Job summary
We are seeking a talented and driven bioinformatician to lead on the development and optimisation of bioinformatic solutions for the national NHS Respiratory Metagenomics Programme and related projects. The role offers a unique opportunity to work within a multi-disciplinary NHS team to support transformative innovation in the diagnosis of infectious disease across the UK and internationally through the development of pipelines, curated databases and analytic tools to translate long read metagenomic sequencing into clinical services. The role has a significant external facing component, leading deployment and troubleshooting support across 30+ NHS and international sites, and growing metagenomics capabilities in NHS teams through national working groups and peer support. The successful candidate will work closely with colleagues across the NHS, UKHSA, ONT and academia to support mutual success. In addition to a very active development programme, the candidate will work with colleagues in Synnovis to support existing diagnostic services across GSTT and KCH, and provide remote support for services at network sites.
In addition to having strong technical skills and experience in pathogen sequencing or NGS pipeline development, the successful candidate will be a strategic thinker in developing tools for clinical deployment at scale across a range of end users. They will have excellent communication skills and an ability to work collaboratively across organisational boundaries.
Main duties of the job
Hosted by CIDR within the Department of Infection at St Thomas' Hospital, the post will primarily lead on the development, deployment and continuous improvement of bioinformatic solutions to support clinical service delivery for sites across the UK in the NHS Respiratory Metagenomics Programme. As part of a multi-disciplinary team, the post holder will provide bioinformatics expertise in the translation of nanopore long-read sequencing-based technologies into routine diagnostic service to support daily patient testing. They will be responsible for the selection, development, maintenance and curation of databases and bioinformatics tools and resources. They will work closely with other bioinformaticians across our NHS, UKHSA, academic and industry partners to develop, validate, maintain and optimise metagenomics pipelines for clinical use across the NHS and to support the digital genomic bridge with UKHSA. The individual will provide support for other members of CIDR and partners in the diagnostic laboratory to enable and enhance the overall objectives of the NHS Respiratory Metagenomics Programme.
The post holder will also provide support across a variety of development projects in the diagnostic laboratory to enable the translation of novel NGS diagnostics into service, including the development and optimisation of pipelines for metagenomics, 16S/ITS and bacterial isolate sequencing.
About us
The NHS Respiratory Metagenomics Programme has been commissioned by the government's Department of Science, Innovation and Technology, in collaboration with NHS England, to revolutionise the diagnosis and surveillance of infectious disease in the UK through cutting edge genomic technology. The programme is a partnership between the NHS, UK Health Security Agency (UKHSA), and Oxford Nanopore Technologies (ONT) to embed pathogen agnostic metagenomic testing in NHS microbiology labs and ICUs by 2029, providing same day clinical detection and real-time data signals to UKHSA's proof of concept national surveillance platform. Guy's and St Thomas' NHS Foundation Trust is leading this national programme on behalf of the NHS, implementing the initial use case in respiratory infection and leading on translational research efforts with the potential to scale across multiple clinical settings. The programme will serve as a test bed for the accelerated adoption of innovation in healthcare and a proof of concept in the use of a clinical diagnostic backbone in an 'always on', real-time UK pathogen surveillance system. At GSTT, the programme is being delivered by an expert clinical, scientific and bioinformatic team within the Center for Clinical Infection and Diagnostics Research, with additional expertise from our pathology provider, Synnovis, and with programme management support from the South East Genomic Medicine Service.
Job description
Job responsibilities
- Lead the bioinformatics support for translation of nanopore metagenomics assays into pilot clinical services. This includes sequencing of bacteria, fungi and viruses and a particular focuson respiratory infections, including SARS-CoV-2, other coronaviruses and influenza.
- Provide bioinformatics support for developmental projects evaluating high throughput real time targeted sequencing of respiratory viruses of public health and infection control significance
- Responsible for the development and maintenance of analysis pipelines to support clinical service delivery across the NHS network, ensuring the approach supports longer term scalingand sustainable use, including developing a strategy for updating methods of pipeline delivery, with particular reference to ensuring service continuity and improvement.
- Lead in the development, implementation and management of analytical tools for the service pipelines. Tasks will include the development of database and related tools for data retrieval,manipulation, analysis and visualisation and producing ISO compliant documentation (validation, SOPs).
- Lead in the deployment of bioinformatic pipelines across NHS Trusts and international sites, including liaison with relevant scientists, network engineers, governance and clinical departments; and drafting and maintaining clear guidance documentation for bioinformaticians and non-bioinformaticians alike
Please see the supporting documentation for a full Job Description and Person Specification.
Job description
Job responsibilities
- Lead the bioinformatics support for translation of nanopore metagenomics assays into pilot clinical services. This includes sequencing of bacteria, fungi and viruses and a particular focuson respiratory infections, including SARS-CoV-2, other coronaviruses and influenza.
