June 24, 2009
Category: 23andme • personal genomics • regulation
Pharmacogenetics Reporter has
a lengthy article (subscription required) on the California bill SB 482, sponsored by personal genomics company
23andMe, which seeks "to distinguish so-called "post-CLIA bioinformatics services" from entities providing laboratory services".
In other words, 23andMe is pushing to have companies purely providing analysis of genetic data regulated separately from those doing the actual laboratory testing. Since 23andMe out-sources its testing to an external laboratory, this would exempt the company from some regulatory requirements. The move follows
some fairly serious regulatory controversy over direct-to-consumer testing in California a year ago.
However, this isn't simply an attempt to make the situation easier for direct-to-consumer genetic testing companies. The bill also proposes regulations that would raise the bar for genetic testing companies, and hopefully close out some of the shadier operators in the space:
Read on »
Posted by Daniel MacArthur at 8:35 PM • 8 Comments
Category: direct-to-consumer genetic testing
GenomeWeb reports that the advocacy group
Genetic Alliance is lobbying the FDA for the construction of a public registry of genetic tests:
[Genetic Alliance Director of Genetics and Health Policy Kristi] Zonno said FDA should create a public registry for genetic tests to "enable transparency and promote informed decision making for consumers and providers." She said that registry "could and should include the myriad of genetic, genomic, and pharmacogenomic testing available to the US market."
Open to the public, the registry should at the very least include the name of the lab performing a test, the name of the test developer, and information to support the test's usefulness in obtaining results and improving clinical care, Zonno added.
This move is long overdue - there have been discussions of the need for such a database in many circles for well over a year, but there has been no visible progress yet. This is an enormously complex industry, and consumers need guidance from independent bodies (certainly more than they need over-zealous regulation of the industry). If Genetic Alliance can convince FDA to make a real effort here that would be a major step in the right direction.
Posted by Daniel MacArthur at 7:10 PM • 9 Comments
Category: conference blogging
Geoff Brumfiel has done a great job in
this article for Nature News on the promise and perils of conference blogging. On the promise side there is discussion of the
wildly successful FriendFeed coverage of last year's ISMB meeting, which ended up being aggregated into
a journal article; in the perilous direction, I get a mention for
my mildly disastrous foray into conference blogging at the recent Cold Spring Harbor Biology of Genomes meeting.
Brumfiel does a good job of conveying the currently chaotic state of conference policies towards the use of social media by participants:
Read on »
Posted by Daniel MacArthur at 6:01 PM • 1 Comments
June 23, 2009
Category: direct-to-consumer genetic testing • personal genomics
Update: In the comments below, SNPedia co-founder Michael Cariaso notes that Duncan has already lost his crown to the anonymous European NA07022, recently sequenced by Complete Genomics, who weighs in with 5891 associations to Duncan's 5321. Records don't last long in the age of high-throughput genomics!
Author David Ewing Duncan now officially has
the most annotated genome of any human being; but given that the majority of those annotations are wrong and most of the remainder only weakly predictive, he's also a powerful illustration of how far we still have to go before the era of personal genomics comes to fruition.
Duncan isn't the person with the largest portion of his genome sequenced (
Craig Venter,
Jim Watson and
Seong-Jin Kim are the named individuals currently competing for that honour), but he has so far cast his net the most widely in examining the potential functional information within his DNA. His 5,321 current associations come courtesy of
SNPedia, a public database of genetic associations maintained by
Michael Cariaso.
The majority of those associations, unfortunately, are
pure noise - the detritus left behind by the noxious wave of false positives that was the era of the candidate gene association study, prior to the advent of modern, robust genome-wide association studies. Of the relative minority that are likely to be genuine, most are common variants with very small effects on disease risk and thus extremely limited predictive value. Wading through the sheer mass of loosely annotated data in
Duncan's SNPedia report provides sharp insight into the challenges of navigating large-scale genetic data.
