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Illumina Launches Personal Genome-Sequencing Service Using Genome Analyzer II


This article, originally published June 10, has been updated to include further information from Illumina and comments from Complete Genomics.

Illumina launched a personal genome-sequencing service last week, taking its first step from the research market into the marketplace for consumer genetics.

The company will offer its service for $48,000 on its Genome Analyzer II platform through a physician, and will conduct the sequencing at its recently CLIA-certified laboratory in San Diego. It will provide customers with a list of SNPs and structural variations in their genomes, such as insertions, deletions, and rearrangements.

Illumina will not provide, however, data-interpretation services, such as disease- risk assessments, ancestry analyses, or information about inherited traits. For that, it has teamed up with direct-to-consumer genomics companies 23andMe, Navigenics, Decode Genetics, and Knome. Customers can select from these non-exclusive partners to receive analyses of their data for an additional fee.

Illumina is not the first company to offer whole-genome sequencing to individuals — Knome has been providing such a service, including data interpretation, since early 2008 and currently charges $99,500 (see In Sequence 5/19/2008), and Medomics offers a "diagnostic genome" service at an undisclosed price, although it has not yet had a customer for it (see In Sequence 5/26/2009). But Illumina is the first sequencing-technology provider to open its service business to individual customers for non-research purposes.

According to Illumina President and CEO Jay Flatley, although the consumer market may currently be small, entering it now means the company can put in place the infrastructure needed for the future, when the cost of sequencing drops and the market grows.

"We believe it's time to begin to work on developing the infrastructure inside and outside of Illumina to enable it to work well," Flatley told In Sequence last week. This includes building a physician network, a data-analysis "ecosystem," and addressing regulatory questions and issues of clinical validation.

"We want to get in front of those issues and deal with them now, as opposed to when the market potential is huge, say, when we are at the $2,000 to $4,000 genome," he said.

That time may arrive soon, Flatley said. "We do recognize that at $48,000, this is not a big market yet, and that is accessible only to a few people, but … the price curves are very steep, so the prices will continue to fall."

Flatley suggested that the current market potential could be on the order of hundreds of customers. "We think there is quite a number of people who want to be among the first 10 named genomes in the world, or the first 100, or the first 1,000, so I think there is some market here," he said.

But Illumina's main goal for now is "to begin to open the discourse about how we are going to do this in the future, and use it medically within the appropriate regulatory and ethical infrastructures."

Customers interested in the service can learn about it on Illumina's website,, where they can also select a physician who is familiar with Illumina's process, as they will need a prescription to have the scan performed. Alternatively, they can choose to work with their own physician. Before the analysis gets underway, they will need to meet with their doctor to sign a consent form and service agreement, to provide blood and saliva samples, and to have the service ordered.

After a waiting period of at least seven days during which they can change their minds, customers receive an invoice and pay half of the service fee, and the doctor sends a written confirmation to Illumina to proceed.

The company will then sequence the customer's DNA, derived from the bar-coded blood sample, at 30-fold coverage, using paired-end technology on its Genome Analyzer II, and map the reads to the human reference genome. It will also genotype DNA from both the blood and saliva samples using microarray technology as an identity-match step. Samples will be analyzed at an Illumina laboratory in San Diego that recently became CLIA-certified.

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After completing the analysis, Illumina will send the results to the customer's physician on an Apple iMac computer, along with its GenomeStudio genome browser software, which allows users to look at their SNPs and structural variations but that is "very much designed as a research tool, not as a consumer-friendly web-based interface," Flatley said. Customers also receive an invoice for the remaining 50 percent of the service fee at that time.

Interpretation Options

Once customers receive their data from Illumina, the four data-analysis partners come into play. Customers can select any of the four to interpret the data in terms of disease risk, ancestry, or other traits, in most cases for an additional fee.

Once company that customers can hire for data interpretation is Knome, whose KnomeEssential service uses the same KnomeXplorer genome browser software that Knome empoys in its own genome-sequencing services.

In addition, the analysis will include customized reports for specific conditions at the request of the customer, Knome CEO Jorge Conde told In Sequence last week. Customers can also purchase annual update services. As of press time, Knome had not finalized the price of KnomeEssential.

The key difference between Knome's and other DTC genomic-service companies' analyses of the Illumina data is that "we have been working with full-genome information from the beginning," Conde said. "We already have the ability to analyze both common and rare SNPs, and can display any genomic-related data because we have already built the application."

