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…
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: Collins said that sequence-wise, the tests "appear to be highly accurate": there were almost no differences in the genotype information…
Regular readers will be aware that my last attempt to report on the presentations at last month's Cold Spring Harbor Laboratory Biology of Genomes meeting resulted in some controversy, as well as some fruitful (if sometimes heated) discussion on the topic of conference blogging. My next attempt will likely prove less divisive: I was kindly invited to write a meeting report by the journal Genome Medicine, and the full text of the article is now available free online. Given the brevity of the article and the scope of the journal I've focused my coverage on the presentations most relevant to…
I've stumbled rather late across a very promising new blog on the experience of a consumer genomics customer, Fantastic Voyage. The blog is primarily written by Grant Wood, the senior IT strategist for a clinical genetics institute in Salt Lake City; the premise of the blog is that Wood will discuss his own experience of consumer genetic testing (via a 23andMe genome scan), while receiving input from two advisors: Marc Williams, a medical geneticist, and Janet Williams, a genetic counsellor. In the two posts so far the highlights have been the insights from Marc Williams. For instance, on his…
Harvard biostatistician Peter Kraft (co-author of an excellent recent article on genetic risk prediction in the New England Journal of Medicine) has just added an interesting comment on his experience of this week's Consumer Genetics Show: I just wanted to share what for me were two stand-out moments at the CGS. First was Zak Kohane's discussion of the "Incidentalome"--a great turn of phrase that captures something I've been mulling over myself. (A less eloquent statement of this idea made it into the recent Nick Wade NYT article on genetic risk prediction). Basically, the idea is that even…
The buzz leading up to this week's Consumer Genetics Show in Boston suggested that a major announcement would be made by the CEO of genomics technology provider Illumina, Jay Flatley. Illumina provides the most popular second-generation sequencing instrument currently on the market, the Genome Analyzer II, and has been making noises about moving into the personal genomics industry since at least the beginning of the year, so the announcement itself was not exactly a shock: Illumina is launching a personal genome sequencing service. The launch comes with a new website, the appealingly titled…
From Emily Singer's article yesterday in Technology Review: A number of companies offering direct-to-consumer genetic testing have cropped up in the past two years to capitalize on these advances, from 23andMe and Navigenics, which offer genome-wide scans to identify specific disease-linked genetic variations, to Knome, which offers whole-genome sequencing to the wealthy. Any doubts that personal genomics is making its way into the mainstream can be assuaged with a look at Interleukin genetics, a startup that sells genetic tests for heart-disease risk, B vitamin metabolism, and other factors…
Not my highlights, sadly - I would have loved to attend the Consumer Genetics Show but was curiously unable to get anyone to pay for my plane tickets... Fortunately for me, others have done a sterling job of covering day one of the meeting. The freshest coverage by far is coming in 140-character bursts from Dan Vorhaus and Emily Singer, who are both live-tweeting the conference with gusto (for Twitter afficianados, commentary on the meeting is being aggregated with the hash-tag #CGS). Emily Singer also has an overview piece in MIT Technology Review with the promise of more to come. Meanwhile…
David Dooling has a great post that starts with the conference blogging issue, and then leaps off in a different but related direction - the curious double standard in the data release policies applying to large genome sequencing centres compared to other genomic researchers. As David notes, the advent of second-generation sequencing technologies means that medium-size genomics labs can now generate more sequence in a month than the entire Human Genome Project was able to generate in a year; indeed, a single Illumina Genome Analyzer can now produce a high-quality entire human genome sequence…
A reader has pointed me to the latest issue of the American Journal of Bioethics, which is devoted to social networking and personal genomics. I'm still working my way through the many interesting articles, but for now I wanted to cover some useful points in the editorial (entitled "A Pragmatic Consideration of Ethical Issues Relating to Personal Genomics"), which was written by a series of big names from personal genomics company 23andMe, including both co-founders. The article is designed to address some of the more popular misconceptions surrounding personal genomics; here's a quick run-…
There has been some very interesting online discussion in a number of venues today about the topic of social media and scientific conferences. For those who missed my post yesterday, the discussion was sparked by an article in ScienceInsider reporting that Cold Spring Harbor Laboratory had produced a new policy on the use of social media at its conferences, which essentially states that attendees should ask permission from presenters before discussing their work online (it's worth noting that this policy is one that CSHL has long applied to affiliated reporters). The policy release was…
