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Illumina's New DTC Sequencing Service Addresses Ethical Quandary by Requiring Prescription


BOSTON — In launching its consumer whole genome sequencing service this week, Illumina will involve the physician much more directly in educating and advising its customers than other direct-to-consumer genomic firms currently do.

Debuting the service here at the Consumer Genetics conference, Illumina said that it will charge $48,000 to analyze patients' DNA by whole-genome sequencing. But unlike DTC genomics firms, which allow customers to order gene scans over the Internet and receive sample collection kits in the mail, Illumina’s service will require a prescription from their doctor or from a physician in Illumina’s Personal Genome Network before obtaining their genomic-risk data.

Illumina will do the primary raw data analysis, but offer its customers the option of going through four DTC genetic companies — 23andMe, Navigenics, Decode, Knome — to learn about the risk and potential lifestyle impact conferred by their gene variations.

“We’ve learned some things from the regulatory challenges that the DTC companies have faced,” Illumina CEO Jay Flatley told Pharmacogenomics Reporter at the conference.

Health regulators from California and New York warned several consumer genomics firms last year for directly marketing genetic screening services to state residents without the involvement of a licensed physician.

DTC genomics firms have argued that they employ physicians who order the genetic tests bought by customers through their websites. However, industry observers have stressed that customers' own physicians, not just those employed by genetic testing firms, should be involved in interpreting an individual's genetic risks [see PGx Reporter 06-25-2008].

Illumina’s approach is a hybrid of the DTC and medical genetic testing model. “We’ve spent a year with our ethics company helping us understand what is the best way to go about this, [figuring out] what’s the most responsible way to go about this,” Flatley said.

He added that Illumina plans to meet with the US Food and Drug Administration to get advice on how to structure the DTC aspects of its business and involve the physicians.

As Illumina's process currently stands, once the firm performs the genome sequencing and customers have discussed the preliminary data with their physicians, they will have the option of signing up with one or more of the DTC consumer genomics firms to learn more about their genetic risk associations.

“All these companies have different business models, but whatever they charge will be incremental to the $48,000” fee for sequencing through Illumina.

As of May, Knome’s whole genome sequencing service cost $99,500, 23andMe’s Personal Genome Service cost $399, Navigenics’ HealthCompass Service cost $2,500, while its pared-down Annual Insight offering is $499. Meanwhile, Decode charges $985 for a complete scan of one’s genetic risk for 38 diseases and traits, $225 to scan for cancer genes, and $195 to scan for genes related to increased risk for various cardiac conditions.

It is unclear if DTC firms will offer a different price point to Illumina sequencing customers.

Prior to this sequencing collaboration, many of the partners were already working with Illumina.

Decode and 23andMe use Illumina’s genotyping chips in their services. Knome, for its whole-genome sequencing service, oursources sequencing to BGI, which mainly uses Illumina technology. Navigenics uses Affymetrix chips for its genome scans.

Flatley noted that in five years, sequencing technology will be as ubiquitous in labs as PCR.

Illumina decided to launch its whole genome sequencing service because “costs have come down enough to make this accessible to a thin slice of the market,” he noted.

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Also, by operating the service with a small number of customers, the industry will be able to gain experience with sequencing technology, and “perfect the process before large-scale use.”

The Illumina Process

Customers interested in getting their genome sequenced can visit Illumina’s website (, which will direct them to call a hotline and speak to a representative. The Illumina representative will tell the customer to either speak to a physician within Illumina’s Personal Genome Network or their own doctor. If customers choose to speak to their own physicians, Illumina’s Flatley said the company will educate them about its service.

Once customers have discussed the sequencing service with a doctor, they can then order a sample collection kit from Illumina’s website, which the company sends to the doctors along with consent forms. The customers will work with genetic counselors and physicians to understand the literature, sign the consent forms, and pay Illumina half of the service fee.

At this point, Illumina gives customers seven days to think over the material discussed and change their mind about investing nearly $50,000 to learn about their genetic risks. “It’s sort of like when you buy a car you have a couple of days to change your mind,” Flatley said. “We want to make sure the consumer has time to think about this and if they want to change their mind, they can.”

After the week, if the customer agrees to go through with the service, the physician must write a prescription for a human genome sequence, and collect blood and saliva samples.

“The prescription is required. The prescription will come into Illumina and be the order to run the sequence,” Flatley explained. The first doctor’s prescription for a human genome scan was written for Flatley, as he was the first person to be analyzed under Illumina’s sequencing service.

