dgmacarthur | November 24, 2009Misha Angrist has a very brief but eloquent rant in response to the genomics nay-sayers in this Nature News piece on the bankruptcy of deCODE Genetics.
Here's a taste:
I agree: GWAS is of limited value and this probably contributed to deCODE's demise. But whatever deCODE's fate, if whole human genomes can be sequenced for < $2000, isn't it about time we stopped kicking GWAS's ever-stiffening corpse? Second, just because something is not a medical necessity, does it follow that it is worthless?
Here's the rest.
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dgmacarthur | November 19, 2009Pharyngula, via a reader, points me to the most aggressively bad attempt at a genetic testing product I have ever encountered, coupled with a truly horrific attitude to parenting.
The tag line alone is hilariously inept:
"Our Technology Spawned from Human Genome Project led by US Scientists. The Industry is Featured by CNN, CBS News"
The idea that is being spruiked here is that genetic testing can help you determine your child's "inborn talents", which you can then use to ruthlessly jam them into whatever career the test results suggest.
The presenter notes that he "wasted a lot of time…
dgmacarthur | November 18, 2009European Genetics and Anthropology has a neat little tutorial that may be of interest for genetic hobbyists: it provides instructions on how to run the program STRUCTURE on your own genetic data generated by a personal genomics company such as 23andMe or deCODEme.
STRUCTURE is an extremely popular tool among researchers working in population genetics, which allows you to generate plots showing estimates of the proportion of an individual's genome belonging to different population clusters.
The tutorial on the blog shows you how to run your analysis using a subset of just 125 markers…
dgmacarthur | November 16, 2009I was just sent this email by a deCODEme customer:
As a valued subscriber to deCODEme, we wanted to write to you directly to
let you know about some important developments in the company and how we
believe these will underpin our ability to continue to keep you in the
forefront of understanding what the latest advances in genetics mean to you.
For the past several months, deCODE has been working on restructuring its
operations. One of the principal goals of this effort has been to enable us to
find new investment that will continue our work in human genetics and to offer
to our customers…
dgmacarthur | November 16, 2009 Struggling Icelandic biotech deCODE Genetics has finally reached the point of formal insolvency. A press release today announces that the company has filed for chapter 11 bankruptcy in a US court:
In a filing with the U.S. Bankruptcy Court for the District of Delaware late on Monday, deCODE listed total assets of $69.9 million and total debt of $313.9 million, as of June 30.
deCODE launched in 1996, basing its business plan on its unique access to biological samples and genealogical and medical records from the small, homogeneous Icelandic population. Since its launch it has proved wildly…
dgmacarthur | November 15, 2009Added in edit: for superb analysis of the announcement from multiple angles, you should also check out Dan Vorhaus' three incisive articles on Genomics Law Report.
Personal genomics company 23andMe announced yesterday on its blog (and in an email to customers) of impending changes to its product line. Until now 23andMe has offered only two products: its $399 full scan, and a $99 Research Revolution product that offers limited functionality and a focus on common disease risk prediction.
There are two major components of the altered product line. Firstly, customers will now be able to…
dgmacarthur | November 11, 2009Medland et al. (2009). Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. The American Journal of Human Genetics DOI: 10.1016/j.ajhg.2009.10.009
A couple of weeks ago I reported on a presentation by 23andMe's Nick Eriksson at the American Society of Human Genetics meeting in Honolulu, in which Eriksson presented data on a series of genome-wide association studies performed by the company using genetic and trait data from its customers.
Along with genetic analysis of a variety of other traits (such as asparagus anosmia and photic sneeze) Eriksson…
dgmacarthur | November 4, 2009 Yesterday I posted a brief rant about the need for researchers to think about the best way to return genetic research data to participants, spinning off an equally brief opinion piece I wrote for the ongoing ELSI series at Genomics Law Report.
Today Dan Vorhaus has posted an excellent piece on the same topic over at GLR, triggered by an exchange between 23andMe's Anne Wojcicki and Kaiser Permanente. Go check it out.
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dgmacarthur | November 3, 2009 My contribution to Genomics Law Report's superb "What ELSI is New" series is up now.
The gist of my argument: as we move into an era of large-scale whole-genome sequencing studies and the utility of genomic information grows, researchers will increasingly frequently be faced with the discovery of highly medically relevant information within their subjects' genomes. Yet under the consent procedures established for most modern genetic research projects the anonymised subjects would never have a chance to learn about this information.
As such, people will die from breast cancer and other…
dgmacarthur | November 3, 2009New-technology DNA sequencing provider Complete Genomics will provide near-complete genome sequences of 100 individuals to the Institute for Systems Biology, driving the first ever association study for a complex trait using whole-genome sequencing. Here's the press release, and GenomeWeb has some additional information.