Regular readers of this blog will be well aware that we are currently in the middle of a technology-driven revolution in genetics, which promises both advances in our understanding of human biology and profound social transformation. As we move into the genomic era, developing familiarity with the basic concepts of genetics - so-called genetic literacy - will be increasingly important. The goal of Mark Henderson's 50 Genetics Ideas You Really Need to Know is thus ambitious but timely: to distill the complexity of genetics into a series of digestible bite-sized chunks suitable for public…
Razib from Gene Expression has a frankly heroic post up dissecting a recent paper on genetic variation around the FUT2 gene, which encodes a cell surface protein involved in the pathway that produces the ABO blood group antigens. The story illustrates some of the difficulties associated with extracting information about human evolution from genetic sequence data. There is fairly compelling a priori evidence for natural selection having a strong effect on this gene during recent human evolution, but even with data on genetic variation from a large sample of worldwide populations it is…
I've just been pointed to a post on ScienceInsider that mentions my recent coverage (also on Twitter) of the Cold Spring Harbor Biology of Genomes meeting, and the resulting request for clarification from some professional science reporters: In addition to reporting on genetic variation in a gene that is active in fast muscle fibers at The Biology of Genomes meeting, MacArthur wrote several on the spot blog posts covering advances discussed by the participants. Francis Collins also mentioned results on his new Web site. A specialized Web-based news service, Genomeweb, complained. To attend…
BioArray News (subscription required) reports that genomic analysis technology provider Illumina has launched a new family of genotyping chips designed to simultaneously assay 4 million sites of variation in the human genome. The chips are a major step up from the 1-million-feature chips that currently represent the state of the art, and take advantage of several public projects generating catalogues of human genetic variation (such as the 1000 Genomes Project). Illumina has also increased the density of markers in and around genes, and fleshed out regions that have previously been…
Personal genomics is a rapidly evolving game, with a clear end goal in sight: offering consumers an accurate, affordable and complete genome sequence, and providing them with tools to dig out the useful nuggets of information contained therein. That goal remains out of reach, and while DNA sequencing technology continues to mature companies in the personal genomics space are offering products at various points on the trade-off curve between information content and cost. At the low-information/low-cost end, companies such as 23andMe and deCODEme offer cheap (sub-$1000) genome scans looking at…
It's difficult to distill down a meeting as data-rich as the Cold Spring Harbor Biology of Genomes meeting, but here's a first-pass attempt. We're sequencing lots of peopleOne of the highlights of the meeting was the update on progress from the 1000 Genomes (1KG) Project. I was fortunate enough to have been given a sneak peek at the data at the 1KG satellite meeting earlier in the week (which you can download yourself if you're so inclined), but it was still impressive to see it all put together in the presentation today by Goncalo Abecasis. Abecasis reported on the data emerging from the…
The GenomeWeb crew have been doing a great job of covering the Biology of Genomes conference - for more detail on the 1000 Genomes Project presentation see here (or here if you happen to have a subscription to In Sequence), and for a review of the panel discussion on genetic privacy (which I missed) see here.  Subscribe to Genetic Future.
A couple of weeks ago I reported that personal genome sequencing company Knome had launched a publicity stunt: selling a complete genome sequence on eBay. I argued that the current information content in a human genome doesn't come anywhere near justifying that cost for most of us, although it could potentially be worthwhile for patients suffering from a severe and undiagnosed genetic disease. Nonetheless, the auction closed a few days ago with a single bid at the opening price of $68,000. At the time I was unsure whether the purchaser was a prankster or a genuine bidder, and that's still a…
I'll be spending the next few days at the Biology of Genomes meeting at Cold Spring Harbor, NY - one of the most awaited events on the genomics calendar. I plan to blog here about the major themes emerging from the meeting; you can also follow me on Twitter if you want shorter, punchier updates, and I've set up a FriendFeed group for more complex topics. The meeting kicked off last night with a session on cancer genomics that gave a sense of the serious amounts of data currently being generated on the genetic origins of tumour development. Most of the work in this area has a fairly…