(Added in edit: In hindsight the paragraph above could be read as a criticism of SNPedia, which it isn't - SNPedia simply provides a catalogue of the genetic associations in the literature along with links to the relevant papers, and it's up to the user to decide what standards of evidence to apply in deciding whether or not an association is useful. So just to be clear - the emotive language in the paragraph is aimed towards the appallingly high levels of false positives in published genetic association studies and not towards SNPedia's decision to list them.)
It's clear that consumers will need tremendous guidance in that navigation - but it's still unclear exactly who will be the best at providing that guidance. The medical establishment certainly wants you to think that they are the only qualified providers, but upstart private personal genomics companies like
23andMe are giving clinicians a run for their money, and crowd-sourced efforts such as SNPedia remain a wild card.
In the meantime, Duncan isn't resting on his laurels - he says he plans to have his entire genome sequenced "soon" as part of
a broader process of self-exploration. It's worth keeping an eye on Duncan as the model of an extremely enthusiastic early adopter of personal genomic technologies - the obstacles to understanding his genetic information will soon be things that the rest of us need to wrestle with as well.
Posted by Daniel MacArthur at 8:15 AM • 6 Comments
June 21, 2009
Category:
This is slightly unusual subject matter for this blog, but I found
this presentation by 2001 Nobel Prize winner Paul Nurse absolutely fascinating. It's an account of his slow unravelling of his family background, told to an audience at the
World Science Festival in New York last week.
The full video is beneath the fold:
Read on »
Posted by Daniel MacArthur at 9:58 AM • 1 Comments
June 19, 2009
Category: conference blogging
Added in edit: the original version of this post implied that the Nature editorial was recent, when it was in fact published in February this year; I was sent a link to it today and assumed it was new. I've edited the post to reflect this.
One of the major reasons for concern from presenters and conference organisers about the notion of conference bloggers is that having unpublished work discussed online may violate the embargo policies of journals and damage their chances of publication.
We do have clarification of this issue from one major journal.
Nature has
an editorial posted back in February that continues its long-term theme of encouraging scientists to engage in the blogosphere, and also includes this important statement:
At the same time, however, our cardinal rule has always been to promote scientific communication. We have therefore never sought to prevent scientists from presenting their work at conferences, or from depositing first drafts of submitted papers on preprint servers. So Nature journalists or those from any other publication should hear results presented at a meeting, or find them on a preprint server, the findings are fair game for coverage -- even if that coverage is ahead of the paper's publication. This is not considered a breaking of Nature's embargo. Nor is it a violation if scientists respond to journalists' queries in ensuring that the facts are correct -- so long as they don't actively promote media coverage.
Sounds good to me, and I hope to see similar clarification from other journals in the near future.
Posted by Daniel MacArthur at 7:37 PM • 3 Comments
Category: personal genomics • trugenetics
Misha Angrist points me to the launch of
TruGenetics, which basically looks like just another genome scan company with a unique gimmick:
they're giving 10,000 scans away free.
Your questionnaire responses and genetic information will be used for genetic research. One of the main goals of TruGeneticsâ„¢ is to develop a unique research database for conducting genetic studies. Your decision to use TruGenetics'â„¢ services indicates that you are willing to contribute your questionnaire responses and genetic information to the TruGeneticsâ„¢ research database. [...] TruGeneticsâ„¢ may conduct this research, or may partner with another organization, including non-profit and commercial entities, to conduct research. TruGeneticsâ„¢ may charge a fee for conducting research using this database.
[...]
You will not benefit directly from contributing your information to the research database. However, important discoveries might be made through this research, and this might significantly help other people. If these discoveries are validated and accepted by the scientific community, we will provide you with this information as it pertains to your genes. This research may also lead to the development of a commercial product. You will not receive any payments if this occurs.
Looks to me as though the business model here is pretty much the same as 23andMe's fundamental strategy - recruit customers, get them to provide both genetic and phenotypic data, look for novel associations and then (the tricky step) figure out a way to monetise said associations by selling them on to pharma or biotech companies. The only difference is that TruGenetics is willing to absorb more of a loss than 23andMe in developing that potentially saleable resource.