Knome will continue to offer its own $99,500 whole-genome and $24,500 exome-sequencing and -analysis services, for which the Beijing Genomics Institute has provided the sequencing. Last week, Knome and SeqWright announced a partnership under which SeqWright will also provide sequencing services for Knome, performed at its CLIA-certified lab (see other article in this issue).

Knome's own services are more personalized than Illumina's, Conde said. They include, for example, a meeting with experts to help explain the results to customers. Also, Conde said, Knome does not store customers' genome data in a centralized database but provides it to them on a memory stick. It was not immediately clear whether Illumina stores the data after returning it to customers.

Finally, he said, Knome's offering is technology-agnostic. Although the company has mainly used Illumina's Genome Analyzer for its services so far, it has "also started to focus on [other] platforms that we can plug in our system, whether it's 454, SOLiD, or any other number of other approaches," he said.

Dietrich Stephan, co-founder and CSO of Navigenics, also stressed that his company's partnership with Illumina is non-exclusive. "We are going to be the company that sits on top of the genome and interprets the genetic risk factors, so they can be understood and acted upon in a medical setting," he told In Sequence last week.

While Illumina is the first, and currently the only, company that provides whole-genome sequencing data for Navigenics to analyze, "we are excited about the other technologies, specifically Pacific Biosciences," Stephan said.

He added that because whole-genome sequence data, unlike SNP-genotyping data, provides information on carrier status for monogenic disease, "it is absolutely critical to have genetic counseling surrounding that type of information, as it can be extremely devastating information." Navigenics provides such counseling as part of its service for Ilumina customers.

Navigenics has not yet set a price for analyzing data from Illumina's personal genomics service, according to Stephan.

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The company, he said, was built from day one "to have the ability to interpret the whole genome and deliver that information to individuals and their doctors. We have always known that the technology would evolve, and we would get to sequencing."

Illumina customers can also employ 23andMe, which until June 2010 will provide at no cost the same personal genome service to Illumina's customers as it does to its own customers, according to a company spokesperson. After that, the initial analysis will cost $499 for new customers, plus a $19.95 monthly fee.

23andMe's service interprets genotyping information from the customized array the company uses for its own offering, which includes some rare variants. As such, it will not take full advantage of the whole-genome data initially. However, the company may add more analyses in the future, the spokesperson told In Sequence last week.

No information about Decode Genetics' analysis services was available before press time.

Flatley's own DNA was the first sequenced by Illumina as part of the company's CLIA-certification process, and he plans to submit his genome sequence to a public database within the next few months.

The lab is in the process of sequencing three more individuals: Hermann Hauser, a partner of UK venture capital firm Amadeus Capital Partners, an investor of Solexa, who also plans to make his genome publicly available; Henry Louis "Skip" Gates, a professor and director of the W.E.B. Du Bois Institute for African and African American Research at Harvard University; and his father, Henry Louis Gates, Sr.

Illumina will be able to use customers' data anonymously in research studies, according to Flatley. Illumina's website states that providing de-identified data for research studies is optional. However, since the company is not collecting any phenotypic information, the data will be of limited use, for example for such purposes as discovering novel SNPs, he said.

"We won't have the ability to use it for doing the equivalent of genome-wide association studies," Flatley said.

In addition, Illumina plans to create a "social community for the education and exchange of information from those who have had their genomes sequenced," according to a company statement. At the Consumer Genetics conference in Boston last week, Flatley demonstrated how customers will be able to access and share their genome information on an iPhone.

'Where the Action Is'

Other firms are not as anxious to jump into the consumer market. Complete Genomics plans to launch its own human genome sequencing service this summer — priced at $5,000 per genome if multiple genomes are ordered — but intends to target the research rather than the consumer sector, at least in the short term.

"We really see the primary market today for complete human genome-sequencing services being still in the research community," Cliff Reid, CEO of Complete Genomics, told In Sequence last week. "Our primary focus is selling to academic researchers and pharmaceutical researchers."

"We really think that's where the action is today, understanding the genome, not providing people with information about their genomes."

He said that Complete Genomics, which had initially planned to launch its human genome sequencing service in late June, plans "a big announcement" sometime in July, relating to both its service and its fundraising activities. He did not elaborate.

In April, the company cut its expenses, including staff salaries, in response to a delay in its Series D funding round (see In Sequence 4/14/2008).

Since then, the company has not had any layoffs or decrease in its capacity, Reid said last week.