Mapping the Personal Genomics Landscape
Last week saw the first annual Genomes, Environments, Traits (GET) Conference, in Cambridge, Massachusetts. Timed to coincide with DNA Day 2010, the conference marked one decade since the publication of the draft consensus human genome sequence. The GET Conference was billed as “the last chance in history to collect everyone with a personal genome sequence on the same stage to share their experiences and discuss the important ways in which personal genomes will affect all of our lives in the coming years.” Not quite everyone with a public personal genome sequence attended – Craig Venter, Desmond Tutu, Glenn Close were all unavailable – but a majority of the genomic pioneers were in attendance and the GET Conference was a one-of-a-kind event.
For those who missed the GET Conference, several high quality recaps are available. The most detailed is A Day Among Genomes, by Carl Zimmer of Discover’s blog The Loom. More targeted reflections on the conference and related events come from Emily Singer of Technology Review summarzing key trends highlighted by the genome pioneers (Singer also has a related piece on the difficulties of understanding human genomes), David Dobbs of Neuron Culture on genomes, cool conferences, and what the hell to tell people about behavioral genes, and Turna Ray of Pharmacogenomics Reporter on the recent Myriad Genetics decision, and its impact on the business of patenting genes. If you’d like even more detail, the Twitter community provided real-time play-by-play.
While there’s no need for a further summary, the GET Conference does provide an occasion to look at the evolving personal genomics landscape in a more holistic fashion.
Past, Present and Future of Genomes, Environments and Traits: 140 Characters at a Time
The first annual Genomes, Environments, Traits (GET) Conference took place yesterday. The GET Conference was an incredible success, with panels, breakout sessions and presentations from all manner of genomic pioneers and futurists, as well as a tremendous audience, both in person and online. In the next few days I’ll share a few thoughts about what we learned at the 2010 GET Conference, as well as what we might expect by the time the 2011 event rolls around. There will also be video from portions of the GET Conference available soon.
In the meantime, if you missed the conference, there was plenty of live Twitter coverage. Everything I tweeted from @genomicslawyer can be found below, and there’s much more at the #GET2010 twitter notebook. Thank you to all those who helped cover the conference online, including GET Conference pioneers (Rosalynn Gill, Misha Angrist), moderators (Carl Zimmer, David Dobbs, Dana Waring Bateman), journalists (Edward Winstead, Emily Singer, Kevin Davies, Aaron Rowe), sponsors (Priscilla Oppenheimer), exome sequence winners (Jonathan Eisen) and many, many more.
Now for Genomes, Environments and Traits in 140 character snips:
The Havasupai Indians and the Challenge of Informed Consent for Genomic Research
Pulitzer Prize-winning journalist Amy Harmon, of The New York Times, reports that a long-running dispute between Arizona State University (ASU) and the Havasupai Indians over the allegedly improper research use of DNA from members of the tribe has been settled.
The research began two decades ago, ostensibly to search for a genetic variant that might be contributing to the increasing rate of diabetes in the tribe. The diabetes research proved unfruitful, but the blood donated by the Havasupai tribe members, and the DNA extracted from it, led to a number of follow-on research projects, grants and publications. It was that research – including searching tribe members’ DNA for variants linked to schizophrenia, and inferring the likely ancestral origins of the tribe’s founders – that led to lawsuits, millions in legal fees and, ultimately, the settlement.
Implications of the Havasupai Settlement. Harmon’s article provides a concise background to the dispute, and briefly describes the $700,000 settlement between ASU and the tribe to “remedy the wrong that was done.” Harmon and unnamed “legal experts” suggest that the settlement is significant because “it implied that the rights of research subjects can be violated when they are not fully informed about how their DNA might be used.”
In some respects, this is a trivial conclusion. One of the most important and well-known elements of the Common Rule – the regulatory regime that governs federally-funded human subjects research – is that researchers must seek, and participants provide, informed consent. Participants that are uninformed cannot provide valid consent and, thus, their rights as subjects are violated. In that respect, at least, the Havasupai case tells us nothing new. (I have not seen the settlement, but I doubt that it will (a) be made public or (b) contain an express admission of guilt from ASU, both factors that will limit its relevance to future similar scenarios.)
Genomic Privacy and Re-Identification Redux
New research published this week in the Proceedings of the National Academy of Sciences from Loukides et al. offers up a new method for preserving individual privacy while linking genomic and healthcare data. (“Anonymization of electronic medical records for validating genome-wide association studies.”) Daniel Cressey of Nature News and Katharine Gammon of Technology Review have concise (and free) summaries.
