Another Stop on the Road to the $1,000 Genome
The latest stop on the road to the $1,000 genome? San Francisco, CA, where J.P. Morgan’s 28th Annual Healthcare Conference is in full swing. There is an abundance of real-time Twitter coverage from the conference, but certain announcements warrant a more detailed discussion.
The announcement generating the biggest buzz today came from Illumina, Inc., whose CEO Jay Flatley unveiled a new genome sequencing machine, the HiSeq 2000. According to Matthew Herper of Forbes.com, Illumina’s new machine “will decode a person’s DNA in one week using $10,000 worth of materials – five times cheaper than any other competing gadget on the market.” Herper adds that the machines will begin shipping in February with a cost of $690,000 (compared to $500,000 for Illumina’s current model). Illumina’s own product page for the HiSeq 2000 provides more technical details, including coverage (~30x) and read length (2×100 bp). There have also been unconfirmed rumors that the machine will come equipped with an iPhone user interface, a concept that Flatley first pitched at last summer’s Consumer Genetics Show.
If it performs as advertised, the HiSeq 2000 is likely to be a huge hit with large genome sequencing centers, as evidenced by the announcement that the BGI (formerly the Beijing Genomics Institute) has agreed to purchase a whopping 128 of the new sequencing systems. But what, if anything, does the Illumina announcement mean for individuals consumers interested in receiving a complete genomic sequence?
Federal Privacy Regulation and the Financially Troubled DTC Genomics Company
Last month, the Genomics Law Report prepared a three-part series entitled What Happens if a DTC Genomics Company Goes Belly Up? The series, which was originally published on Genetic Future (see Parts 1, 2 and 3), reviewed the privacy policies of several genomics companies to determine whether they prohibit the transfer of private data to third parties. We also discussed the fact that a bankruptcy court may approve such a transfer notwithstanding a policy to the contrary. In this post, we examine whether federal regulations may restrict the dissemination of private genomic data—including the new rules proposed earlier this month under the Genetic Information Nondiscrimination Act of 2008.
1. Is DTC Getting HIPAA? The Health Insurance Portability and Accountability Act of 1996 (HIPAA), the most prominent federal regulation governing the privacy of medical records, established the Privacy Rule to provide national standards for protected medical records. HIPAA’s Privacy Rule currently applies only to “covered entities” and business associates of covered entities. A covered entity is a health plan, health care clearinghouse, or a health care provider. Since a company providing genomic sequencing services is not a health plan or a health care clearinghouse, HIPAA will apply only if such a company is determined to be a health care provider or a business associate of a covered entity.
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The Scientific Foundation for Personal Genomics: Recommendations from the Joint NIH-CDC Workshop
Last December, some of the true heavyweights in the field of personal genomics convened for a two-day workshop cosponsored by the CDC and NIH to review the science and implementation of personal genomics. Participants included scientific luminaries (e.g., Francis Collins, George Church and Bob Green), personal genomics companies (e.g., 23andMe, Knome, Navigenics, deCODE Genetics and DNA Direct) and policy groups (e.g., Genetic Alliance, Personalized Medicine Coalition and Genetics and Public Policy Center). The workshop and its participants’ recommendations were summarized (pdf) late last month in the journal Genetics in Medicine.
The workshop focused on a review of the “scientific foundation for using personal genomics in risk assessment and disease prevention,” developing five specific recommendations for the future development and use of personal genomics.
1. Develop and implement scientific standards for personal genomics. Of primary importance was the development of scientific benchmarks for evaluating personal genomics testing. Heavily emphasized was the need to establish standards for measuring the clinical validity (how well a genetic variant identifies or predicts an individual’s clinical status) and clinical utility (the health and other benefits of a test balanced against its harms or costs) of personal genomics tests. The importance of voluntary industry guidelines (pdf), randomized clinical trials and economic analysis of personal genomics testing were all discussed.
