Genomics & Society
Why the State of Personal Genomics is Not as Dire as You Think
Another Tale of the Struggle of Personal Genomics, Full of Sound and Fury, Signifying…What? After a while, the personal genomics news cycle can begin to feel predictable. Recently, and not for the first time, there have been rumblings that personal genomics pioneer 23andMe is struggling. The most recent “news” appears to be a December SEC filing disclosing a $4 million payment to an unidentified 23andMe executive. Gene Expression and BNET have taken the opportunity to recycle some of the company’s previous financial struggles, including co-founder Linda Avey’s departure and a well-publicized round of fall layoffs, and to speculate broadly about the state of morale at the company in addition to the well-being of the personal genomics industry more generally.
Avey herself, perhaps unintentionally, has fueled speculation that something may be afoot with a pair of recent posts (the original post has now been combined with an update) on her own blog. Avey has launched a preemptive strike against what appears to be an upcoming New York Times piece that will “question[] the viability” of the personal genomics industry and “hits too close to home” for Avey not to comment. (Or, as GenomeWeb headlines it, Linda Avey Versus the New York Times.)
Perhaps all of the smoke signifies a smoldering fire at 23andMe. Then again, it may represent nothing more than periodic reverberations from the social media echo chamber, where common memes are repackaged and recycled at regular intervals.
Personal Genomics in the News: Desmond Tutu and the GET Conference
It’s been a busy twenty-four hours in the world of personal genomics. Yesterday, as announced in the journal Nature, the number of individuals who have had their genomes sequenced and made publicly available increased by two. Archbishop Desmond Tutu and !Gubi, a tribal elder from a Bushman (or Khoisan) community in Namibia, joined the ranks of personal genomics pioneers that include scientific and cultural luminaries such as James Watson, George Church, Skip Gates, Jr. and Stephen Quake.
Hot on the heels of the Nature paper (which has been exceptionally well-covered elsewhere, including by Not Exactly Rocket Science, the Technology Review, and the New York Times) comes this morning’s announcement that many of those same genomics pioneers, including Watson, Church, Gates, Quake and others, will be sharing the stage together at the inaugural GET (Genomes Environments Traits) Conference. From the conference announcement:
“The GET Conference 2010 marks the last opportunity in history to gather a majority of individuals in the world with public personal genome sequences in a single venue,” says George Church, founder and principal investigator of the Personal Genome Project and professor of genetics at Harvard Medical School. “With rapid advances in technology, the number of individuals with personal genome sequences is expected to rise dramatically, from dozens today to thousands by 2011 and a million or more individuals within the next few years.”
The morning portion of GET Conference 2010 will feature wide-ranging discussions during which personal genome pioneers and globally recognized leaders of genomic science and industry, including Misha Angrist, George Church, Jay Flatley, Henry Louis Gates, Jr., Rosalynn Gill, Seong-Jin Kim, Greg Lucier, James Lupski, Stephen Quake, Dan Stoicescu and James Watson, will share their experiences and discuss the future of personal genomics. Award-winning science journalists Carl Zimmer and Robert Krulwich will moderate the discussions.
SACGHS Gene Patent Recommendations Still Controversial
The Secretary’s Advisory Committee on Genetics, Health and Society (SACGHS) for the Department of Health and Human Services (HHS) convened again on Friday for a snow-shortened session. One of several items on the Committee’s agenda was a report that the GLR has covered several times (see here and here): Gene Patents and Licensing Practices and Their Impact on Patient Access to Genetic Tests. With the threat of a blizzard looming, the meeting was unexpectedly short, with only a pair of public comments followed by the Committee’s vote to approve the report.
The report itself will not be available for several weeks, but the six recommendations on gene patenting and licensing approved by the Committee this past October continue to provoke a heated response. The Biotechnology Industry Organization (BIO), along with former Senator Birch Bayh (of Bayh-Dole Act fame) and others, held a Friday press conference to denounce – again – the report’s recommendations.
The SACGHS Recommendations. Most of the recommendations are uncontroversial, urging the Secretary of HHS to convene stakeholders to “explore” and “encourage” strategies to improve access to genetic testing, enhance patent licensing and ensure that the USPTO is “kept current with the latest scientific and technological developments related to genetic testing and technology.”
