November 4, 2009
Category:
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.
Posted by Daniel MacArthur at 1:15 PM • 0 Comments
November 3, 2009
Category:
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 diseases even though someone out there possesses genetic information
they would have needed to avoid this that could have been used to guide additional screening to detect such cancers early.
Throwing medically actionable data away without the subjects ever having a chance to learn about it is unconscionable -
we need to start changing the way we think about the rights of research subjects to their own data.
It's important not to understate the challenges posed by returning research data to research subjects - such as balancing against the need for privacy and data security, or unduly alarming people with inaccurate results - but these are not reasons to avoid data return. They are simply obstacles we need to overcome.
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Posted by Daniel MacArthur at 10:15 AM • 8 Comments
Category: complete genomics • disease genetics • huntington's • whole-genome sequencing
New-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:
Read on »
Posted by Daniel MacArthur at 7:30 AM • 5 Comments
October 27, 2009
Category: law
The rather worrying conclusion is that "at present it does not appear that there is any federal regulation--including HIPAA--that clearly restricts the transfer of customers' information as part of a sale of assets by a troubled DTC genomics company." Given that uncertainty, Moore and Sherlock conclude:
...the most practical advice at this time, for existing and potential customers, continues to be to understand the terms and conditions offered by each individual DTC genomics company with respect to their customers' information--and to recognize that, in bankruptcy, genomic data may be transferred to a similar company without regard to those terms and conditions.
There's also a tantalising promise of posts to come in the near future exploring the implications if impending regulatory changes in the DTC genomics area push testing companies firmly into the realm of clinical diagnostics.
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Posted by Daniel MacArthur at 12:00 PM • 2 Comments
October 25, 2009
Category: 23andme • ashg2009 • consumer-driven research • direct-to-consumer genetic testing • genetics of normal variation • genome-wide association studies • participant-driven research • personal genomics
It'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 overview of the potential of the 23andMe cohort for association studies: all 23andMe customers have genetic information for over 500,000 common genetic variants, and they are also encouraged to provide self-reported phenotype data on a wide range of traits ranging from the presence of detached earlobes to longitudinal tracking of Parkinson's disease symptoms. Eriksson reported that the company now had sufficient numbers of returned surveys to perform genome-wide association studies for 22 traits, with sample sizes ranging between 2500 and 6000 individuals - reasonable sample sizes for an initial look at the genetic architecture of a complex trait.
The company seems to be doing a reasonable job of identifying and controlling for the various potential confounders that plague genome-wide association studies, such as population structure. However, 23andMe faces an unusual challenge that standard academic GWAS consortia don't: the possibility that a subject will give a biased trait report after seeing their own genetic data.
Read on »
Posted by Daniel MacArthur at 5:30 AM • 10 Comments
October 14, 2009
Category: 23andme • ashg2009 • conference blogging
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.
Read on »
Posted by Daniel MacArthur at 7:15 PM • 8 Comments
October 13, 2009
Category: 23andme • genome-wide association studies • personal genomics
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 family studies that many (but not all) traits related to athletic performance are highly heritable; researchers just haven't been able to track down the vast majority of the genetic variants responsible yet, and this study is no exception.
What 23andMe have actually shown here is that
the limited subset of genetic variation captured by their genotyping chip (which almost exclusively targets genetic variants with a frequency of greater than 5%) doesn't include any variants with an extremely strong association with NFL prowess.
That shouldn't come as a surprise to anyone who's been following advances in human genetics for the last few years; a genome-wide association study on a highly complex trait with a sample size of 100 has, historically speaking, a vanishingly small chance of yielding any positive results at all. (Yes, there are exceptions, but I don't think a sensible prior expectation would be that athletic performance has a similar genetic architecture to macular degeneration.)
The press release argues that the results "speak to the breadth of the genetic research the company is undertaking". That may be so, but I certainly hope they aren't indicative of the general quality of 23andMe's research program. Much as I hate to say it about a company whose work I generally admire, this study carries all the hallmarks of being pure PR fluff. If you want to do a GWAS for athletic performance, at least wait until you have a homogeneous sample that's well-powered enough to have a fighting chance of detecting real associations.
On the bright side, 23andMe has been building up much more sensible sample sizes for other projects, including
4,500 older amateur athletes and over
3,000 Parkinson's disease patients. I'm hopeful that we'll see something a little more interesting than this NFL story roll out of the company over the next few months.
Posted by Daniel MacArthur at 12:30 PM • 23 Comments
October 7, 2009
Category: 23andme • commercial genetic testing • direct-to-consumer genetic testing • navigenics • personal genomics • risk prediction
Four 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 individuals were tested by the companies
23andMe and
Navigenics, which examine ~580,000 and ~923,000 sites of common genetic variation (SNPs), respectively. It's worth noting that in both cases the scans were performed before the companies were required to comply with CLIA standards (meaning that genotyping accuracy may have improved somewhat since these scans were done).
The first result is reassuring: the concordance between the genotype calls from the companies was excellent, with disagreements at fewer than one in every 3,000 sites. Previous comparisons (see comments on
this article) between 23andMe and deCODEme have found even smaller discrepancy rates, closer to one error in every 25,000 sites - the difference appears to be due to
a substantially higher error rate on the Navigenics platform compared to 23andMe (compared to research-quality typing performed on the same samples, Navigenics had a 0.29% discordance compared to 0.01% for 23andMe). Overall, though, it's clear that the levels of technical accuracy being achieved by the genotyping platforms used by major personal genomics companies are perfectly acceptable.
The real challenge is not with generating the raw genetic data, but rather with converting it into disease risk predictions - and here, the authors argue, the results of the comparison are less than ideal:
Read on »
Posted by Daniel MacArthur at 9:20 PM • 17 Comments
Category:
The
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.
Any of these would provide ample fodder for a post, but right now I only have time to write about one. Hmmm...
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Posted by Daniel MacArthur at 6:30 PM • 1 Comments
October 6, 2009
Category: ibm • next-generation sequencing • oxford nanopore technologies • whole-genome sequencing
IBM'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 the near future. Rather, the press release seems to have been triggered by
yesterday's announcement that IBM had been awarded a $557,000 grant from the National Human Genome Research Institute to help develop the sequencing technology.
IBM's proposed technology (which would make use of solid state nanopores, basically tiny holes in a silicon membrane) would certainly offer substantial advantages over existing sequencing platforms, but there remain some serious challenges to developing this tech. A friend working in the nanopore area proposed these as the most serious obstacles ahead:
Read on »
Posted by Daniel MacArthur at 11:00 AM • 3 Comments
