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Does Illumina Have the First $1,000 Genome?

Illumina announces a new high-end sequencer made for “factory-scale” sequencing of human genomes.

The $1,000 genome has been a catchphrase of the sequencing industry for years, but despite bold promises from different companies, this benchmark hasn’t been met. Now, thanks to a new sequencing machine from Illumina, it may finally be within reach.

Humans only: A new high-throughput sequencing machine from Illumina is optimized to sequence thousands of human genomes in a year.

At the J.P. Morgan Healthcare Conference on Tuesday, Illumina CEO Jay Flatley announced a new high-end sequencing machine that could accurately sequence whole human genomes at a cost of less than $1,000 each. Competitor Ion Torrent (later bought by Life Technologies) announced in 2012 that it had developed a machine capable of doing so (see “Device Brings $1,000 Genome Within Reach”), but that capability has yet to materialize. Illumina’s new machine is scheduled to reach its first customers in March. Faster chemistry and better optics—Illumina’s machines read DNA sequences by analyzing patterns of fluorescent nucleotides—have allowed costs to come down.

The $1,000 price tag is often seen as vital to making whole-genome sequencing cost-effective for medical testing and personalized medicine. At this cost, it might become reasonable for well-off patients to have their genomes sequenced for potential medical information.

Still, Illumina’s new machines will be out of reach for most labs. The ultrahigh-throughput sequencers will be sold in systems of at least 10 machines each, at a starting price of $10 million. According to Flatley, the $1,000 cost does take into account the cost of the machines, chemicals to do each run of sequencing, sample prep, and more. But these are machines intended to sequence tens of thousands of genomes each year.

Illumina emphasizes that the new machines will speed population-level genome sequencing for large projects aimed at understanding human disease and natural genetic variation. In his presentation, Flatley predicted an explosion of demand for “factory-scale” sequencing of human genomes. He pointed to a few large-scale projects already in the works, including the U.S. Veterans Affairs project to sequence the genomes of thousands of former soldiers  and the U.K.’s 100K Genomes project, which will sequence the genomes of National Health Service patients to help guide their care and to study genetic disease (see “Why the U.K. Wants a Genomic National Health Service”).

Researchers still struggle to understand how changes in DNA sequence cause disease and influence health. Large-scale sequencing projects can help reveal associations between a particular DNA variant and a disease or a healthy outcome. “Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine,” said Eric Lander, founding director of the MIT and Harvard genomics center the Broad Institute, in a released statement.

The Illumina machine was built specifically for human genomes, says Flatley, and it can sequence human genomes accurately enough to reliably identify DNA variants 10 times faster than its predecessor, another high-end Illumina machine. While other machines may sequence human genomes more quickly, they cannot produce the same quality of sequence data at that speed, says Joel Fellis, a senior manager of product marketing at Illumina.

Flatley says the new machine can partially sequence five human genomes in a day. A complete run takes three days, during which time it can produce 16 human genomes at a quality level widely accepted by the sequencing community.

This means that if just four labs were running 10-unit installations of the new machines in 2014, they could produce more human genome sequences than had ever been produced by all the other labs in the world, says Flatley.

The first three customers are all powerhouses of genome sequencing: Macrogen, a genomic services company in Seoul; the Broad Institute in Boston; and the Garvan Institute of Medical Research in Sydney.

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