So what prompted Bayh’s charge that the recommendations represent “an attempt to send us back to a time when it appeared that American innovation was on its last legs and our economy was in deep distress”?
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Up Next in Gene Patents: Waiting for a Ruling (Again) and SACGHS Meets (Again)
GenomeWeb has a recap of today’s hearing in the Myriad case, including the not-at-all-surprising decision that there was no summary judgment decision issued from the bench. From all accounts the case appears to have been argued along the lines set forward by the parties in their briefs, with no obvious surprises presented by either party during oral argument. As for a decision, according to GenomeWeb, “Judge Sweet did not say today when he expects to make a decision in the case.” Interested observers, including the Genomics Law Report, can expect to wait some time – at least several weeks, if not months – before a decision is handed down. That decision, no matter which way it falls, is likely to produce an appeal to the Second Circuit.
In the meantime, those that simply cannot get enough of the gene patent debate are reminded that the Secretary’s Advisory Committee on Genetics, Health and Society (SACGHS) is convening again this week to finalize its report on biotechnology patent and licensing policy. As previously reported by the GLR, the last SACGHS meeting reviewed and approved several recommendations (pdf) from its Gene Patents and Licensing Task Force, including proposed exemptions from liability for infringing patents when (i) making, using, ordering, or selling tests for patient care purposes or (ii) “in the pursuit of research.”
While the SACGHS approved the recommendations, final review and approval of the Committee’s report on Gene Patents and Licensing Practices and Their Impact on Patient Access to Genetic Tests was tabled until the February meeting. The recommendations and the draft report generated some pushback last fall so, Friday morning, the Committee will be reviewing those additional comments and “coming to closure” (pdf) on the report. The GLR will be listening in. Interested readers can find information about the SACGHS meeting here.
Newborn Blood Spot Litigation: 70 Days to Destroy 5+ Million Samples
Sometime in the next few months, Texas will destroy more than 5 million blood samples collected from newborn babies across the state over the past seven years. The lawsuit that led to this result—agreed to as part of a settlement reached between the state and a civil rights group representing a group of parents—illustrates a number of interesting points about the law and litigation of genetics issues.
As we discussed in A Closer Look at Biobanking of Newborn Blood Spots, states collect blood samples from most infants born in the United States each year, with the goal of detecting and treating a variety of potentially serious conditions. The Texas Department of State Health Services (DSHS) has been collecting newborn blood samples from babies born within the state since the 1960s. Texas currently tests for conditions including cystic fibrosis, endocrine disorders, fatty acid disorders, and others—28 disorders in all (pdf). At least some of the samples are apparently subjected to genetic testing for hemoglobinopathy, phenylketonuria, and galactosemia.
Life Technologies Fires Latest Sequencing Salvo
Another week, another drop in the cost of whole-genome sequencing. The latest announcement comes from Life Technologies, which yesterday announced the launch of its SOLiD 4 sequencing system. The details of the announcement are well-covered by GenomeWeb and Matthew Herper of Forbes.com.
In brief, the SOLiD 4 generates 100 gigabases of data per run at a cost of $6,000 per genome, a cost that appears to account solely for the consumables and does not include the cost of the machine or of interpreting all of that sequence data. According to GenomeWeb, Life is also promising an upgrade to its system – SOLiD 4hq – in the second half of 2010 which it expects to triple the data output at half of the cost: 300 megabases per run, $3,000 per sequence.
As for the impact of Life’s SOLiD 4 announcement, Matthew Herper hits the nail on the head:
But although the news is good for Life and will keep it in the game as the price of decoding the genetic code continues to drop, the specs of this new machine don’t seem good enough to upset Illumina’s place as the first choice of geneticists. “It’s a solid improvement, but I don’t think this changes the game,” says Isaac Ro, an analyst at Leerink Swan who follows both companies.
Five Questions for Personal Genomics in 2010
Death, taxes and January prediction columns: these things are inevitable. So what? A new year offers a convenient—if arbitrary—time to review the year that was and contemplate what lies ahead. Without further ado, here are five of the questions the Genomics Law Report is asking as we kick off 2010.
1. Will the $1,000 genome live up to the hype? Affordable whole-genome sequencing is coming, possibly as early as this year depending on whom you ask. But when the day inevitably arrives, after the media frenzy has subsided, will the $1,000 genome prove anti-climactic?