Whole-Genome Sequencing and Gene Patents Coexist (For Now)
In a recent post, John Conley analyzed the ACLU’s lawsuit challenging Myriad Genetics’ patents on the BRCA-1 and BRCA-2 “breast and ovarian cancer susceptibility” genes. Several readers responded with the same general inquiry: if an individual undergoes a whole-genome sequence analysis, will the individual (or the company providing the sequence) be required to pay royalties to Myriad because the BRCA-1 and -2 loci will have been sequenced?
Although focused on the BRCA genes, the question is broadly applicable to the entire genome sequencing industry: when sequencing all or a portion (e.g., the exome) of an individual’s genome, are individual gene patents infringed upon by either the company providing the sequence or the individual purchasing or requesting it? The answer is not entirely clear, but, at least in the case of Myriad and the BRCA genes, it appears to be no. Or at least, not yet.
Let’s begin with what is not patented, which includes a majority of genes and the vast majority of the human genome. Genes—those stretches of DNA that encode for proteins—make up approximately 2% of the human genome. The estimate of the exact number of genes ranges from between roughly 20,000 to 30,000 and, of those, a 2005 study in the journal Science found that only 20% of human gene DNA sequences are patented (subscription). Although those numbers are certainly subject to change, the reality is that, today, it is likely that less than 1% of the entire human genome has been patented.
Of course, that very small number belies the fact that the genes which have been patented consist of some of the most important identified genes associated with the prediction or determination of human health and disease. The high-profile BRCA genes are an excellent example and thus make for a good case study.
The Genome In Silico and the Future of Whole-Genome Sequencing
In my previous post summarizing last weekend’s conference on Genetics and Ethics in the 21st Century I briefly mentioned Professor John Robertson’s discussion of the “genome in silico.” Using Illumina’s recently announced $48,000 whole-genome sequencing service as an example, Robertson wondered whether the future of whole-genome sequencing lies in converting the genome to silicon storage (in silico) or whether on-demand sequencing of short genetic segments (or even whole genomes) will continue to be done as and when patients present with specific clinical conditions (in vivo). To put it another way, will the patient of the future present his doctor with the equivalent of Illumina’s concept iPhone app or Knome’s USB drive, or will she come prepared to undergo a more traditional blood draw or tissue biopsy.
Following Illumina’s announcement at the Consumer Genetics Show, Daniel MacArthur at Genetic Future speculated that Illumina, in focusing “on the sequence generation side…[was] restricting itself to the least attractive segment of the personal genomics market.” And I agreed, arguing that the bioinformatics portion of the genome sequencing market — interpreting and functionalizing raw sequence data — appeared to be both larger and less well-developed, thus presenting a more promising commercial opportunity.
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Pathway Genomics Launches and a Look Back at Two Years of DTC Genomics
Pathway Genomics became the latest entrant in the consumer genomics space when it publicly launched its new direct-to-consumer (DTC) genotyping service this morning. Pathway provides genotyping (or SNP testing) for a variety of genetic traits and markers including ancestral testing for $199, health and disease testing for $249 and both the health and ancestry service for $349, which is a $50 price drop over the current market leader, 23andMe. Blaine Bettinger (of the Genetic Genealogist and a consultant for Pathway) previewed the service back in March and today’s Bio-IT World also has a detailed summary.
What’s new about Pathway Genomics? From a narrow perspective, perhaps not much. On its surface, the Pathway offering is comparable to products already on the market from 23andMe, deCODEme and Navigenics. Although it’s too early to evaluate Pathway’s promises of “better science, deeper results, and a better price,” the genotyping service appears competitive with existing industry offerings, with the ancestry testing component positioned to be an industry leader. However, unlike the last major DTC genomics announcement, there does not appear to be anything fundamentally new about Pathway’s technology or market-shattering about its price point.
Even though Pathway does not appear to offer a breakthrough technology or business model, its launch is still a significant event. It represents yet another bet by investors on the commercial potential of consumer genomics and ratchets up the competition for DTC market share. Moreover, Pathway’s service is indicative of how the consumer genomics industry continues to shift.
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).
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 (slides) 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
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.
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