NU50CK000629
Cooperative Agreement
Overview
Grant Description
New England Pathogen Genomics Center of Excellence - The Massachusetts Department of Public Health (MADPH) is proposing the formation of the New England Pathogen Genomics Center of Excellence (the Center) in response to the US Public Health Pathogens Genomics Centers of Excellence (CDC-RFA-CK22-2204) funding opportunity. This application is for the mandatory components (core, response implementation) and also includes the optional component (Lead PGCOE for education).
The Center's mission is to enhance regional capacity for the generation, analysis, and integration into public health response of pathogen genomic data, increasing the scale, speed, sensitivity, and quality of data generated. The Center leverages the complementary strengths of its regional and academic partners, including public health, genomics, data visualization, clinical medicine, and education. It will be led by MADPH, with the Broad Institute of MIT and Harvard as lead academic partner and other members from Massachusetts and Connecticut.
To serve all of New England, it will draw on existing links between state health departments, MADPH's role leading the regional network of the CDC's Bioinformatics Regional Resource Capacity-Building Program, and a range of cooperative efforts during the SARS-CoV-2 (SC2) pandemic. More broadly, the team is deeply involved in national and international efforts to build public health capacity for pathogen genomics.
In the first year, the Center will address two priority pathogen types, respiratory pathogens and sexually transmitted infections, with the latter focused on Neisseria gonorrhoeae infections. We will combine unbiased and targeted approaches to:
1) Differentiate the underlying cause and monitor the transmission dynamics of infections;
2) Develop tools to identify pathogen genomic risk profiles related to drug resistance; and
3) Implement rapid detection and genotyping technologies.
To support such pathogen-specific use cases, the Center will work to codify workflows and standardize data and its translation for public health decision making. We will streamline sample access and handling (physical and regulatory); develop sequencing for new sample types; improve unbiased metagenomic sequencing for use in public health labs; develop standardized data visualization and reporting; and advance CLIA-grade sequencing for clinical applications. We aim to develop methods, processes, and tools that are scalable, generalizable, and applicable to users domestically and abroad.
In parallel, the Center will prepare for rapid deployment of tools and processes to respond to an emerging infectious threat. This will require creating flexible plans to deploy available resources for scalable sequencing and appropriate data analysis, visualization, and reporting tools for integration of information into public health response; these will be based on experience with local (mumps), regional (hepatitis A), and international (Zika/SC2) outbreaks. To overcome potential regulatory delays, multi-institutional and interstate IRB protocols and MTAs will be established in advance.
The core education components of the Center will focus on practical training in the tools described above. Initial goals will include training in bioinformatics analysis through the Terra.bio platform and support for efforts like the MassCPR viral variants call series that brings together basic and translational researchers and public health practitioners. Additional goals will be identified through a needs assessment of public health professionals.
For the national training lead center, we propose:
1) A comprehensive landscape analysis of needs in genomic training and capacity;
2) A dedicated PGCOE portal, accreditation program, and curated online training offerings; and
3) New opportunities for advanced and nontraditional learning.
The Center's mission is to enhance regional capacity for the generation, analysis, and integration into public health response of pathogen genomic data, increasing the scale, speed, sensitivity, and quality of data generated. The Center leverages the complementary strengths of its regional and academic partners, including public health, genomics, data visualization, clinical medicine, and education. It will be led by MADPH, with the Broad Institute of MIT and Harvard as lead academic partner and other members from Massachusetts and Connecticut.
To serve all of New England, it will draw on existing links between state health departments, MADPH's role leading the regional network of the CDC's Bioinformatics Regional Resource Capacity-Building Program, and a range of cooperative efforts during the SARS-CoV-2 (SC2) pandemic. More broadly, the team is deeply involved in national and international efforts to build public health capacity for pathogen genomics.