Whole-genome sequencing is a means to an end and not an end in itself. The understandable excitement surrounding Complete Genomics’ November announcement that it had sequenced three genomes for an average cost of $4,400 often neglected to focus on what the price tag did not cover: the substantial costs associated with interpreting the genomic data.
For genomics researchers, the falling cost of whole-genome sequencing is a continuing cause for celebration, enabling increasingly ambitious research projects. But the success of personal genomics, which is what really matters to consumers, patients and healthcare providers, requires more than inexpensive genomic data. The real breakthrough in personal genomics will come when we can offer individuals affordable access to their whole-genome sequence as well as to the genomic tools and knowledgebase necessary for those individuals to put that data to use.
Personal Genomics: A Participatory Activity
Last week the GLR covered deCODEme’s announcement that it was offering existing customers of its main competitor, 23andMe, the opportunity to have their genomic data interpreted by deCODEme’s own service. For free.
Although somewhat surprising from a short-term commercial perspective, I generally liked the move by deCODE as a means to improve the company’s genomic data interpretation abilities. Here’s what I wrote at the time:
If interpretation proves to be one of the key differentiators between DTC genomics companies, as expected, deCODE (and other companies) should embrace opportunities to hone their interpretative platforms now, while the DTC commercial market remains relatively small.
As both Peter Aldhous of New Scientist and Daniel MacArthur of Genetic Future have pointed out, it appears that there is some honing to be done on deCODEme’s end. From ancestry confusion to interpretative errors in evaluating Alzheimer’s risk, deCODEme’s first attempt at genomic data migration has been an imperfect one. Would deCODEme have preferred a seamless launch to their 23andMe data migration service? Of course. But if the experiment now pays off in smoother data migration and interpretation for the company in 2010 and beyond, these first bumps in the road will soon be forgotten.
Genetic Discrimination Comes in Many Colors
An email from a regular Genomics Law Report reader notes that we have been engaging unwittingly in genetic discrimination. Dr. Bob West is color-blind, and he points out that our treatment of hyperlinks—to date we have used red hyperlinks against black text in our posts, without any other markings to distinguish linked from ordinary text—creates a real problem for him.
Red-green color blindness, which is the most common form, is an X-linked genetic condition that affects an estimated 7-10% of men in the United States (because it is X-linked, it affects far fewer women). People with red-green color blindness have a difficult time distinguishing red from black characters, which made locating links on the GLR very difficult. To compensate, Dr. West was forced to print out the GLR columns (default print settings typically causes hyperlinks to become underlined, regardless of how they appear on screen) in order to identify the hyperlinks.
The GLR is responding. You will now notice that hyperlinks in the body of GLR columns, including this one, appear red and underlined (beige if you’ve previously visited the link), allowing readers two ways (color and style) to identify hyperlinks.
Remember to share your other comments and suggestions—from examples of inadvertent genetic discrimination to ideas for future columns—by contacting us. Thanks.
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Is deCODEme Taking a Page from the 23andMe Playbook?
Daniel MacArthur of Genetic Future provides coverage of the decision by direct-to-consumer (DTC) genomics service provider deCODEme to offer existing 23andMe customers the ability to upload their raw 23andMe data to the deCODEme service. For free.
MacArthur correctly notes that the value of the genome scans provided by companies such as 23andMe and deCODEme lies not in the actual creation of raw genetic data but in the interpretation of that data, and wonders why deCODEme has decided to give that away for free. Here’s MacArthur’s take:
So, why the free offer? I’m guessing deCODEme is gambling (quite reasonably) that offering free uploads will attract a non-trivial number of 23andMe customers over to deCODEme’s interface. That then provides the Icelanders with an opportunity to give people a fair trial of their own interface, and hopefully to impress them with the quality and accessibility of the data provided.
That seems reasonable, and many 23andMe customers are likely already familiar with porting their raw genetic data to other interpretive tools – Promethease, for example – so perhaps this puts deCODE in front of a group of individuals who would not otherwise be in the market for a duplicative genome scan. (23andMe appears unconcerned by the prospect of a side-by-side comparison of its service with that of deCODEme.)
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