On 26th October 2015 the BBSRC Veterinary Vaccinology Network hosted a Bioinformatics workshop at The Roslin Institute, Edinburgh. The workshop was attended by over 50 delegates from a variety of organisations around the UK and the USA. This workshop was held after a joint US-UK Funders and Research workshop hosted in Washington earlier on in the year had established the need for further collaborative discussions on applying bioinformatics to veterinary vaccinology. The aim of this workshop was to understand what is currently being worked on, what resources are currently available, highlight gaps in current knowledge and resources, and ultimately identify future research priorities.
Dr John Hammond, The Pirbright Institute opened the workshop by discussing the potential of functional genomics to improve animal health, setting the scene for the day. The workshop identified several aims including identifying pipelines and sharing methods within bioinformatics applicable to comparative and veterinary immune research.
Applications of studying bioinformatics in veterinary vaccinology were highlighted:
- response to vaccination v natural infection
- tissue or cell specific interactions
- markers or correlates of protection
- splice variation
Dr. Hammond's presentation led on to discussing the importance of characterising variable immune gene complexes including repetitive immune gene complexes, highlighting research on KIR and MHC genes. Dr Hammond emphasized that at present the human genome is used as a gold standard for research and there remains many gaps in livestock genome assembly and annotation. Of greatest scrutiny and target of improvement are the often variable genes associated with reproduction and the immune system. Further research should consider the quality of reference genomes used.
Dr Tim Connelley, The Roslin Institute outlined T cell receptor repertoire analysis identifying new bioinformatic programs including miTCR and MIGEC whilst a complementary presentation from Dr Anna Fowler, University of Oxford focused on collaborative work with The Pirbright Institute on analysing antibody repertoires in the absence of a germline sequence. Dr Adaikalavan Ramasamy provided a background on the transcriptomics facility based at Jenner Institute based at the University of Oxford and described current research on the analysis of immune function during vaccination.
The workshop also included presentations from scientists from the United States Department of Agriculture Animal Research Service. Dr Tim Smith, US Meat Animal Research Centre discussed the use of improving reference genomes with long read length sequencing methods including strategies to counteract assembly issues using hybrid strategies, piecing short reads together. Dr Derek Bickhart took this discussion further by discussing optical mapping technologies used with PacBio-based assemblies whilst Dr Tyler Thaker provided an overview of the work his research group have conducted on transcriptomic analysis of TB infection in cattle.
The final three presentations were conducted by researchers from The Roslin Institute, Dr Tom Freeman, highlighted network based analysis and visualization of biological databases. Notably www.biolayout.org and www.virtuallyimmune.org which includes a model of the influenza A life cycle and host defense systems. Integrating omics data between host and parasites were discussed by Dr Tom Michoel.
The final presentation of the workshop was presented by Dr Mick Watson who provided an overview of the recently established FAANG network (Functional Annotation of Animal Genomes Network). www.faang.org @faangomics. Dr Watson highlighted the aims of the network which includes standardising:
- Bioinformatic pipelines
- Pre-publication sharing of data
Before ending with a comparison of different transcriptomic mapping strategies, highlighting problems and potential solutions.
The workshop provided a platform to map out the current research in bioinformatics and will hopefully enable more joined up, collaborative approaches with regard to future research in the area.
Special thanks go to the staff at the Roslin Institute for supporting the workshop.
An official report of the proceedings will be published in the following weeks.
Photo: Dr John Schwartz - Postdoctoral Researcher, The Pirbright Institute with Dolly the Sheep