About

The Northwest Pathogen Genomics Center of Excellence (NW-PaGe) The Northwest Pathogen Genomics Center of Excellence (NW-PaGe) seeks to accelerate public health agencies’ ability to leverage pathogen genomic data in public health investigations, epidemiological surveillance, and public health decision making.

Making use of pathogen genomic data for applied epidemiology requires new molecular approaches in the laboratory, development of bioinformatics pipelines to assemble sequencing reads into analyzable genomes, and evolutionary and comparative genomics analyses and visualizations to investigate the data. The public health workforce needs to be able to deploy these methods nimbly during field investigations or infectious disease events.

NW-PaGe enables iterative collaboration between academia and public health. Our Center helps facilitate the translation of new and cutting-edge approaches from academic labs into public health practice. We also seek to guide academic research and technology development in ways that serve public health needs.

We support innovation across five different domains:

Microbiological approaches for generating pathogen genomic data
Bioinformatic pipeline development to support genomic data quality control, assembly, and analysis
Data modernization to support genomic and epidemiological data integration, data hygiene, and data sharing
Analysis and visualization of pathogen genomic data to enhance surveillance and outbreak response
Deployment of pathogen genomic data to support public health investigations in the field

Who We Are

NW-PaGe brings together epidemiologists at State and County public health agencies and microbiologists and public health bioinformaticians from the State Public Health Laboratory. Our collaboration also extends to academic groups working in pathogen genomics, genomic epidemiology, and veterinary health.

Our Partners

Fred Hutchinson Cancer Center – Bedford Laboratory

The Bedford Laboratory at Fred Hutchinson Cancer Center are leading experts in the application of computational and statistical methods to pathogen genomic sequence data to understand infectious disease dynamics, epidemic growth, and pathogen geographic spread. The Bedford Laboratory contributes to the Center academically by developing novel genomic epidemiologic methods and helping public health departments learn to apply them. Furthermore, as co-developers of the Nextstrain software suite, the Bedford Laboratory works with public health partners in the Center to ensure that Nextstrain software development meets public health’s priorities and needs.

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Public Health – Seattle & King County

As a Local Health Jurisdiction, Public Health – Seattle & King County (PHSKC) has different needs, authority, and resources than a state or federal-level public health agency. Within the Center, PHSKC provides a critical vantage point towards how genomic surveillance can be applied to support epidemiological field investigations, which are often conducted at the county-level. PHSKC’s partnership ensures that work developed by the Center can support pathogen genomic data access and use at the local level.

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University of Washington – Greninger Laboratory

The Greninger Lab uses next-generation sequencing to understand viral transmission, evolution, and host interaction, and is tightly integrated with the clinical laboratories at University of Washington Medical Center. The Lab contributes their academic expertise in novel sequencing assay development, as well as their experience translating and validating assays to clinical standards, to help guide sequencing protocol development by the Center. The Greninger Lab also provides surge sequencing capacity, particularly for viral genomic surveillance.

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University of Washington – Northwest Center for Public Health Practice

Drawing on their extensive background in training and outreach between academic and public health practice communicates, the Northwest Center for Public Health Practice contributes to the Center through design and evaluation of educational resources and training materials delivered by NW-PaGe.

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University of Washington – Starita Laboratory

The Starita Lab primarily works in human genomics to improve genomics-guided precision medicine. Due to its size, characterizing human genomic data typically requires labs to harness new technologies and automated approaches to enable sequencing at scale. With extensive experience performing high throughout sequencing studies for human genomic characterization and for the respiratory disease sequencing during the Seattle Flu Study, the Starita Lab supports the Center by ensuring that sequencing approaches developed by the Center leverage new technologies and robotic approaches designed to handle the scale of specimens received by public health laboratories.

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Washington State Department of Health – Data Integration and Quality Assurance team

Much of the utility of genomic epidemiology comes from the joint analysis of pathogen genomic data and linked epidemiologic data. However, these data sources are often disparate and disjoint. The Data Integration and Quality Assurance team contributes to the Center through development of databases, data schemas, and data flows to ingest and link epidemiological data with genomic data. We contribute to the Center through efforts to make data linkage processes as automated and generalizable as possible, such that our data integration processes can be deployed across pathogens and across public health agencies.

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Washington State Department of Health – Molecular Epidemiology Program

The Molecular Epidemiology Program at WA DOH seeks to strengthen applied epidemiologists’ ability access and leverage pathogen genomic data to support outbreak investigations and routine epidemiologic surveillance. We contribute to the Center by piloting and implementing new techniques for pathogen genomic analysis and visualization; helping to design and coordinate pathogen genomic surveillance systems; and providing didactic and enquiry-based training to help applied epidemiologists interpret and use pathogen genomic data in their public health activities.

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Washington State Public Health Laboratory

The Washington State Public Health Laboratory contributes to the Center through validation and optimization of wet lab sequencing protocols for public health applications; development and implementation of bioinformatic pipelines for genomic data assembly, quality control, and analysis; and providing training to other public health departments seeking to develop pathogen genomic surveillance capacity.

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Washington State University – Washington Animal Disease Diagnostic Laboratory

The Washington Animal Disease Diagnostic Laboratory is a state-of-the-art, Level 1 animal health laboratory within the National Animal Health Laboratory Network. By supporting animal disease diagnostics and surveillance, they help to safeguard animal health, the food supply, and human health at the animal-human interface. WADDL’s participation in the Center ensures that NW-PaGe developed sequencing protocols, data analysis pipelines, and data capture and collation processes are generalizable across human and animal specimens and surveillance goals, thereby supporting One Health pathogen genomic surveillance.

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