Can the Scottish Genomes Partnership rival Genomics England?

Philippa Brice

14 January 2015

Scotland has declared ambitions to join the genomics revolution, in the form of a new £15 million collaboration.

Illumina, official commercial partner of the English £300 million 100,000 Genomes Project (100KGP), is also partnering with the Universities of Edinburgh and Glasgow to provide a facility with fifteen HiSeq X DNA sequencers. These high-throughput Illumina machines are currently the market leaders in low-cost sequencing, having been the first to break the crucial ‘$1000 genome’ barrier. Working at full capacity each full human genome sequence will reportedly cost under £750 to sequence, although this figure of course excludes data alignment, analysis and clinical interpretation (see Clinical whole genome analysis: delivering the right diagnosis).

Clinical focus

Whilst the 100,000 Genomes Project is focusing solely on cancer and rare diseases, the new Scottish initiative will also look at central nervous system (CNS) disorders and unspecified ‘population studies’, moving on to infectious disease agents (pathogens), plant and animal genomes. It is perhaps surprising that both projects are initially focused on human genome sequencing rather than pathogen genome sequencing, since the latter arguably offer the quickest means to deliver improvements in health protection and disease treatment.

However, in terms of health care cancer seems to be the dominant field for the SGP, since the partnership says that linking genetic and clinical information will enable more precise diagnoses and safer, more personalised treatment. Illumina CEO Jay Flatley commented that they would “better understand cancer and rare diseases and ultimately transform how they are diagnosed and treated”.

Infrastructure

The Scottish Genomes Partnership (SGP) is between the University of Glasgow’s Wolfson Wohl Cancer Centre and Edinburgh Genomics. Professor Jonathan Seckl of the University of Edinburgh said: “Edinburgh is home to the UK’s national supercomputer facility, which will provide the high performance data processing ability needed to analyse the vast volume of information that will be generated from this research”.

The University of Edinburgh’s press release notes that Scotland has ‘well established and approved methods of linking electronic health records to medical research programmes, governed by NHS and academic regulations’. The ScottisH Informatics Programme (SHIP) is a national research platform for electronic patient records, supported by the Information Services Division of NHS Scotland in partnership with the Universities of Edinburgh, Dundee, Glasgow and St Andrews.

Fair comparisons?

In some respects, comparing this new Scottish initiative with the 100KGP is not really appropriate, given the disparities between the two. The scale of both funding on the one hand, and the challenge on the other, are much greater for Genomics England than for the SGP. Moreover, the goals of the two may be somewhat divergent; whilst the SGP refers to the genomics revolution in healthcare and clearly has clinical goals, it also has ambitions to create a DNA sequencing facility for much broader-ranging research.

Conversely, the 100KGP is seeking not only to create a health-linked research resource with a view to wealth generation as well as the development of new diagnostics and treatments but also to set up a genomic medicine service for the NHS and bring benefit to patients. Sequencing aside, this is no mean task, with various barriers to be surmounted as set out by the Foundation’s Clinical genome analysis project.

Ultimately, the sheer size of the resource arising from the 100KGP should make it more valuable for health research, given the ambitions for full clinical interpretation. However, the much smaller size of the Scottish population combined with pre-existing links between electronic patient records and research could make the SGP a crucial test-bed for combining clinical whole genome sequencing with research. It could also yield early results in health-related areas that will not be pursued in the initial phases of the 100KGP.

Overall, the more clinical genome sequencing and analysis we have on national and international levels, the better. However, the rapid expansion of ambitious clinical genomics projects around the world underline the urgency of efforts to develop standards and mechanisms to facilitate data sharing across and between projects, as led by the Global Alliance for Genomics and Health.