This is pretty exciting stuff:
The Institute for Systems Biology (ISB) and Complete Genomics Inc. announced today that they are embarking on a large-scale human genome sequencing study of Huntington`s disease (HD). ISB has engaged Complete Genomics to sequence 100 genomes,…
dgmacarthur | October 27, 2009A while back Dan Vorhaus and Lawrence Moore wrote a fantastic series of guest posts here on Genetic Future on the issue of what would happen to customer data in the event that a direct-to-consumer genetic testing company went bankrupt - here's the introduction, a detailed analysis of the implications of bankruptcy law, and a summary of the implications for consumers.
Lawrence Moore and Emily Sherlock now have a follow-up post over at Genomics Law Report digging into the implications of federal privacy regulations in the event of a DTC genomics company collapse.
The rather worrying…
dgmacarthur | October 25, 2009It's been an intensive week of genomics here at the American Society of Human Genetics meeting, and I haven't been able to grab time to blog as much as I'd have liked. In fact there's a whole load of genomics news I'll be trying to cover in some detail over the next couple of weeks; for the moment, though, I couldn't let today's presentation from personal genomics company 23andMe go by without at least some comment. (For other coverage of the conference, do check out Luke Jostins' blog coverage and the stream of live analysis on Twitter.)
The 23andMe presenter (Nick Eriksson) delivered an…
dgmacarthur | October 14, 2009I'll be away for the American Society of Human Genetics meeting in Hawaii for most of the next couple of weeks - I'll be covering the conference primarily via Twitter, and you can follow all of the tweets from the conference using the #ASHG2009 hashtag.
Genetics bloggers/tweeters should also pencil in the "tweetup" on Thursday 22nd from 4:30 to 5:15 in the ASHG Press Office (Room 318 in the Convention Center), organised by Chris Gunter; anyone interested should RSVP via email. This should be a good chance to put faces to many of the names in your Twitter and RSS feeds.
There's a lot of…
dgmacarthur | October 13, 2009 Details are pretty sketchy, but a press release announced today suggests that personal genomics company 23andMe has performed a genome-wide association study comparing 100 current or former professional NFL players with a set of controls of unspecified sample size.
The shocking result:
The study did not find the tested players to be genetic outliers, suggesting that genetics may not be a good predictor of athletic success.
It's unsurprising that the results of this study are negative (more on this below), but the conclusions they draw from this are fallacious. In fact we know from twin and…
dgmacarthur | October 7, 2009Four scientists - including the omnipresent J. Craig Venter (left) - have penned an opinion piece in the latest issue of Nature based results from five individuals genotyped by two separate personal genomics companies. The article highlights some deficiencies in the way that genetic data are currently used by direct-to-consumer companies to generate risk predictions and to present them to customers.
The identity of the tested individuals isn't made explicit in the article, except to note that there were two males and two females from the same family and one unrelated female. All of the…
dgmacarthur | October 7, 2009The latest issue of Nature contains an embarrassment of riches for those of us interested in personal genomics, and indeed I'm having trouble figuring out which article to write about first.
Just look at the options: there's a review on approaches to tracking down the missing heritability of common diseases; there's a potentially highly controversial plea from Chicago researcher Bruce Lahn for acknowledgment that "genetic diversity contributes to variation across numerous physical, physiological and cognitive domains" between human populations; and there's an advance online publication…
dgmacarthur | October 6, 2009IBM's announcement that it will be entering the DNA sequencing technology race (which I mentioned briefly earlier today) has created a tremendous amount of mainstream media interest. That's understandable given IBM's size and history of innovation, but how likely are they to represent serious contenders for the potentially lucrative sequencing market?
Firstly, it's important to note that this announcement represents more of an expression of interest in the field rather than anything close to a mature technology; IBM will not be rolling out a machine to sequence your genome at any stage in…
dgmacarthur | October 6, 2009Things are as usual moving at ludicrous speed in the world of genomics, but sadly I only have time to post a few pointers to some of the most striking developments.
IBM is moving into the third-generation sequencing arena. The company is developing a new sequencing technology based on tiny nanopores - a field already being explored by the understated British nobility of sequencing, Oxford Nanopore. This is all over the news, but Dan Vorhaus has an introduction and is promising to follow up on further developments. You can also watch a pretty but largely content-free animation of the process…
dgmacarthur | October 6, 2009
Last week I noted a highly controversial plan by the UK Border Agency to begin using DNA and isotope testing to help determine the geographical origins of refugees, for use in making decisions about whether or not to grant asylum.
A reader has just pointed me to this recent post on ScienceInsider indicating an apparent change in policy: the Border Agency has now stated that the trial will be "proof of concept" only, and that "no decisions on individual cases will be made using these techniques, and they will not be used for evidential purposes". As ScienceInsider notes, this represents a…
dgmacarthur | September 29, 2009ScienceInsider reports that plans by the UK Border Agency to employ DNA and isotope testing to test the origins of asylum seekers are being met with outrage by scientists and refugee advocates.
There's not much information about the precise tests that will be employed, but what information has been made available has horrified a number of scientists including the University of Leicester's Alec Jeffreys:
After reviewing the Border Agency's plans, Jeffreys echoed those criticisms in an e-mail to Science: "The Borders Agency is clearly making huge and unwarranted assumptions about population…