As we’ve written earlier (“Back to the Future: NIH to Revisit Genomic Data-Sharing Policy”), the ability to link – and to share – genotype and phenotype data (including medical records, particularly treatment and outcome data) will be essential to the development of the next generation of genomic research. One of the most common ways to link genotype and phenotype data is to combine genomic data with electronic medical records (EMRs). A particular patient’s EMR may contain everything from basic biographical information to family medical history to current diagnoses, including ICD codes. When it comes to associating genes with medical conditions, researchers rely on International Classification of Disease (ICD) codes to categorize individual patients by disease type and search for shared genetic variations that might play a causal role.
Cracking the Codes. Obviously identifying information (e.g., biographical information) is generally required to be removed pursuant to HIPAA regulations. ICD codes, however, are sometimes retained for purposes of genetic association research and, in some circumstances, a set of otherwise anonymous ICD codes pulled from an EMR can be traced backwards to identify the specific individual supplying the codes.
Disclosure of Patients’ Genetic Information Without Their Consent–Is the “Public Interest” Really a Sufficient Justification?
New guidance issued by the U.K. General Medical Council (GMC) regarding a physician’s ability to disclose to a patient’s relatives the diagnosis of such patient’s genetic illness1 has recently been a hot topic of discussion on several online forums.2 The guidance, which became effective on October 12, 2009 and addresses medical privacy issues in a variety of contexts (not just genetic information sharing), recognizes that the diagnosis of a patient’s genetic illness may indicate the likelihood of the same illness in the patient’s close blood relatives. The GMC suggests that a physician’s first obligation after diagnosing a genetic illness is to explain to the patient the likelihood that close relatives are also at risk and to encourage the patient to discuss his or her illness with relatives. However, should the patient refuse to voluntarily disclose the illness to at risk family members, the physician may disclose such information if disclosure would be “justified in the public interest.” Physicians are instructed to balance their duty to provide care to the patient against their duty to protect others from serious harm.3
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.
Read the rest of this entry »
Is There an Obligation to Return Genetic Data to Research Participants? Kaiser Responds to 23andMe’s TEDMED Criticism
Earlier today, in the latest installment of the What ELSI is New? series, Daniel MacArthur asked a question that has cropped up repeatedly in recent weeks and months as part of the broader discourse surrounding genetic research and commerce: what rights should individuals have to gain access to their personal genetic or genomic data?
MacArthur’s position – that research participants should generally be provided with complete access to their own genetic data upon request – is one that continues to remain a minority position. It finds support in research initiatives such as the Personal Genome Project (PGP) and (to a lesser extent) the Coriell Personalized Medicine Collaborative (CPMC), but returning research results has generally been eschewed by other large-scale genetic research projects, including Kaiser Permanente’s recently announced Research Program on Genes, Environment, & Health (RPGEH).
Last month, the Genomics Law Report examined the RPGEH and its reluctance to return genetic data to a participant population that is expected to quickly grow to 100,000 or more Kaiser patients. RPGEH’s decision not to return data to its participants was under the microscope again last week at TEDMED 2009 when 23andMe co-founder Anne Wojcicki criticized Kaiser for planning to genotype RPGEH participants without offering them the ability to review their data.
Read the rest of this entry »
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:
Back to the Future: NIH to Revisit Genomic Data-Sharing Policy
As first reported by GenomeWeb, last week the NIH issued a “Notice on Development of Data Sharing Policy for Sequence and Related Genomic Data.” Although the title doesn’t exactly trip off of the tongue, the NIH’s announcement provides an opportunity to review where we are and where we have already been when it comes to genomic data-sharing.
At the heart of the NIH’s announcement is a desire to increase the availability of genomic datasets. From last week’s notice:
.
Consistent with the NIH mission to improve public health through research and the longstanding NIH policy to make data publicly available from the research activities that it funds, the NIH has concluded that the full value of sequence-based genomic data can best be realized by making the sequence, as well as other genomic and phenotype datasets derived from large-scale studies, available as broadly as possible to a wide range of scientific investigators.
For NIH-funded genomic researchers, this language should have a familiar ring. In 2007, the NIH published a policy covering data-sharing for genome-wide association studies (GWAS) that required all NIH-funded GWAS research be deposited in a central data repository. Here’s the mission statement from the 2007 policy:
Read the rest of this entry »
Kaiser’s Massive Genetic Database Leverages Its Patient Population (But It’s A One Way Street)
This 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:
Read the rest of this entry »