In the first year, the Center will address two priority pathogen types, respiratory pathogens and sexually transmitted infections, with the latter focused on Neisseria gonorrhoeae infections. We will combine unbiased and targeted approaches to:
1) Differentiate the underlying cause and monitor the transmission dynamics of infections;
2) Develop tools to identify pathogen genomic risk profiles related to drug resistance; and
3) Implement rapid detection and genotyping technologies.
To support such pathogen-specific use cases, the Center will work to codify workflows and standardize data and its translation for public health decision making. We will streamline sample access and handling (physical and regulatory); develop sequencing for new sample types; improve unbiased metagenomic sequencing for use in public health labs; develop standardized data visualization and reporting; and advance CLIA-grade sequencing for clinical applications. We aim to develop methods, processes, and tools that are scalable, generalizable, and applicable to users domestically and abroad.
In parallel, the Center will prepare for rapid deployment of tools and processes to respond to an emerging infectious threat. This will require creating flexible plans to deploy available resources for scalable sequencing and appropriate data analysis, visualization, and reporting tools for integration of information into public health response; these will be based on experience with local (mumps), regional (hepatitis A), and international (Zika/SC2) outbreaks. To overcome potential regulatory delays, multi-institutional and interstate IRB protocols and MTAs will be established in advance.
The core education components of the Center will focus on practical training in the tools described above. Initial goals will include training in bioinformatics analysis through the Terra.bio platform and support for efforts like the MassCPR viral variants call series that brings together basic and translational researchers and public health practitioners. Additional goals will be identified through a needs assessment of public health professionals.
For the national training lead center, we propose:
1) A comprehensive landscape analysis of needs in genomic training and capacity;
2) A dedicated PGCOE portal, accreditation program, and curated online training offerings; and
3) New opportunities for advanced and nontraditional learning.
Funding Goals
NOT APPLICABLE
Grant Program (CFDA)
Awarding Agency
Place of Performance
Massachusetts
United States
Geographic Scope
State-Wide
Related Opportunity
Analysis Notes
COVID-19 $9,700,000 (48%) percent of this Cooperative Agreement was funded by COVID-19 emergency acts including the American Rescue Plan Act of 2021.
Amendment Since initial award the total obligations have increased 335% from $4,600,000 to $20,019,577.
Amendment Since initial award the total obligations have increased 335% from $4,600,000 to $20,019,577.
Massachusetts Department Of Public Health was awarded
NE Pathogen Genomics Center of Excellence
Cooperative Agreement NU50CK000629
worth $20,019,577
from National Center for Emerging and Zoonotic Infectious Diseases in September 2022 with work to be completed primarily in Massachusetts United States.
The grant
has a duration of 5 years and
was awarded through assistance program 93.084 Prevention of Disease, Disability, and Death by Infectious Diseases.
The Cooperative Agreement was awarded through grant opportunity US Public Health Pathogens Genomics Centers of Excellence.
Status
(Ongoing)
Last Modified 3/20/25
Period of Performance
9/30/22
Start Date
9/29/27
End Date
Funding Split
$20.0M
Federal Obligation
$0.0
Non-Federal Obligation
$20.0M
Total Obligated
Activity Timeline
Transaction History
Modifications to NU50CK000629
Additional Detail
Award ID FAIN
NU50CK000629
SAI Number
NU50CK000629-4242896943
Award ID URI
SAI UNAVAILABLE
Awardee Classifications
State Government
Awarding Office
75CDC1 CDC Office of Financial Resources
Funding Office
75CVL0 CDC NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES
Awardee UEI
DLKMR1QVDX34
Awardee CAGE
3JKS4
Performance District
MA-90
Senators
Edward Markey
Elizabeth Warren
Elizabeth Warren
Budget Funding
| Federal Account | Budget Subfunction | Object Class | Total | Percentage |
|---|---|---|---|---|
| CDC-Wide Activities and Program Support, Centers for Disease Control and Prevention, Health and Human Services (075-0943) | Health care services | Grants, subsidies, and contributions (41.0) | $9,700,000 | 100% |
Modified: 3/20/25