The samples arrive in anonymous packaging, so the laboratory will not be able to link samples to an individual.

Illumina also runs the samples through its genoyping chips. “We do this to match the samples up at the end, to make sure the samples are the same,” Flatley said.

Approximately two to three months after the samples are sequenced, Illumina will send the results to the physician to be shared and discussed with the customer.

Addressing Ethical Quandary

Integral to customers getting their sequencing data through Illumina is the involvement of physicians. Thus, it will be critical to educate doctors about Illumina’s service, Flatley noted.

“We will qualify physicians around the country who are trained in the Illumina process,” he said. Illumiina plans to train physicians and bring them into its Personal Genome Network through out major US cities in the next three months. In the coming months, the company plans to extend its training program nationally and internationally.

The American Medical Association issued a statement last year opposing the kind of direct-to-consumer genetic testing offered by firms like Navigenics, 23andMe, and Decode Genetics’ DecodeMe. The group’s policy states that genetic susceptibility testing marketed directly to consumers should be performed under the care of a qualified health-care professional [see PGx Reporter 08-20-2008].

As the field evolves, “it could be in the long-run that [physician involvement] is not a requirement,” Flatley said. “We thought it’s better for us to do it this way in the beginning, to take the highest road we could find.”

Flatley noted that Illumina plans to hold meetings with the FDA about how to structure the DTC and physician involvement aspects of its service.

The FDA has said it is watching the bourgeoning field of DTC genomic testing with interest but has not expressed any intent to regulate the field. In the absence of federal guidelines regulating the field, some DTC genetic testing firms have come together to standardize certain aspects of their business. Each company still has their own way of calculating and reporting genetic risk, however [see PGx Reporter 04-15-2009].

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By involving physicians from the launch of its personal genome-sequencing service, Illumina is preparing for any potential regulatory changes down the line.

“The challenges will be when people start to use these data sets clinically,” Flatley said.

“What we have to be aware of as time goes by, the data sets being produced by the DTC genetic companies and Illumina will be increasingly valuable from a diagnostic and prognostic perspective,” he added. “How do you do clinical validation of a whole-genome? That’s not really possible to do. So, we need to evolve the thinking of the FDA and others about how clinical data sets are used.”

Flatley noted that he didn’t foresee federal regulations for the field in the near future.

“We want to get involved with the FDA to sort of get ahead of that problem to figure it out now while the [data] volume is low and this isn’t a massive market yet,” he explained. “So, when the big opportunity comes down the stream we’ve got that worked out.”

What DTC Firms Do Best

In partnering with Knome, 23andMe, Decode, and Navigenics, Illumina is taking advantage of what the instruments provider and the DTC firms are best equipped to do.

The sequencing analysis, done at 30x coverage, will be performed at Illumina’s own CLIA-certified laboratory. Through an iMac interface, Illumina will initially report to consumers the “primary data,” including comparisons between the sequence with the reference genome, SNP detection, structural variants in the genome, and copy number variations.

“So we’ll provide that raw set of information,” Flatley said. “But what we won’t do or have no plans to do in the future is connect that data with medical outcomes, with traits.”

Particularly since Illumina’s iMac interface might be “a little bit intimidating” for most customers, they will have the option of signing up with a DTC genomics firm, with a more consumer-friendly interface, to learn more about their genetic risk associations.

The DTC firms will “be working with us to provide the consumer layer on top of our datasets,” Flatley said. “The consumer can choose to use all of them, one of them, or none of these companies if they like,” he added.

Initially the DTC firms will be extracting from Illumina’s sequencing data the same types of data that the companies analyze through their chip scans. “Because the sequencing gives you everything, over time [the DTC firms] will be able to give more information that they couldn’t give customers through their genotype chips,” Flatley said.

“They can put in more information on structural variation, more pharmacogenomics information, so the richness of the data set will improve over time,” he added.

Flatley noted that Illumina will not be advising customers which DTC firm to go with. “We’re trying to level the playing field here,” Flatley said.

Illumina is also in the process of designing an iPhone application that will allow consumers to check and share their personal genome for genetic markers related to ancestry, traits, and health on their phones as those data get updated. Flatley demonstrated a prototype of the iPhone application at the conference but did not say when the technology might be available for consumer use.

An iPhone application of his type would certainly be step closer to introducing genomics to a much broader, mainstream audience.

“If people are spending too much time analyzing their genomes at work and their boss walks in, all they have to do is shake [their iPhone] and the data will be gone,” Flatley quipped.