This month, the Wessex Genome Medicine Centre, based at University Hospital Southampton, will have been open for a year. It has seen nearly 450 people stepping forward to have their genomes analysed.

100,000 Genomes

The centre is the South Coast node of the 100,000 Genomes project, a Government sponsored transformation plan to introduce genome testing into NHS care and change the way patients are treated. The project has focused on rare inherited diseases and cancer as this is where genome analysis is likely to provide early results that make a difference.

However, as one of the main issues is interpreting the relevance of genome differences between humans, being able to amalgamate data on 100,000 samples will make a big change to our knowledge of what is important for disease and what is normal variation. In this way every single sample will tell us more and the hope of the project is that genome testing will change our approach to diagnosis and direct personalised treatment.


There are some challenges in introducing such testing into routine care which the Southampton team recognises. Do patients understand the extent of the information that the test can provide, for example, identifying new risk factors for diseases that had not been considered previously?

The Faculty CELS team, led by Anneke Lucassen, is researching how patients cope with this knowledge in an extensive study on the ethics of genome testing. How do we assess whether a genomic variant is the cause, a consequence, or an incidental finding?

Many scientists in the Faculty are developing tools to demonstrate how a genome variant changes function. For example, Diana Baralle has a ‘splicing pipeline’ project making some genome variants easier to interpret. The genome informatics research group, led by Sarah Ennis, is researching new ways to optimise picking out novel disease-causing DNA variation. Furthermore, every patient in the study has agreed to have additional blood samples taken for other ‘omics samples (to look at proteins, molecules that bind to DNA, and RNA species) and so are an important potential source for computer science based approaches to disease discovery e.g. Ben MacArthur and his team using mathematical methods to understand cellular dynamics.

Cancer genomes

The cancer arm of the project is changing the way we work and showing the vital role played by cellular pathology in assessing which tissue should be analysed and how to optimise it once it leaves the body, work led by Emily Shaw. Without this step the genome analysis is irrelevant. The project benefits from Christian Ottensmeier who established a pilot genomes project in lung cancer using the same processes and analyses are currently underway.

Cancer genomes still need significant research to be used in the clinical setting but increasingly, treatment trials are now stratified by genome variants and this is likely to be the future direction as our understanding improves.

Major opportunities

So what started out as a NHS project, with clear aims to improve patient treatment, has also provided major opportunities for basic and translational research which Southampton is particularly set up to capitalise on. Furthermore, the new MSc in Genomics Medicine, run by the Faculty of Medicine is teaching the next generation to use the data effectively.

The first genome sequences from the project are eagerly awaited. It might take time for these to impact treatment but it is so important to establish the processes, make discoveries so that we become more effective and above all be part of the vanguard that are starting to try.

100,000 genomes

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