Boost for data science training for researchers and healthcare professionals working in pathogen genomics

A Wellcome Connecting Science collaboration with the Centre for Genomic Pathogen Surveillance receives a UK Research and Innovation grant to support urgent capacity building for data science applications in pathogen genomics and surveillance

Genomics is fast becoming pivotal to the work of researchers and healthcare professionals in the UK. However, there is a growing skills gap in their application of genomics and data science tools to understand and manage disease. As the incorporation of big data and genomic sequencing is now common in healthcare, the need for training to support the increasing demand for analysing and interpreting complex data has become imperative.

In the field of infectious pathogens, fast and large-scale delivery of genomic sequence information underlines the importance of strengthening capacity for pathogen data science skills, in order to guide clinical care and for the accurate and timely provision of public health interventions. Thanks to a grant awarded by UK Research and Innovation (UKRI), a collaborative training initiative between the Centre for Genomic Pathogen Surveillance (CGPS), Big Data Institute, University of Oxford and Wellcome Connecting Science aims to scale-up accessible training skills development using a Train the trainer approach, specifically designed for pathogen genomics and surveillance. This innovative collaboration will focus on equipping professionals with relevant competencies to train others through the application of standardised guidance and digital training resources. Combining their expertise in development of genomics software tools and training delivery, CGPS and WCS will build upon a successful collaboration on a Train the trainer course in 2019, which aimed to strengthen capacity for genomic surveillance of antimicrobial resistance in low and middle-income countries.

Genomic Surveillance of Antimicrobial Resistance - Train the Trainer Course (2019)

The new project entitled Train the trainer – Data Science for Pathogen Genomics and Surveillance (T3Connect) will train researchers, healthcare and academic professionals in effective dissemination of basic and applied data science skills for pathogen genomics in the UK. This approach provides an effective framework for scaling up the capacity for analysis and interpretation of genomics data useful for the management and surveillance of infectious diseases. Developing training resources which are accessible and compatible with the professional demands of scientists and clinical staff is a key objective for the successful expansion of genomics data science training.

The funded training programme will apply a blended format consisting of a combination of online and face-to-face training, and will involve:

1. Implementing a series of Train the trainer courses to promote forward direct training, by providing researchers, educators and healthcare professionals, with the skills to train other professionals in data science applications for pathogen genomics.

2. Cultivating a community of professionals that offer training, mentorship and networking opportunities in pathogen genomics and surveillance.

3. Building and publishing freely available training resources that are accessible to all professionals.

Our Train the Trainer approach provides a sustainable and scalable solution to developing training skills tailored resources and mentored networks for genomics and data sciences. Collaborating with The Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, and in consultation with relevant stakeholders, the project will build lasting strategies to strengthen capacity for data science for pathogen genomics through trainer communities, thereby expanding the potential for wider reach and impact in healthcare.

Alice Matimba (Wellcome Connecting Science) 

This project builds upon previously developed Train the Trainer methods focused on genomic surveillance of antimicrobial resistance and will enable broadening of the approach for pathogen genomics, data science and surveillance more generally. We are excited to collaborate with the Wellcome Genome Campus Advanced Courses and Scientific Conferences to engender this route to training and delivery.

Professor David Aanensen from The Centre for Genomic Pathogen Surveillance, University of Oxford

Wellcome Connecting Science

Wellcome Connecting Science’s mission is to enable everyone to explore genomic science and its impact on research, health and society.

We connect researchers, health professionals and the wider public, creating opportunities and spaces to explore genomic science and its impact on people. Connecting Science inspires new thinking, sparks conversation, supports learning and measures attitudes, drawing on the ground-breaking research taking place on the Wellcome Genome Campus.

Big Data Institute

The Big Data Institute is located in the Li Ka Shing Centre for Health Information and Discovery at the University of Oxford. It is an interdisciplinary research centre that focuses on the analysis of large, complex data sets for research into the causes, consequences, prevention and treatment of disease. Research is conducted in areas such as genomics, population health, infectious disease surveillance and the development of new analytic methods. The Big Data Institute is supported by funding from the Medical Research Council, the UK Research Partnership Investment Fund, the National Institute for Health Research Oxford Biomedical Research Centre, and philanthropic donations from the Li Ka Shing and Robertson Foundations.

Further details are available at

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