Does Illumina Have the First $1,000 Genome? – MIT Tech Review

Article link: http://www.technologyreview.com/news/523601/does-illumina-have-the-first-1000-genome/?utm_campaign=newsletters&utm_source=newsletter-daily-all&utm_medium=email&utm_content=20140115

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.
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 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 price, 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 price tag 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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By timmreardon

One comment on “Does Illumina Have the First $1,000 Genome? – MIT Tech Review

  1. Dear James,I’m glad that you are appreciative of the reselae of the peach genome, and recognize the high quality of this genome. The peach genome v1.0 represents a major effort by numerous labs around the globe. Please rest assured that we are aware of the unique and special nature of the peach genome, and what it has to offer the plant community.As such, we are gratified that you are restraining yourself from a lot of simple stuff I could do in a couple of days that would steal a lot of thunder out of what’s in the usual genome paper . Having said that, those types of analyses and the material in this blog, while it does not seem to jeopardize any planned publications, is not in the spirit of the Fort Lauderdale agreement. The comparative analyses on CoGe are blatantly violating that spirit, and I have requested that it be removed from the public domain. I hope that you and other scientists will respect the International Peach Genome Initiative’s desire to make the data available to the research community, while simultaneously keeping certain analyses protected for the researchers who produced the data.Now that that’s out of the way, to Party Cactus: the diversity that exists in peach is very broad, and includes genotypes that do not produce a stone. Unfortunately this trait has not been incorporated into developed varieties. There are also varieties that produce a sweet pit not unlike almond (sister species), but I don’t believe anybody has worked on incorporating that trait into a peach variety, the stones are rather tough after all. Regardless, these traits are likely to be incorporated into accepted peaches without GM in the future. Other interesting traits that occur in peaches that you may not be aware of: weeping form (like the willow), doubled flowers (like the rose), I could go on. To make a long story short, it is amazing that so many forms and biotypes can exist with so little DNA!I wish the same could be said for plum pox virus. I am not aware of any resistant peach germplasm to that disease, and the US is in continued danger of having the disease occur. The USDA plum that is mentioned above is highly promising and will hopefully be successfully field tested in Europe in the coming years for durable PPV resistance. If the mechanism for resistance is robust, it will likely be incorporated into other stone fruits and into US germplasm to protect against any future US PPV outbreaks.In closing, thanks for your interest in peaches and the peach genome, and rest assured we are working on the publication!Best regards,Bryon SosinskiCo-coordinator for the International Peach Genome Initiative

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