Recap from the Consumer Genetics Show: Illumina Gets Personal in Advance of the Coming Bioinformatics Bottleneck

The first annual Consumer Genetics Show took place last week (June 9-11) in Boston, MA. With much anticipation — and some uncertainty about what to expect from the inaugural event — research, commercial and thought innovators from across the country came together to discuss the present and the future of consumer genetics technologies and services and the research and science that is driving the development of those technologies.

Highlights from the show — which was attended by most of the GLR team — included Francis Collins’s anonymous genome sequencing and Zak Kohane’s discussion of the “Incidentalome.” In addition, the GLR’s own David Clark presented a well-received talk on the Emerging Legal Issues in the Expanding Genomics Space.

But arguably the most newsworthy event of the show came courtesy of Illumina’s  CEO, Jay Flatley, who officially launched Illumina’s personal genome sequencing service. The announcement was covered extensively by Genetic Future, Forbes, GenomeWeb and others, and Illumina has produced its own site — http://www.everygenome.com/ — to explain the service. The short version is this: for $48,000 — just under half of the previous low-water mark of $99,000 established by Knome earlier this year — consumers can purchase a whole-genome sequence and, after consulting with a physician, completing a consent form and confirming their interest after a one-week waiting period, have it delivered to them on their own Apple iMac.

Illumina's personal genome sequencing service

Illumina's personal genome sequencing service

But perhaps the most interesting feature of Illumina’s service is what you don’t get for your $48,000 investment. Although your iMac comes loaded with some 3 billion base pairs representing your genome, Illumina does not provide any data interpretation, relying on third party providers to assist consumers and their doctors with the all-important process of attempting to understand the significance of all of those newly-delivered As, Ts, Cs and Gs.

As Daniel MacArthur points out in his superb piece over at Genetic Future, Illumina is providing a consumer-facing service while simultaneously outsourcing the most important component of the consumer relationship to its DTC competitors 23andMe, Knome, Navigenics and deCODEme:

Sequencing a whole genome with short-read technology is difficult, but the real challenge is the next bit: translating the assembled sequence into useful information. Illumina will not be doing the interpretation of genome sequences themselves, but will instead draw on the expertise of relatively well-established personal genomics companies 23andMe, deCODEme, Navigenics and Knome. Customers will apparently have the option of choosing which of these providers they go through for their analysis, who can then add their own additional fees for this crucial stage.

I can see why farming out interpretation is an attractive option, given Illumina’s major strength in sequencing technology and the enormous investment in databases and people required to build up a complete interpretation service, but in focusing on the sequence generation side Illumina (like Complete Genomics before them) is restricting itself to the least attractive segment of the personal genomics market. Sequence generation is a competitive space dominated by a single bottom line: whoever can generate an accurate genome sequence more quickly and cheaply than its competitors wins, and there is no room for complacency; there will always be new technologies popping up over the horizon. Illumina has carefully invested in third-generation technologies to keep its edge, but there’s no guarantee that this will last.

Interpretation, on the other hand, is a niche with nuance: here there is more than one axis of competition, and potentially a much slower decline in profit margins. At current rates of progress it is only a matter of years before generating a genome sequence costs in the tens of dollars; since most people will only need their genome sequenced once* very cheap sequencing will rapidly result in a depletion of the sequence generation market. Interpretation, on the other hand, is the gift that keeps on giving: as new research uncovers more details about the functional portions of the genome and their interactions with environmental risk factors customers will always need their reports updated and re-analysed in increasingly more sophisticated ways.

Illumina’s consumer genomics service, which straddles the fence between sequencing and interpretation, is neither unique nor surprising. In some respects Illumina is merely joining Knome, albeit at a lower-for-now price point, as a provider of whole-genome sequencing to consumers. But as it at least contemplates shifting its focus from its traditional area of expertise (data generation) to a potentially larger and longer-term market segment (data interpretation), Illumina’s actions reflect a much broader trend in the field.

At the Biology of Genomes meeting in early May, Daniel MacArthur reported in the journal Genome Medicine that “the single dominant message emerging from [the meeting] was simple: advances in DNA sequencing technology are now enabling the generation of biological data at a frightening (and accelerating) pace. Increasing sequencing capacity promises rapid advances in biological understanding, but it also brings tremendous challenges in terms of storing, disseminating and analyzing vast quantities of data.”

The challenges of extracting meaningful understanding from mountains of data is a theme that has been picking up steam within both the research and commercial genetics communities for some time.  It’s a theme that was emphasized earlier this month at the AAAS/FDLI colloquium on Personalized Medicine and echoed again at the Consumer Genetics Show. While the race to generate data is at full throttle, the market for interpretation and functionalization of that data appears to be both larger and less well-developed, leaving the door open for new entrants both big and small.

Recently, for instance, Washington-based CombiMatrix decided to abandon its core business of developing microarrays for sale to R&D laboratories — ceding that business to equipment manufacturing giants Illumina and Affymetrix — and to reinvent itself as a supplier of cancer diagnostic services directly to physicians and other medical providers. Another Washington-based company, Microsoft, recently announced its acquisition of Rosetta Biosoftware from Merck, a move intended to provide needed expertise in the development of Microsoft’s own Amalga Life Sciences data management and integration platform.

Nearly unthinkable less than a decade ago, most academic and commercial leaders now believe that the era of the $1,000 genomic sequence is now just a matter of time, with its arrival expected as early as the end of this year (George Church) or, more conservatively, by 2015 (Francis Collins, as announced during his keynote address at the Consumer Genetics Show). But powerful technologies and plummeting costs mean that a bioinformatics bottleneck is almost certainly looming.

What will bear watching over the remainder of 2009 and into 2010 is whether and how emerging and existing companies, including Illumina, work to position themselves to provide the all-important service of funneling the coming tidal wave of genomic data through new interpretive tools and services, leaving consumers with a manageable, informative and personalized understanding of their genomes.