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Illumina Offers $10K Human Genome for Research; Sees 'All-In' $1,000 Genome in Three to Five Years

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By Julia Karow

Illumina is "routinely" offering human whole-genome sequencing services to researchers for under $10,000 under its recently launched Illumina Genome Network, and believes that the total cost of human genome sequencing will come down to $1,000 within three to five years, according to the company's CEO.

The company has also seen a growing interest in its Individual Genome Sequencing service — which is targeted at consumers and doctors and priced between $9,500 and $19,500 per genome — in particular for clinical applications, including cancer and to help diagnose inherited genetic diseases.

At the UBS Global Life Sciences Conference this week, Illumina CEO Jay Flatley provided an update on the company's human whole-genome sequencing service, which it offers through its own lab, as well as through subcontractors that are part of the Illumina Genome Network it launched this summer (IS 8/3/2010).

Flatley said that for Illumina, the human whole-genome sequencing service business will be "interesting in the next couple of years" but that it will probably remain "way smaller" than the instrument and reagent business. In the last six months, he said, the company has seen an increased interest among researchers to do large human whole-genome sequencing studies that involve on the order of 100 samples.

Illumina serves as the point of contact for researchers interested in sequencing services through IGN, and accepts projects comprising at least 50 samples, or pilot projects for studies of that size.

According to the website, the service includes whole-genome sequencing at 30-fold average coverage, using paired-end reads from a single short-insert library. Illumina provides an alignment of the reads, a list of SNPs and indels, a genotype report, data visualization, as well as raw reads and quality scores. For "premium data analysis," it refers to its network partners. Typical projects of 50 genomes "may be completed" in 12 to 16 weeks, and faster for a higher fee.

Researchers receive a quote from Illumina, along with a list of IGN partners who can perform the service. At the moment, the network consists of Illumina's own FastTrack Services Laboratory, Macrogen at the Genomic Medicine Institute at Seoul National University, and the National Center for Genome Resources. Illumina said previously that it is in the process of signing up additional partners.

Flatley said that customers will be offered a discount if they allow Illumina to subcontract the project. Asked to provide a price range for the service, he said that Illumina "routinely" offers it for under $10,000 now, partly depending on the volume of the project. Flatley said that its network partners do not bid against each other in the process.
According to the company's website, the per-genome cost "will be on the same level as a similar service done using less-accepted technologies performed by less-experienced users" — a veiled reference to Complete Genomics' human whole-genome sequencing service.

After receiving a quote, researchers rank-order the IGN partners according to their preference. Illumina then approaches the partners in that order, and once the project is accepted, customers send their samples directly to the partner and receive their data back directly from them. Illumina is responsible for billing for the service.

Personal Genomes for Clinical Applications

Flatley also offered an update on Illumina's Individual Genome Sequencing service. This spring, the company lowered the price for that service to $19,500 for an individual, $14,500 per genome for groups of five using the same physician, and $9,500 for individuals with serious medical conditions where a genome sequence could be of help in diagnosis or therapy selection (IS 6/8/2010).

To date, the company has sequenced the genomes of 24 individuals through the service, Flatley said, among them eight with clinical conditions. The proportion of clinical samples has been growing in part because of the price cut but also because of a growing scientific interest, Flatley said. Clinical samples sequenced to date include both cancer samples and their matched controls, as well as samples from children with a disease that could not be diagnosed otherwise and where there was hope "that sequencing will provide some additional insight." He added that the company is "beginning to use sequencing on a fairly regular basis" for clinical purposes.

Asked about the cost of whole-genome sequencing, he said that any HiSeq customer today can sequence a human genome for under $10,000 in reagent costs, based on reagent list prices. Large genome centers that receive reagent discounts can do the same "significantly cheaper," he added.

Within three to five years, Flatley estimated, the "all-in" cost of human genome sequencing will reach $1,000, including not only reagents but also bioinformatics, instrument amortization, and other costs. He did not say whether that target could be reached using existing sequencing platforms.

An estimated 400 human genomes or so have been sequenced at high coverage to date, he said, adding that those sequenced at low coverage could bring that number to as many as 4,000.

This week, Illumina launched a "World Personal Genome Registry" that aims to track the number of individuals sequenced. It currently contains 38 genomes, half of them named and half anonymous. Flatley said that the company hopes to hand the registry off to an "appropriate standards body" for hosting within six months.

The database contains only those individuals "who we have been able to track," he said, the majority sequenced using Illumina technology. It appears to be incomplete, omitting, for example, the genomes of several individuals sequenced with Life Technologies' SOLiD and Complete Genomics' sequencing technology.

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