Drawing on discussions about instruments, sequencing costs and projects at the ESRC Collaboratory on Next Generation Sequencing for Genomics, this posting questions the likely impact of the 100,000 Genome Project.
The discussion about instruments was stimulated by the image below, produced by Professor Adrian Mackenzie from Lancaster University.
This graph shows that most of the datasets in the SRA have been produced by Illumina instruments, the Illumina HiSeq2000 in particular. The dominance of Illumina-produced datasets deposited in the SRA has also been reported here.
Adrian posed the question, ‘Why does this graph look like this?’ The response was that it was not so much that Illumina instruments were superior, but rather a result of path-dependency. A significant factor in positioning Illumina was the use of its instruments for high profile sequencing projects, including the 1000 Genomes Project. As a result, more pipelines and infrastructures have been developed around these instruments which attracts others to use them, in addition to which using the same or similar instruments enables researchers to fully utilize existing datasets produced used them. The outcome seems to be some kind of stabilization with Illumina in a dominant market position.
The next discussion was about sequencing costs.
Most accounts of changes in genomics over the past 10 years refer to the dramatic drop in sequencing costs since the advent and diffusion of NGS instruments, typically using the data and graph produced by the NHGRI.
However, as Professor Neil Hall from the Centre for Genomic Research at Liverpool University pointed out, the steepness of the downward curve has in fact been leveling out. One explanation proffered at the collaboratory for this flattening was that Illumina’s dominance in the market reduced its incentive to reduce costs further.
Speaking about DNA variants for rare diseases, Dr Lucy Raymond from the University of Cambridge spoke about a pilot study for a major new sequencing project.
The new project, called the 100,000 Genome Project, plans to sequence the genomes of up to 100,000 NHS patients by the end of 2017 and link their genome data with their medical records. The project will be run by Genomics England Ltd (GeL). Wholly owned by the Department of Health, GeL has a dual remit. On the one hand its objective is to improve individual and public health through building the infrastructure for the delivery of genomics medicine. On the other, it seeks to encourage innovation, reduce sequencing costs, create jobs and bring investment to the UK.
As part of its strategy to drive down costs, GeL’s tendering process will encourage competition between next generation sequencing providers to operate and equip its sequencing centres .
So what is the likely impact of GeL’s strategy? Will competition between commercial providers of sequencing technologies drive costs down? Will a new market leader emerge? And if so, what will the impact be on existing infrastructures and pipelines and the costs of downstream processing and analysis?