dgmacarthur | August 12, 2009The announcement of the Helicos genome sequence (which I've already discussed in detail) engendered a huge amount of media interest, sometimes for the wrong reasons.
Having the media attention directed elsewhere in the third-generation sequencing space was clearly an unwelcome experience for Helicos competitors Pacific Biosciences, who have responded with a press release announcing the successful raising of $68M to finance further development of their single-molecule real-time (SMRT) sequencing platform.
To be fair, raising that sort of capital in the current economic climate is no mean…
dgmacarthur | August 11, 2009David Dooling has an entertaining take on the Helicos genome sequence I discussed yesterday entitled "Another rich white guy sequences own genome".
I noted in my post yesterday that the alleged price drop for the Helicos sequence over current technologies was an illusion, but David includes a much more thorough analysis of the relative genome sequencing costs thrown around over the last couple of days and makes it very clear that the price Helicos is quoting is really no advance over the current prices for second-generation sequencing technologies:
They report reagent costs that are on par…
dgmacarthur | August 11, 2009A reader pointed me to this press release on the dire financial state of Icelandic biotech deCODE Genetics.
The slow financial train-wreck that is deCODE has been sliding off the rails for years (see stock price chart below), but things look set to reach their final resolution one way or another within the next few months: the company currently has $3.8 million in cash reserves, but is bleeding out $12 million per quarter, and "believes it has sufficient resources to fund operations only into the latter half of the third quarter".
Where to from here? In the press release, deCODE CEO Kari…
dgmacarthur | August 10, 2009Pushkarev, D., Neff, N., & Quake, S. (2009). Single-molecule sequencing of an individual human genome Nature Biotechnology DOI: 10.1038/nbt.1561
Yes, it's yet another "complete" individual genome sequence, following on the heels of Craig Venter, James Watson, an anonymous African male (twice, and not without controversy), two cancer patients, a Chinese man, and two Koreans.
There is a new twist, though: this is the first genome to be sequenced using single molecule sequencing technology - also known as "third-generation" sequencing, to distinguish it from first-generation Sanger…
dgmacarthur | August 6, 2009CNN reports:
At the Chongqing Children's Palace, experts are hoping to revolutionize child-rearing with the help of science. About 30 children aged 3 to 12 years old and their parents are participating in a new program that uses DNA testing to identify genetic gifts and predict the future.
The test is conducted by the Shanghai Biochip Corporation. Scientists claim a simple saliva swab collects as many as 10,000 cells that enable them to isolate eleven different genes. By taking a closer look at the genetic codes, they say they can extract information about a child's IQ, emotional control,…
dgmacarthur | August 4, 2009While I continue my work-induced blog coma, here's a guest post from Luke Jostins, a genetic epidemiology PhD student and the author of the blog Genetic Inference, delivering a fairly scathing critique of a recent whole-genome sequencing paper based on Life Technologies' SOLiD platform.
McKernan et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding Genome Research DOI: 10.1101/gr.091868.109
In prepublication at the moment is a
paper from the labs of ABI,
makers of the SOLiD sequencing system.…
dgmacarthur | August 3, 2009Those interested in the commercial, technical or ethical issues around the emerging industry of personal genomics now have a chance to put their questions to the co-founder of 23andMe, Anne Wojcicki. The NY Times blog Freakonomics is inviting readers to add their questions to the comments section of this post; Wojcicki will respond in a later post.
The questions are already pouring in: one reader asks if Wojcicki believes that there is a genetic component to intelligence; another asks for advice on getting a tattoo made from his 23andMe raw data; another reader is looking for a job.
This is…
dgmacarthur | July 17, 2009Purcell et al. (2009). Common polygenic variation contributes to risk of schizophrenia and bipolar disorder Nature DOI: 10.1038/nature08185
Neil Walker has been doing a spectacular job of serving up useful information in the comments recently, so I asked him to write the first ever guest post on Genetic Future - something that (as I will be announcing shortly) I intend to do fairly regularly over the next couple of months.
The topic is a paper that has created a rather perplexed buzz recently in the complex disease genetics community: the genome-wide association study (GWAS) for…
dgmacarthur | July 9, 2009A quick pointer to a new blog on the genomics scene that's just been officially launched: Genomics Law Report, a corporate blog from legal firm Robinson, Bradshaw and Hinson. One of the contributors, Dan Vorhaus, is an advisor to the Personal Genome Project and provides one of the highest signal-to-noise ratio genomics feeds on Twitter.
Dan's latest post, an excellent analysis of 23andMe's latest push into consumer-driven research, is a good place to start reading.
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dgmacarthur | July 8, 2009I just received the following email from the Nuffield Council on Bioethics - I'd recommend anyone interested in the future of personalised medicine in the UK consider submitting their views to the inquiry. I'll be putting together my own submission, which I'll also post here on Genetic Future.
Medical profiling and online medicine: the ethics of 'personalised' healthcare in a consumer age
The Nuffield Council on Bioethics is currently running a consultation on Medical profiling and online medicine: the ethics of 'personalised' healthcare in a consumer age. The paper provides background…
dgmacarthur | July 7, 2009Personal genomics company 23andMe has always differentiated itself from its more sober competitors through an emphasis on collaborative, consumer-driven research - essentially, encouraging its customers to contribute their genetic and trait data to internal research projects designed to find new genetic associations. It is widely believed that generating novel associations between genetic variants and traits is actually the core business strategy for the company, although the precise mechanism for converting such associations into cash-flow remains unclear.
The company's initial attempt at…
dgmacarthur | July 7, 2009The UK House of Lords Science and Technology Committee has published the long-awaited report (PDF) from its inquiry into genomic medicine.
Mark Henderson at The Times has been busy today, putting out three excellent pieces on the report: a summary of the major implications, an opinion piece pushing the need for the health service to respond quickly to the arrival of genomic medicine, and a lengthy blog post praising the report and providing his views in more detail.
I find little to disagree with in Henderson's coverage, and certainly agree with his overall opinion of the report: this…
dgmacarthur | July 6, 2009A while back I pondered the possibility of creating icons for conference presenters to add to their first slide to alert bloggers/tweeters in the audience about whether the presented data was "blog-safe". This was provoked by a recent episode illustrating general confusion among bloggers (in this case, me) and scientists about the use of social media at conferences.
Fellow Australian-turned-UK-resident-scientist Cameron Neylon has now put together a handy set of slides for presenters to label both "blog-safe" and "no-blogging" presentations. The slides have a ccZero license and so are freely…
dgmacarthur | June 24, 2009Pharmacogenetics 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…
dgmacarthur | June 24, 2009GenomeWeb 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…
dgmacarthur | June 24, 2009Geoff 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:…
dgmacarthur | June 23, 2009Update: 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…
dgmacarthur | June 19, 2009Added 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…
dgmacarthur | June 19, 2009Misha 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.
What's the business model here? The registration page provides some hints:
Your questionnaire responses and genetic information will be used for genetic research. One of the main goals of TruGenetics⢠is to develop a unique research database for conducting genetic studies. Your decision to use TruGenetics'⢠services indicates that you are willing to contribute your questionnaire responses and genetic information to…
dgmacarthur | June 18, 2009Readers 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…