Title: NIHR HPRU in Genomics and Enabling Data at University of Warwick
Funder: Department of Health and Social Care

Abstract: Public Health England (PHE), the University of Warwick, the Wellcome Sanger Institute and the University of Cambridge propose to jointly create the NIHR Health Protection Research Unit (HPRU) in Genomics and Enabling Data. Our mission is to provide the methodological backbone required to improve English public health using new rich data sources. In particular, recent and ongoing developments in whole-genome sequencing technologies have a widely acknowledged great potential to help us improve public health, but this potential is currently incompletely realised due to a lack of sound and scalable methodology to interpret the data in the correct epidemiological context. Working in close collaboration with other HPRUs, we will develop new analytical methods that exploit large scale genomic, metagenomic and epidemiological data available on infectious diseases, in order to learn about the ways pathogens evolve, spread and cause diseases. These new methods will be based on robust statistical methodology, thoroughly tested on both simulated and real datasets, and implemented into open source software tools that will be easy to deploy and apply. Probabilistic models and Bayesian inference will be used to keep a clear understanding of any assumptions made and a full quantification of uncertainties inherent to any public health system. Particular attention will be given to the scalability of the methods to large amounts of data, and the practicality of their application in real-time situations, including the feasibility to respond to public health emergencies. We will pursue four complementary themes respectively aimed at (1) detecting and analysing outbreaks, (2) integrating genomic and enabling data into traditional infectious disease epidemiology, (3) developing and implementing user-friendly databases and interfaces and (4) analysing and predicting evolutionary dynamics and in particular antimicrobial resistance trends. The HPRU will benefit from a broad wealth of relevant expertise available at PHE, Warwick, Sanger and Cambridge. These institutions include many world-leading experts in microbial genomics, infectious disease epidemiology, public health, mathematical modelling and computational statistics. We have an extensive track record of successful collaboration with each other and other Universities and public health bodies, and have selected our objectives and research projects based on the specific needs of PHE and other HPRUs to use genomic and enabling data to inform public health decisions. We will build upon these exceptionally strong foundations to deliver world-class research and implementation of genomic epidemiology.

Lay abstract: Public Health England (PHE), the University of Warwick, the Wellcome Sanger Institute and the University of Cambridge propose to jointly create the NIHR Health Protection Research Unit (HPRU) in Genomics and Enabling Data. Our mission is to provide the methodological backbone required to improve English public health using new rich data sources. In particular, recent and ongoing developments in whole-genome sequencing technologies have a widely acknowledged great potential to help us improve public health, but this potential is currently incompletely realised due to a lack of sound and scalable methodology to interpret the data in the correct epidemiological context. Working in close collaboration with other HPRUs, we will develop new analytical methods that exploit large scale genomic, metagenomic and epidemiological data available on infectious diseases, in order to learn about the ways pathogens evolve, spread and cause diseases. These new methods will be based on robust statistical methodology, thoroughly tested on both simulated and real datasets, and implemented into open source software tools that will be easy to deploy and apply. Probabilistic models and Bayesian inference will be used to keep a clear understanding of any assumptions made and a full quantification of uncertainties inherent to any public health system. Particular attention will be given to the scalability of the methods to large amounts of data, and the practicality of their application in real-time situations, including the feasibility to respond to public health emergencies. We will pursue four complementary themes respectively aimed at (1) detecting and analysing outbreaks, (2) integrating genomic and enabling data into traditional infectious disease epidemiology, (3) developing and implementing user-friendly databases and interfaces and (4) analysing and predicting evolutionary dynamics and in particular antimicrobial resistance trends. The HPRU will benefit from a broad wealth of relevant expertise available at PHE, Warwick, Sanger and Cambridge. These institutions include many world-leading experts in microbial genomics, infectious disease epidemiology, public health, mathematical modelling and computational statistics. We have an extensive track record of successful collaboration with each other and other Universities and public health bodies, and have selected our objectives and research projects based on the specific needs of PHE and other HPRUs to use genomic and enabling data to inform public health decisions. We will build upon these exceptionally strong foundations to deliver world-class research and implementation of genomic epidemiology.

Research activity codes: 2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: INFECTION