Public Health England focus on infectious disease genomics

Philippa Brice

14 July 2014

Public Health England (PHE) is developing new systems for storage and analysis of big data with a view to underpinning genomic analysis of infectious disease agents, or microbial pathogens.

Infectious diseases were originally identified as one of the priority areas for action by the UK government funded 100,000 Genomes Project. Genome analysis offers the potential for much faster and more accurate identification and characterisation of infectious agents, allowing prompt diagnosis and treatment (including with a view to antibiotic resistance) as well as surveillance of infectious disease outbreaks and public health threats.

Now PHE is said to be using a new big data storage system from DataDirect Networks with implementation and support from big data management and analysis company OCF. It is also reportedly working to further expand the capacity for data storage and analysis to support research access to the big data from pathogen sequencing and enhance collaboration.

Managing Director of service provider OCF said that PHE would: “set the standards for the rest of the world to follow” in the provision of microbial DNA sequence data storage.

It is not clear how far the PHE approach will be consistent with that of the 100,000 Genomes Project run by Department of Health owned company Genomics England, which is busy developing data storage and analysis capacity as well as measures for secure integration of confidential patient data. It is intended that this will eventually form a unique research resource that public and commercial researchers may pay fees to access. A similar revenue-generating model for the PHE database could be problematic, since data on current and emerging infectious disease cases, patterns and threats are potentially highly sensitive, albeit in a different manner from human genome sequence data. Similarly, pathogen genomes differ significantly from human ones (principally in their much smaller size which makes sequencing and data analysis much faster, and also cheaper) s o approaches to data storage and interrogation are likely to differ.

Last week PHE announced plans to move an important centre of scientific expertise from Porton Down in Wilshire to Harlow in Essex, between Cambridge and London. PHE Chief Executive Duncan Selbie said this was essential for realisation of their ambition to provide modern scientific facilities, in allowing them to retain and can attract the world’s best scientists and researchers”. PHE has previously said that it hopes to relocate all their infectious disease facilities from Porton Down, Colindale and Whitechapel to a single site in Harlow to create a unified science hub.

The PHG Foundation is currently undertaking a major project looking at the implementation of pathogen genome sequencing in the UK; a comprehensive overview of the current picture of service provision across the country and expert recommendations for PHE and other stakeholders is due for release early next year.