Lead Genomic Data Scientist

Job summary The Lead Genomics Data Scientist is an exciting new role designed to lead the development and implementation of a robust computational biology / bioinformatics strategy to meet the needs of Work-packages [WP] 1 & 2 (rapid Whole Genome Sequencing [WGS] and other omics & Myeloma multi-target next generation sequencing (NGS) panel) of the NHS Haemato-oncology Genomic Network of Excellence [NoE] which is a new national initiative at the interface of translation genomic research and clinical service.
Duties of this post will encompass bioinformatic, analytical and administrative activities in addition to national educational and engagement roles.
Main duties of the job 1.
Design, develop, implement and take through ISO15189 accreditation: a. an appropriate bioinformatics pipeline for the analysis of all variant types for a tumour-only Next Generation Sequencing panel for plasma cell dyscrasias.
b. appropriate bioinformatic pipeline(s) for the analysis of all variant types from tumour-only and tumour: matched germline Whole Genome Sequencing for a range of different haematological malignancies.
2.
Work with other Genomic Laboratory Hubs (GLHs) on the national implementation of the tumour-only Next Generation Sequencing panel for plasma cell dyscrasias, by designing and implementing appropriate engagement and education programmes around the bioinformatics and interpretation and analysis components of the panel.
3.
Work with other stakeholders nationally including Genomics England and NHS England's Genomics Unit in the design, development and implementation of a strategy and mechanism for local WGS with central bioinformatics pipeline provision and local clinical interpretation and reporting, acknowledging that the Haematological Network of Excellence rapid local WGS programme is a national pilot programme of a new sequencing implementation strategy in cancer.
4.
Design, develop and implement the necessary analysis tools for other 'omics' which may include but not be limited to short read RNA sequencing / whole transcriptome sequencing, long read WGS and hybrid long read WGS and targeted sequencing assays.
About us Oxford University Hospitals NHS Foundation Trust is one of the largest NHS teaching trusts in the country.
It provides a wide range of general and specialist clinical services and is a base for medical education, training and Trust comprises four hospitals - the John Radcliffe Hospital, Churchill Hospital and Nuffield Orthopaedic Centre in Headington and the Horton General Hospital in Banbury.
Our values, standards and behaviours define the quality of clinical care we offer and the professional relationships we make with our patients, colleagues and the wider community.
We call this Delivering Compassionate Excellence and its focus is on our values of compassion, respect, learning, delivery, improvement and excellence.
These values put patients at the heart of what we do and underpin the quality healthcare we would like for ourselves or a member of our family.
Watch how we set out to deliver compassionate excellence via the OUH YouTube channel.
Job description Job responsibilities Main duties and responsibilities of the post Leadership and Management Develop and implement a computational biology / bioinformatics strategy to allow the success of WPs 1 & 2 of the NHS Haemato-oncology Genomic Network of Excellence.
This should include assessment of business-as-usual implementation of the contents of the WPs on both a laboratory and national level.
Implementation of WPs 1 & 2 on a national level will require the post-holder to be able to absorb and ten disseminate highly complex information around the bioinformatics pipelines to both specialist and non-specialist audiences who may be resitant to change.
To ensure broad adoption they will need to be able to communicate in a logical and persuasive manner which takes large numbers of people with them.
Work with NHS Genomics Unit (national oversight group) to ensure that the computational biology / bioinformatics strategy for NoE WPs 1 & 2 aligns with their vision for the future of genomics within the Genomic Medicine Service (GMS).
Assist in the national adoption of WP2 where desired by other GLHs.
Contribute, where requested, to national discussions / meetings around the implementation of WGS at a local level with movement of data to third party suppliers for bioinformatics analysis, realising that WP1 is being used as a national pilot of possible working practices.
Develop a practical and affordable strategy around data-storage for the WPs 1 & 2 in the NoE which includes collaboration with third party suppliers.
Advise on the need for and assist in the appointment and management of any further bioinformatics resource required for NoE WPs 1 & 2 including managing budgets.
Provide representation at national NoE meetings around the progress of NoE WPs 1 & 2 where appropriate, where it will be necessary to present complex information in a way that can be understood by large non-specialist audiences.
Assist in the development of additional collaborations including with academic and commercial partners around the activities of NoE WPs 1 & 2.
Clinical/Scientific Demonstrate and apply a thorough understanding of the scientific principles involved in translational bioinformatics and genomics.
Lead the development, implementation, population, maintenance, validation/verification and utilisation of NGS analysis software and databases to acceptable standards of quality and accuracy suitable for the analysis and interpretation of sequencing data generated by the NoE WPs 1 & 2 such that they are suitable for business-as-usual clinical implementation within Central &South (C&S) and other GLHs.
Oversee the development of bioinformatics pipelines for NoE WPs 1 & 2 to nationally accepted Standards (UKAS or equivalent) in a timely and efficient manner.
Take responsibility for the review, validation/verification and implementation of highly complex and specialist bioinformatic software, tools and applications, and internet resources applicable to medical genetics, to annotate genomic data and aid in the interpretation of novel sequence variants relevant to NoE WPs 1 & 2.
Independently check and validate the bioinformatic findings of registered scientists, non-registered scientists and genetic technologists.
Aid the development and maintenance of external IT systems and accessible databases of relevant scientific and clinical information.
Employ best practice in utilising project management and scientific software development methodologies to create robust, fast, and efficient IT systems and processes that meet the needs of the service.
