
of Contextual InformationIsn’t
STANDARDIZED
•Free text, short hand, granularity, misspelling, paper format
• Ontologies help resolve issues of taxonomy, granularity and specificity
• Reduces time consuming manual processing and mining
Leafy Greens “has_disposition” Transmission Vehicle (E.coli)
Spinach Lettuce
Endive “is_a” Lettuce TypeIcebergSpinacia oleracea
Amaranthus hybridus
S. Africa
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Ontology, A Way of Structuring Information
• Standardized, well-defined hierarchy of terms
• Interconnected with logical relationships e.g. Endive “is_a” Lettuce type
Integrates Epi Exposure data
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GenEpiO: Genomic Epidemiology Application Ontology
Standardize fields/terms used to describe genomics, lab, clinical and epidemiological data critical for food-borne pathogen
outbreak investigations Provincial National Public Health Agency Public Health Agency (Hsiao, co-PI) (Van Domselaar, co-PI)
Academic/Public Brinkman (PI)
www.irida.ca
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GenEpiO: Combining Different Epi, Lab, Genomics and Clinical Data Fields
Lab AnalyticsGenomics, PFGE
Serotyping, Phage typingMLST, AMR
Sample MetadataIsolation Source (Food, Host
Body Product, Environmental), BioSample
Epidemiology InvestigationExposures
Clinical DataPatient demographics, Medical
History, Comorbidities, Symptoms, Health Status
ReportingCase/Investigation Status
GenEpiO(Genomic Epidemiology Application Ontology)
Current Ontology Development Focuses On 3 Key Areas
Food Antimicrobial
Resistance
Disease Surveillance
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(FoodON)(SurvO) (ARO)
See draft version at https://github.com/GenEpiO/genepio/wiki
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Ontologies are commonly encoded using OWL (Web Ontology Language).
• Markup language for sharing ontologies on the web • Machine and human-readable• OWL statements written in RDF • Expressed in XML syntax
• Protégé (editor)• Ontology lookup services:
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Use ontology to identify common exposures, symptoms etc among genomics clusters
Example: Automating Case Definition generationCorrelate Genomics Salmonella Cluster A cases between 01 Mar 2014- 15 Mar 2014 with High-Risk Food Types Chicken Nuggets and Geographical Location of Vancouver
XXXXXXXXXXXXXXGenEpiO Will Help Integrate Genomics and
Epidemiological Data.
Genomic Epidemiology Ontology is like instrumentation for your contextual
information…it needs maintenance and continual
improvement
To achieve consensus and uptake International GenEpiO Consortium
Join us!E-mail: [email protected] 11
(>60 members from 15 countries)
GenEpiO facilitates data sharing!
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Context is everything in foodborne outbreak investigations.
GenEpiO helps fit the data together.
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Project LeadersFiona Brinkman – SFUWill Hsiao – PHMRLGary Van Domselaar – NML
Simon Fraser University (SFU)Emma GriffithsGeoff WinsorJulie ShayMatthew LairdBhav Dhillon
McMaster UniversityAndrew McArthurDaim Sardar
European Food Safety AgencyLeibana Criado ErnestoVernazza FrancescoRizzi Valentina
National Microbiology Laboratory (NML)Franklin BristowAaron PetkauThomas MatthewsJosh AdamAdam OlsenTara LynchShaun TylerPhilip MabonPhilip AuCeline NadonMatthew Stuart-EdwardsMorag GrahamChrystal BerryLorelee TschetterEduardo ToboadaPeter KruczkiewiczChad LaingVic GannonMatthew WhitesideRoss DuncanSteven Mutschall
University of LisbonJoᾶo Carriҫo
European Bioinformatics InstituteMelanie CourtotHelen Parkinson
BC Public Laboratory and BC Centre for Disease Control (BCCDC)Damion DooleyJudy Isaac-RentonPatrick TangNatalie PrystajeckyJennifer GardyLinda HoangKim MacDonaldYin ChangEleni GalanisMarsha TaylorJennifer Law
University of MarylandLynn Schriml
Canadian Food Inspection Agency (CFIA)Adam KoziolBurton BlaisCatherine Carrillo
Dalhousie UniversityRob BeikoAlex Keddy www.irida.ca