- Provide bioinformatics support for developmental projects evaluating high throughput real time targeted sequencing of respiratory viruses of public health and infection control significance
- Responsible for the development and maintenance of analysis pipelines to support clinical service delivery across the NHS network, ensuring the approach supports longer term scalingand sustainable use, including developing a strategy for updating methods of pipeline delivery, with particular reference to ensuring service continuity and improvement.
- Lead in the development, implementation and management of analytical tools for the service pipelines. Tasks will include the development of database and related tools for data retrieval,manipulation, analysis and visualisation and producing ISO compliant documentation (validation, SOPs).
- Lead in the deployment of bioinformatic pipelines across NHS Trusts and international sites, including liaison with relevant scientists, network engineers, governance and clinical departments; and drafting and maintaining clear guidance documentation for bioinformaticians and non-bioinformaticians alike
Please see the supporting documentation for a full Job Description and Person Specification.
Person Specification
Previous Experience
Essential
- PhD or equivalent in genome biology or bioinformatics
Desirable
- Experience of working in a diagnostic laboratory and/or infectious diseases
Previous Experience
Essential
- Developing, implementing and maintaining bioinformatic data analysis pipelines in clinical settings
- Software project leadership skills and experience of commercial and academic molecular biology software packages for mining genome databases
Desirable
- Computer programming in R, Lisp or another functional programming language
- Next Generation Sequence analysis
Additional
Essential
- Excellent communication and liaison skills and the ability to work collaboratively across organisational boundaries with a diverse group of people, including clinical, academic and managerial colleagues
Desirable
- Enthusiasm with the ability to motivate a team in a rapidly changing environment
Qualifications
Essential
- PhD or equivalent in genome biology or bioinformatics
- Evidence of ongoing professional development or knowledge acquisition in NGS bioinformatics techniques and related software
Desirable
- Experience in a diagnostic laboratory
- Experience in infectious diseases
Skills
Essential
- Proven skills in scripted programming languages e.g. Python, PERL
- Proven skills in database design, architecture, and implementation on a variety of platforms
Person Specification
Previous Experience
Essential
- PhD or equivalent in genome biology or bioinformatics
Desirable
- Experience of working in a diagnostic laboratory and/or infectious diseases
Previous Experience
Essential
- Developing, implementing and maintaining bioinformatic data analysis pipelines in clinical settings
- Software project leadership skills and experience of commercial and academic molecular biology software packages for mining genome databases
Desirable
- Computer programming in R, Lisp or another functional programming language
- Next Generation Sequence analysis
Additional
Essential
- Excellent communication and liaison skills and the ability to work collaboratively across organisational boundaries with a diverse group of people, including clinical, academic and managerial colleagues
Desirable
- Enthusiasm with the ability to motivate a team in a rapidly changing environment
Qualifications
Essential
- PhD or equivalent in genome biology or bioinformatics
- Evidence of ongoing professional development or knowledge acquisition in NGS bioinformatics techniques and related software
Desirable
- Experience in a diagnostic laboratory
- Experience in infectious diseases
Skills
Essential
- Proven skills in scripted programming languages e.g. Python, PERL
- Proven skills in database design, architecture, and implementation on a variety of platforms
Disclosure and Barring Service Check
This post is subject to the Rehabilitation of Offenders Act (Exceptions Order) 1975 and as such it will be necessary for a submission for Disclosure to be made to the Disclosure and Barring Service (formerly known as CRB) to check for any previous criminal convictions.
Applications from job seekers who require current Skilled worker sponsorship to work in the UK are welcome and will be considered alongside all other applications. For further information visit the UK Visas and Immigration website (Opens in a new tab).
From 6 April 2017, skilled worker applicants, applying for entry clearance into the UK, have had to present a criminal record certificate from each country they have resided continuously or cumulatively for 12 months or more in the past 10 years. Adult dependants (over 18 years old) are also subject to this requirement. Guidance can be found here Criminal records checks for overseas applicants (Opens in a new tab).
Additional information
Disclosure and Barring Service Check
This post is subject to the Rehabilitation of Offenders Act (Exceptions Order) 1975 and as such it will be necessary for a submission for Disclosure to be made to the Disclosure and Barring Service (formerly known as CRB) to check for any previous criminal convictions.
Applications from job seekers who require current Skilled worker sponsorship to work in the UK are welcome and will be considered alongside all other applications. For further information visit the UK Visas and Immigration website (Opens in a new tab).
From 6 April 2017, skilled worker applicants, applying for entry clearance into the UK, have had to present a criminal record certificate from each country they have resided continuously or cumulatively for 12 months or more in the past 10 years. Adult dependants (over 18 years old) are also subject to this requirement. Guidance can be found here Criminal records checks for overseas applicants (Opens in a new tab).
