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British Government Picks Illumina to Sequence 100,000 Genomes

The world’s largest genome project will be carried out on instruments from the California sequencing company.

The British government says that it plans to hire the U.S. gene-sequencing company Illumina to sequence 100,000 human genomes in what is the largest national project to decode the DNA of a populace.

Gene machine: A sequencing instrument from Illumina can decode a genome in a day.

In a regulatory filing with the U.S. Securities and Exchange Commission, Illumina said it had been picked as the “preferred partner” for the £100 million project.

Genomics England confirmed that it had chosen the California company to carry out the sequencing project. “We’ve been through the ‘bake-off’ process to find the right company to do the sequencing, and will now be entering detailed negotiations,” says Vivienne Parry, a spokesperson for Genomics England.

Illumina’s sequencing instruments dominate the market for unraveling DNA (see “50 Smartest Companies”). Parry says fewer than five other companies bid for the job, one of the largest sequencing projects ever undertaken.

Some other countries are also considering large national sequencing projects. The U.K. project will focus on people with cancer, as well as adults and children with rare diseases. Because all Britons are members of the National Health Service, the project expects to be able to compare DNA data with detailed centralized health records (see “Why the U.K. Wants a Genomic National Health Service”).

While the number of genomes to be sequenced is 100,000, the total number of Britons participating in the study is smaller, about 70,000. That is because for cancer patients Genomics England intends to obtain the sequence of both their inherited DNA as well as that of their cancers.

Genomics England began talking early this year to potential bidders, including Chinese company and Illumina rival BGI (see “Inside China’s Genome Factory”). At the time, the average cost of completing a genome was about $3,000 to $4,000.

Completing all 100,000 genomes would have cost more than twice Genomics England’s budget. The agency said in December it intended to use its negotiating power to drive prices down.

Illumina reacted by releasing a new system, the Hiseq X Ten, which it says would be able to sequence genomes for $1,000 each, crossing a long-anticipated price barrier (see “Does Illumina Have the First $1,000 Genome?”).

That system is actually 10 machines, each costing $1 million. By requiring buyers to invest at least $10 million in equipment, Illumina made sure the lower costs of its new system did not widely affect prices in other parts of the sequencing market, while letting it capture big national jobs like the one in the U.K.

According to users of the new Illumina system, the price per genome is still closer to $2,000 than $1,000.

Parry says Illumina will carry out the sequencing on behalf of Genomics England, and that the two would finalize negotations over the next two weeks. “It’s an enormously exciting project which is at the edge of technology. It’s not something that people have done before,” says Parry. “We will be at the limits of the technology.”

[Update 7/12/14: Illumina will carry out sequencing on behalf of Genomics England of 100,000 genomes. An earlier version of this article said incorrectly that Genomics England intended to sequence the DNA of 100,000 distinct individuals and that it would do so itself with instruments purchased from Illumina.]

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