Ten thousand individuals is enough to power a reasonable genome-wide association study (GWAS) for one complex trait, or 2-5 moderately-powered GWAS for much more simple traits (e.g. drug response). Ideally, customers would be recruited on the basis of falling into specific phenotype categories (e.g. disease cohorts and healthy controls), so it will be interesting to see if customers have to fill in their phenotype survey before they are given any guarantee of receiving a free scan.
The big question is what genetic markers you could possibly find with 10,000 people that won't be scooped up by academic GWAS consortiums before you can finish your analysis and submit your patent applications. You'd need to target a phenotype that was sufficiently medically relevant to be worth selling, but simultaneously sufficiently obscure to not be the target of massive GWAS already in the pipeline.
Alternatively, perhaps the company is most interested in recruiting perfectly healthy individuals from specific populations to serve as a shared control group for disease-specific GWAS being performed by other groups; this could potentially be a fairly valuable resource. I'm speculating pretty wildly now, so I'll leave it there.
I've signed up, but I'll need to hear more details from the company before I commit to handing over my genetic and medical details. I'll let you all know when I do.
Posted by Daniel MacArthur at 7:31 PM • 4 Comments
June 18, 2009
Category: conference blogging
Readers who haven't seen it already may be interested in
the post and subsequent discussion on conference blogging taking place on Dr Isis' blog.
I feel that Dr Isis' post misrepresents my position in several ways (see
this clarifying comment from me), but she does provide an interesting argument against the notion that "open tweeting" should be the default position unless the presenter explicitly states otherwise.
The discussion has given me an opportunity to clarify my thoughts on a few issues. Below the fold I've pasted some snippets from my comments on Dr Isis' post summing up some points I don't think I've ever fully spelled out here on my blog.
Read on »
Posted by Daniel MacArthur at 7:38 PM • 6 Comments
June 17, 2009
Category: blog safe • conference blogging
The
rather contentious result of my live-blogging of the Biology of Genomes meeting last month made it very clear to me that the scientific community needs to do a better job of communicating in advance whether a presentation is off-limits to audience live-bloggers. I've since been involved in a number of discussions about this issue both on- and off-line.
Cold Spring Harbor Laboratory (the host of the Biology of Genomes meeting) has
clarified its own position, stating that potential live-bloggers (or tweeters) need to explicitly seek permission from speakers before writing about their presentations. This fits with CSHL's policy of encouraging the presentation of unpublished data by preventing unauthorised reporting of results, but it puts potential bloggers in an awkward position: it's not always clear in advance which talks will be interesting enough to discuss online, and finding speakers before their presentation to ask them for permission can be both logistically challenging and socially awkward (especially in the cases where it requires explaining to the presenter what this "blogging" business is all about).
Far better would be a situation where presenters stated in writing whether they were happy for their work to be live-blogged in an official format: ideally, stating a preference would be part of the registration process for all attendees, and every entry in the conference abstract book (whether presentation or poster) would indicate explicitly whether the presenter was happy for their results to be freely discussed online. I hope that any conference organisers reading this consider setting up something along these lines for their next meeting.
In the interim, it strikes me that there is room for a more individual approach for speakers who are happy to have their work live-blogged: some sort of standard icon that could be added to a title slide or the corner of a poster, quietly indicating that the presented data is "blog-safe" - i.e. can be blogged/tweeted freely. Such an icon would obviously only be used by the small sub-set of researchers web-savvy enough to know about it, but it might nonetheless help to raise awareness of the issue among the broader scientific community.
The question is, what icon can we use?
Read on »
Posted by Daniel MacArthur at 11:20 AM • 17 Comments
June 16, 2009
Category: personal genomics
Emily Singer has been doing a great job of covering the consumer genetics beat over at Technology Review;
her most recent piece draws on a recent presentation by former head of the National Human Genome Research
Institute Francis Collins.
Collins caused a bit of a stir during his presentation (at last week's
Consumer Genetics Show in Boston) by announcing that he had signed up for several personal genomics services under a false name. His conclusions:
Read on »
Posted by Daniel MacArthur at 7:21 PM • 12 Comments
