a federated platform enabling richer genomic epidemiology ... · a federated platform enabling...

A Federated Platform Enabling Richer Genomic Epidemiology Analysis in a Public Health Environment.

Franklin Bristow2, Josh Adam2, João André Carriço5, Mélanie Courtot 3,1, 10, Bhavjinder Dhillon1, Damion Dooley3, Emma Griffiths1, Judy Isaac-Renton3, Alex Keddy8, Peter Kruczkiewicz7, Matthew Laird1, Andrew MacArthur11, Thomas Matthews2, Aaron Petkau2, Lynn Schriml6, Julie Shay1, Eduardo Taboada7, Patrick Tang2, Joel Thiessen2,9, Geoff Winsor1, Robert G. Beiko8, Morag Graham2,9, Gary Van Domselaar2,9, William Hsiao3,4,The IRIDA Consortium and Fiona Brinkman1. www.irida.ca1Simon Fraser University, Burnaby, BC, Canada;2National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada; 3BC Public Health Microbiology and Reference Laboratory, Vancouver, BC, Canada; 4University of British Columbia, Vancouver, BC, Canada; 5Faculty of Medicine, University of Lisbon, Lisbon, Portugal; 6University of Maryland School of Medicine, Baltimore, MD, USA; 7National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada; 8Faculty of Computer Science, Dalhousie University, Halifax,NS, Canada; 9University of Manitoba, Winnipeg, MB, Canada, 10European Bioinformatics Institute, Hinxton, Cambridge, UK, 11McMaster University, Hamilton, ON, Canada.

The Goal of IRIDA:To support real-time infectious disease outbreak investigations in Canada:

We are developing an open source, interactive, standards compliant resource for public health agencies that aims to release de-identified genome data rapidly, plus enable rich epi-clinical-lab-genome data analysisin a Public Health environment.

Design Philosophy• Dynamic integration of data sources (clinical,

epidemiological and lab sourced) • Privacy protection • Suite of bioinformatics tools for researchers and

public health workers • Data standardization enabling value-added activities

Data Management and Analysis• Easy-to-use tools providing rich analyses in a timely

manner • Controlled parameters and workflows for reproducibility

• Automated raw read uploader• Data organized by Project and Sample• SNV phylogenies with SNVPhyl Galaxy workflow and de

novo assembly and annotation using SPAdes and Prokka• Easy-to-interpret QA/QC, revision tracking

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Data Security and Sharing • Stakeholders maintain local, physical ownership of

sample data • Data sharing facilitated over an HTTP REST API,

authorization with OAuth2

Application Ontology and User Interface• No single existing ontology can adequately describe all the

domains required for genomic epidemiology

• IRIDA ontology leverages existing resources and OBO standards for interoperability

• Metadata gaps identified by extensive user consultation IRIDA ontology available as OWL file

• Dynamic ontology driven user interface, selective de-identification and line list sharing

Identifies genomic islands (GIs), virulence factors, antibiotic resistance genes in complete and draft genomes

Integrates sequence data and geospatial information for phylogeographicanalysis

AMR gene annotation tool for whole genomes or genome assemblies integrated within Comprehensive Antibiotic Resistance Database (CARD)

Background• Most tools/pipelines require considerable technical

knowledge • Cannot easily integrate rich epidemiologic data

IslandViewer

GenGIS

RGI – Resistance Gene IdentifierDatabase & API Modules

User access control + Data Security

Quality

Control

Comparative

Genomics

Molecular

Typing

VisualizationPatho-

genomics

Genomic

Epi/Geo-

tagging

Lab Technician/

Medical

Microbiologist

Epidemiologist Researcher

Customized output

Clinical Data

Sources

Epidemiology

Data

Sources

Laboratory

Data

Sources

Programming Interface, Analysis

Modules, End Users

Data Sources

Value Added

Activities

Epidemiology Investigation

Results

Epi-analysis Ready Data

Outbreak Investigation

IRIDA Platform Design

AcknowledgementsFunded by grants from Genome Canada, Genome BC, the Genomics R&D Initiative (GRDI), Cystic Fibrosis Canada and Compute Canada

Genomics

Pathogen Taxonomy

SOPS

Diagnostic Test

Result Report

Laboratory-test centric

Clinical-patient centric

Epidemiology-case centric

Host Taxonomy

Symptoms

Demographics

Treatment

Vaccines

DrugsGeography

Public Health Intervention

Exposure

Contact

Food

Travel

Environment

Temporal Info