Completing the Personal Genomics Toolkit
The big news buzzing through the world of genomics this afternoon is the publication of a paper in the journal Science announcing the production of three whole-genome sequences at an average materials cost of $4,400. The work was performed by the third-generation sequencing company Complete Genomics Incorporated, along with researchers from George Church’s lab at Harvard Medical School.
The Race for the $1,000 Genome
Erika Check Hayden of Nature’s blog The Great Beyond has an excellent summary of the Complete announcement in which she also attempts to head off some of the inevitable media hype:
Complete’s $4,400 price tag doesn’t include costs for the company’s infrastructure, such as its Silicon Valley data farm and the army of analysts and technicians required to make sense of the data; the company lists more than 60 employees in this paper’s author list. The company is actually selling genomes at $20,000 apiece in minimum orders of five; costs go down as the order size increases. That puts it slightly behind the schedule it set at its launch; the $5,000 genomes won’t be available until next year.
The announcement from Complete Genomics is hardly unexpected. At its launch last fall the company promised that it would deliver $5,000 genomes (and 1,000 of them, not just 3) by the end of 2009.
From a personal genomics standpoint, there is no question that Complete is a viable contender in the race to deliver affordable, individual whole-genome sequences. Spurred by competition from the likes of IBM, Illumina, Pacific Biosciences, Oxford Nanopore and others, the $1,000 genome continues to draw closer. It is no longer a question of if but when that magic number will be attained.
But while the $1,000 genome competition makes for an exciting horserace, the real focus of today’s announcement should be not on how much a genome sequence costs, but on what you can (or cannot) do with that sequence.
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Enabling Responsible Public Genomics
In the few short months since its launch, we’ve found the Genomics Law Report to be a flexible forum for discussing the legal implications of current developments in the fields of genomics and personalized medicine. Often what reaches the pages of the GLR, however, represents only the highlights from more detailed research and analysis that we undertake in order to thoroughly understand these issues and accurately advise our clients.
We have collected some of that more detailed research and analysis in a law review article, “Enabling Responsible Public Genomics,” to be published next spring in the journal Health Matrix: Journal of Law-Medicine. Here’s the abstract for the article:
Co-Founder Linda Avey Leaves 23andMe to Start New Alzheimer’s Foundation
DTC genomics company 23andMe announced late Friday afternoon that co-founder Linda Avey was leaving the personal genomics start-up, effective immediately, to begin work on a new foundation focusing on Alzheimer’s disease. Kara Swisher at BoomTown has the full scoop, including copies of internal emails to 23andMe employees from both Linda Avey and the company’s other co-founder, Anne Wojcicki.
The announcement is certainly fertile ground for speculation. Avey’s own email begins by recognizing “that [23andMe] has reached a critical point in its growth where new leadership can take it to the successful heights we all think it can achieve.” Which at least prompts the question: Was there some element of the old leadership (i.e., Avey and Wojicki) that was deemed incapable of reaching those heights? There has been no public indication that the move is related to 23andMe’s current financing round, which has included investments from Sergey Brin, Google’s co-founder and Wojcicki’s husband, and from Google itself.
Leveraging the Crowd to Understand Your Genome
Earlier this week Peter Aldhous of NewScientist magazine recounted an unusual experience with DTC genomics provider Decode Genetics. In reviewing his genetic data on the deCODEme website, Aldhous uncovered what appeared to be significant and bizarre errors in his mitochondrial DNA. Aldhous turned to Blaine Bettinger, The Genetic Genealogist, for help in diagnosing the problem with his mitochondrial DNA. Bettinger’s response: “This is a strange question, but are you sure this is Homo sapiens?”
Aldous, Bettinger and Decode investigated the problem and ultimately determined that the “errors” in the mitochondrial DNA were actually being introduced by a bug in the deCODEme software interface that allows users to browse their data. (Aldhous carefully points out that the software glitch was a rare one and that it did not seem to affect deCODEme’s disease-risk summaries or analysis.)
More than a simple software error, Aldhous’s experience highlights the complexity inherent in consumer genomes. Translating an individual’s saliva sample into a description of genetically influenced traits and risks is a multi-stage process with potential for error at every step in the chain. Or, as Daniel MacArthur of Genetic Future cleverly puts it, “There’s many a slip ‘twixt spit and SNP.”
Crowd-Sourcing vs. Open-Sourcing in Consumer Genomics
The New York Times yesterday described the emerging phenomenon of utilizing patient and online communities to jumpstart scientific research. In a previous post (Genomic Research Goes DTC) I discussed this trend, as well as a number of the legal uncertainties surrounding this new research model, particularly in the case of genomic research conducted by private companies.
That uncertainty is well covered in the Times article, thanks to Bob Cook-Deegan, Director of Duke University’s IGSP Center for Genome Ethics, Law & Policy, who strikes the proper balance in assessing the exciting but untested model of patient-driven research:
“I’m very suspicious of a company that has tons of private data getting too cozy with the drug or biotech industry,” he said. “But I don’t want to say it’s not going to work, because I can see all kinds of value that could come out of this.”
Where I found the article lacking, however, was in its description and presentation of the patient-driven genomic research model. As the Times describes it:
Supporters of this model—sometimes called crowd-sourcing or open-source research—call it democratization of research and say they are pioneering new models that put patients in control of their data and build bridges between researchers, patients and their doctors. (emphasis added)
It all sounds innovative and patient-friendly, but are “crowd-sourcing” and “open-sourcing” really interchangeable concepts? No, and conflating the two terms obscures one of the key features distinguishing patient-driven research from traditional modes of research.
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Genomic Research Goes DTC
The first generation of Direct-to-Consumer genetic testing and sequencing was populated by companies such as 23andMe, Navigenics and deCODEme that offered genotyping for a limited set of conditions, focusing primarily on genealogy and monogenic traits.
As the cost of generating genetic data continued to decline new companies brought new commercial offerings to the table, including whole-genome sequencing from Knome and, more recently, Illumina, and an increasing focus on the genetics underlying complex diseases and traits.
Recruiting Customers as Research Subjects
Even more recently a new dimension to the field of DTC genetics has emerged: Direct-to-Consumer research. In May of 2008 23andMe’s founders laid out their vision for customer-driven research. 23andWe, as the company’s research arm is known, launched its first significant project in March of this year when, aided by financial support from Sergey Brin, the co-founder of Google and the husband of 23andMe co-founder Anne Wojcicki, 23andMe announced a large-scale study aimed at the genetic bases of Parkinson’s disease. The study aims to recruit 10,000 patients with Parkinson’s disease to enroll. Participants in the study will receive 23andMe’s services for $25, a steep discount from the going rate of $399.
And on Tuesday, 23andMe announced what it is terming the “Research Revolution, a community outreach program that empowers people to drive the direction of genetic research.” In some ways this Research Revolution is genomic research meets American Idol, with the general public invited to vote by participating in the project and choosing from a list of 10 diseases to support. (Participation costs $99 for a stripped-down version of 23andMe’s service that does not include several key features, including ancestry information, carrier testing and access to the underlying raw genetic data).