NB The above duties are likely to require the post-holder to use visual display equipment for long continuous periods of time on most days.
Liaise with other stakeholders both within the laboratory, C&S GLH, Genomics England, NHS Genomics Unit and beyond to identify opportunities for improving genomic services by evaluating new technologies, algorithms, newly commissioned tests and automation of workflows.
Act in an advisory capacity to colleagues outside of the department and outside of the Trust on all bioinformatic aspects of NoE WPs 1 & 2.
Responsible for the development of documentation and training to ensure the bioinformatics pipelines developed for NoE WPs 1 & 2 adhere to GLH Quality Policy and standards.
Co-ordinate collaborative projects that involve sequencing platforms with outside researchers, university investigators, including bioinformatics analysis and data transfer.
Data Management / Clinical Governance Plan, manage and organise own workload to meet priorities and ensure timely completion.
Take responsibility for the accuracy of own work.
The post holder will collaborate with all other staff, to be an effective team member, and achieve optimal use of resources.
Maintain responsibility for writing, updating, and communicating Standard Operating Procedures relating to procedures involving the use of bioinformatics for diagnostic purposes.
Ensure the accuracy and timeliness of all patient results related to the NoE WPs 1 & 2.
Use judgement skills to assess the impact of any trends identified and be able to initiate investigation and remediation.
The post-holder needs to recognise that their role in NoE WPs 1 & 2 is significantly contributing to the development of data which is used to make treatment decisions for patients not just locally but also nationally.
Through deployment of their developed bioinformatics tools in NoE WPs 1 & 2 they are informing access to high-cost medications and patient management strategies.
Ensure the safe and secure storage and retrieval of patient data within the Laboratorys data management systems and that the laboratory complies with requirements of data protection, in accordance with the Data Protection Act and relevant Information Governance policies.
Monitor data storage levels and plan for future increase in capacity.
Lead on any relevant internal and external bioinformatics Quality Assurance testing schemes for NoE WPs 1 & 2 to ensure the highest standards of molecular genetic testing.
The post-holder will also be responsible for transfer of data to national repositories ( Genomics England storage cloud) where appropriate to optimise analysis capabilities.
Maintain responsibility for detailed and rigorous record-keeping, including accurate recording of programming, pipelines, metadata associated with sequencing runs, and strict adherence to quality standards and guidelines.
Support the Quality Manager by leading on quality management relating to NoE WPs 1 & 2 NGS data analysis, storage, root-cause analysis, troubleshooting, audit and managing incidents.
Take a proactive role in maintaining high quality standards to ensure maintenance of the laboratory UKAS accreditation status.
Comply with the departmental risk management and risk reporting strategy within the bioinformatic teams(s) which includes health and safety, quality management, training, recruitment, internal quality control, patient and laboratory records including confidentiality and consent, reporting to the laboratory director.
Propose and implement changes that impact on own and wider specialist area by actively participating in cross-departmental, Trust-wide, GLH-wide, and national training to support development and continuous improvement of best practice in all aspects of bioinformatics Innovation, research, and development Undertake planned and agreed research and service developments relevant to NoE WPs 1 & 2 under the direction of Consultant Head of Laboratory and Clinical NoE leads.
This will include collaboration with third party academic and commercial organisations.
Maintain up to date knowledge of developments and research in the field of expertise to identify and implement translational projects that will bring innovation for the benefit of the services and patient.
Collaborate with research and clinical leaders in the field within OUHFT and the University to contribute to the research aims of the department and the other associated bodies , GMSA.
Present findings/data from case studies, audit and research projects to local/national/international meetings and conferences and through publications in peer reviewed journals Where appropriate lead or assist in the development of new collaborations (including using own network of contacts) and funding bids to help deliver the aims of NoE WPs 1 & 2 and expand the influence of this work.
Education and Training Design and implement the necessary national training programmes around the NoE WPs 1 & 2 national implementation.
Participate in training meetings with other trainers and the Training Officer to ensure a co-ordinated approach and effective delivery of training.
Professional To maintain, or be actively working towards, State Registration with HCPC and to employ all the competences required of a registered Clinical Scientist.
Participate in regular performance review and personal development planning Undertake CPD activities, taking measures to acquire, improve and apply scientific skills and expertise to perform the job to the highest level of quality and reliability; this includes attending internal training sessions, relevant external meetings, courses, study days and conferences, and keeping up to date with current journals and literature Demonstrate emotional resilience in a range of distressing circumstances as experienced through management of the service, and provide support/leadership to other members of staff Display high standards of conduct, behaviour, and professionalism always in line with Trust policy and to promote a culture of compassionate excellence within the department Person Specification Qualifications & Training Essential PhD level education which includes a substantial component of genomic analysis Desirable Professional registration with HCPC Experience Essential Significant experience of developing and implementing pipelines in clinical, academic or industry settings to analyse genomic data for both targeted assays and Whole Genome Sequencing in haematological malignancies.
Desirable Experience of working in genomics analysis at the research / clinical interface.
Skills & Knowledge Essential Excellent skills in coding / programming, mathematical modelling, database construction and how to apply these skills to clinical genomics.
Desirable In depth knowledge of the biology of plasma cell dyscrasias.
Abilities Essential Ability to communicate complex bioinformatic, scientific and confidential information and make the case for change to specialist and non-specialist audiences who may be resistant to new approaches.
Desirable Ability to manage conflict