Completing the Personal Genomics Toolkit

toolkitThe 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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Filed under General Interest, Genomic Sequencing, Genomics & Society, Industry News

Kaiser’s Massive Genetic Database Leverages Its Patient Population (But It’s A One Way Street)

one wayThis week MIT’s Technology Review featured a story about Kaiser Permanente and its plans to use its Northern California patients to construct an enormous genetic database. The acronym-unfriendly Research Program on Genes, Environment, & Health, or RPGEH is funded in large part by a $25 million NIH research grant courtesy of February’s stimulus bill. The program will genotype 100,000 patients using SNP array technology from Affymetrix. If all goes well, the project will expand to as many as 500,000 patients by 2013.

What makes the RPGEH proposal so exciting, from a research perspective, is not just the 700,000 SNPs that will be genotyped for 100,000 patients, although that alone would represent one of the largest genetic research databases currently in existence. The real value lies in the marrying of genetic information with robust medical, environmental and other phenotypic data that Kaiser already maintains as a health care provider. From the RPGEH’s official description:
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Filed under Biobanking, Genetic Testing/Screening, Genomic Policymaking, Genomics & Society

Make Room for Big Blue: IBM the Latest (and Largest) Entrant in the Race for the $1,000 Genome

920905The quest for the $1,000 genome—viewed by many as the point at which whole-genome sequencing will become cost-effective and widely available—is a fierce competition populated by a cast of start-ups and specialized genomics companies.

The most well-known entrants in the next-generation sequencing market are companies such as Oxford NanoporePacific Biosciences and Complete Genomics; names that are hardly familiar to the average patient or consumer. And the wilder the sequencing claims—e.g., a full genome “for less than $100 in under an hour“—the more obscure, at least for the moment, the company: Halcyon Molecular, BioNanomatrix and NABsys among others.
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Whole-Genome Sequencing and Gene Patents Coexist (For Now)

Test Tubes 80In 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.


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Filed under Direct-to-Consumer Services, Genetic Testing/Screening, Genomic Policymaking, Genomic Sequencing, Genomics & Medicine, Myriad Gene Patent Litigation, Patents & IP, Pending Litigation

The Genome In Silico and the Future of Whole-Genome Sequencing

silicon waferIn 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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Filed under Biobanking, Bioinformatics/IT, Direct-to-Consumer Services, Genetic Testing/Screening, Genomic Sequencing, Genomics & Society, Informed Consent, Legal & Regulatory

Genomics and Personalized Medicine: Facts, Fiction, Future?

futurehand80Over the weekend I took part in the 13th Conference on Genetics & Ethics in the 21st Century in Breckenridge, CO. The theme was “Genomics and Personalized Medicine, Facts, Fiction, Future?” Although the altitude (Breckenridge is at 9,600 ft) posed a problem for several participants, the conference otherwise went off without a hitch.

The program kicked off with a focus on the state of genetic and genomic knowledge with an excellent talk by Richard Gibbs of Baylor’s Human Genome Sequencing Center, who provided a progress report on the 1000 Genomes project and predictions for the future of large-scale genomics research. Penn State’s Kenneth Weiss followed with “Genetic Causation: A Fermi Problem” and presented a compelling challenge to the received wisdom of genetic heritability. Some of the most interesting discussion was driven by a question posed to Richard Gibbs: whether there are instances where the ethical, legal and social discourse surrounding genetics and genomics has either failed to keep pace with, or outstripped, the progress of science. Beyond a general consensus that Gattaca-style genetic prediction lies far beyond the horizon (if it will ever be possible), Gibbs seemed to think that on the whole the ELSI discussion was often out in front of the science, but not by an inappropriate distance. This topic provided fodder for considerable debate throughout the remainder of the conference.
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NHGRI Commits $9.5 Million to Spur Innovation

Promote Innovation70This week, the National Human Genome Research Institute (NHGRI) committed an additional $9.5 million to fund advancements in genome-sequencing in pursuit of its goal to “reduce the cost of sequencing a mammalian-sized genome to approximately $1,000.” Through its “Revolutionary Genome Sequencing Technologies—The $1,000 Genome” program, the NHGRI continues to drive a remarkable decline in the cost of genomic sequencing (pdf) that leading experts, including former NHGRI Director Francis Collins, predict will soon produce a $1,000 human genome.

Earlier this week, the GLR noted that the United States Patent and Trademark Office has seen fewer applications for genomics-related trademarks, which could be an indicator of a declining rate of innovation in that area. Whether or not that is actually the case, the NHGRI continues to do its part to keep the ideas – and the funds – flowing.

Filed under Genomic Policymaking, Genomic Sequencing, Industry News, Patents & IP

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

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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Filed under Bioinformatics/IT, Direct-to-Consumer Services, Genomic Sequencing