dgmacarthur | March 4, 2009I received an email a while back from a reader wondering why his friend has had to submit multiple saliva samples to personal genomics company 23andMe without getting a result back. Customers in a similar position may be reassured by a lengthy explanation posted yesterday on 23andMe's blog about their sample processing protocol, penned by the company's Director of Operations.
(Other potential customers may also be reassured to hear that this type of failure is apparently "quite rare", although 23andMe haven't responded yet to my queries regarding the frequency of sample failures; and that…
dgmacarthur | March 3, 2009I discussed the second-generation sequencing company Complete Genomics a couple of weeks ago (see here and here). These guys are unique in that they offer their technology only as a service, rather than the usual business model of selling platforms to genomics facilities, and a highly restricted service at that: Complete has stated fairly categorically that it will only be sequencing human genomes (no plants, algae, or even chimpanzees!).
Whether this business model will prove a commercial success remains to be seen, but the company seems to have impressed the genomics community with its…
dgmacarthur | March 3, 2009Yurii S Aulchenko, Maksim V Struchalin, Nadezhda M Belonogova, Tatiana I Axenovich, Michael N Weedon, Albert Hofman, Andre G Uitterlinden, Manfred Kayser, Ben A Oostra, Cornelia M van Duijn, A Cecile J W Janssens, Pavel M Borodin (2009). Predicting human height by Victorian and genomic methods European Journal of Human Genetics DOI: 10.1038/ejhg.2009.5
Human height is a strongly genetic trait: in well-nourished Westerners somewhere in the vicinity of 80-90% of the variation in height is due to genetic factors; if your parents are tall, there's a very good chance you will be too. That means…
dgmacarthur | February 25, 2009From an editorial in this week's Nature:
Indeed, researchers would do well to blog more than they do. The experience of journals such as Cell and PLoS ONE,
which allow people to comment on papers online, suggests that
researchers are very reluctant to engage in such forums. But the
blogosphere tends to be less inhibited, and technical discussions there
seem likely to increase.
Moreover, there are
societal debates that have much to gain from the uncensored voices of
researchers. A good blogging website consumes much of the spare time of
the one or several fully committed scientists that write…
dgmacarthur | February 23, 2009James Clarke, Hai-Chen Wu, Lakmal Jayasinghe, Alpesh Patel, Stuart Reid, Hagan Bayley (2009). Continuous base identification for single-molecule nanopore DNA sequencing Nature Nanotechnology DOI: 10.1038/nnano.2009.12The clever boys and girls at Oxford Nanopore Technologies - one of the most quietly impressive contenders in the hotly-contested next-generation DNA sequencing race - have a new paper out in Nature Nanotechnology today. The paper demonstrates proof of principle for a crucial step in their approach to DNA sequencing, the accurate recognition of DNA bases as they pass through a…
dgmacarthur | February 21, 2009An article on GenomeWeb Daily News discusses some tantalising but still unpublished data from a team at Penn State University led by Mark Shriver:
The team has already found a handful of genes that seem to influence
different facial features. "I think we've got compelling evidence for
six genes that we tested," Shriver said. The team's data also suggests
that different parts of the face are influenced by different genes.
Variation in face shape is certainly strikingly heritable (all you need to do is look at any family photo to see that), but there's currently little known about the genetic…
dgmacarthur | February 20, 2009I'm struggling to figure out what is more disturbing about this post - the fact that 23andMe are actually trying to say that BRCA gene testing is not "medical genetic testing", or Steve Murphy talking about his "man parts".
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dgmacarthur | February 20, 2009A reader pointed me to this article on the collaborative research project between personal genomics company Navigenics and the Scripps Translational Science Institute. The project aimed to recruit 10,000 people from among employees and patients of Scripps Health and their family and friends. Recruits will receive data from a Navigenics genome scan at a subsidised price of $470, compared to the normal commercial price of $2,500.
The bad news: despite the dramatic price reduction, the project has only succeeded in recruiting 4,000 participants - just 40% of the original goal. Recruitment ends…
dgmacarthur | February 19, 2009Icelandic genomics company deCODE Genetics has received a license to market direct-to-consumer genetic tests (such as the genome scan provided by daughter company deCODEme) in the state of California. This follows the regulatory crackdown by California's public health department last June, which sent nervous ripples through the direct-to-consumer genetic testing industry.
Personal genomics rivals 23andMe and Navigenics both received their own licenses last August, and it's unclear to me why it's taken so long for deCODEme to follow suit (please feel free to speculate wildly in the comments…
dgmacarthur | February 19, 2009Warfarin (a.k.a. Coumadin, Jantoven, Marevan, or Waran) is the most widely-prescribed blood-thinning agent on the market. It's also (in the words of Howard McLeod) a "terrible drug" - it has a very narrow therapeutic window, meaning that the minimal useful dose and the maximal safe dose are very close together. (The effects of over-dosing on warfarin - reduced blood clotting - are so severe that the drug is also used as a highly effective rat poison.)
To further complicate things, the dosage of the drug that is both effective and safe differs widely between individuals, and is known to be…
dgmacarthur | February 18, 2009I'm guessing a lot of us have been waiting for John Hawks to comment in detail about the release of low-coverage sequencing of the Neanderthal genome - well, wait no longer.
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dgmacarthur | February 18, 2009I was surprised by the response to my brief post on the question of whether group (race or gender) differences in intelligence are a valid topic for scientific investigation: not only because of the volume of comments, but also because the ensuing debate was largely civil and on-topic. The post was sparked off by two conflicting essays in the most recent issue of Nature, one by Steven Rose opposing research into such differences, and another by Ceci and Williams arguing that sealing off certain lines of enquiry - however contentious - is dangerous and unscientific.
There's now more on this…
dgmacarthur | February 16, 2009Just in case anyone has missed it, the pair of duelling essays in the latest issue of Nature is well worth a read. The topic is whether there is any justification for scientific exploration of associations between gender or race and intelligence; Stephen Ceci and Wendy M. Williams from Cornell argue the affirmative, while Steven Rose takes up the opposing case.
The debate continues as a lively discussion on Nature Network, which contains many thoughtful comments from both sides.
I find it pretty hard to stomach the notion that any field of scientific enquiry should be completely off the table…
dgmacarthur | February 15, 2009Steve Murphy is up in arms about a recent email from 23andMe to its customers advertising the use of genetic variants on its V2 chip to predict individual risk of statin-induced myopathy and breast cancer.
Of course, Steve does have a strong financial interest in 23andMe staying as far away as possible from the area of clinical diagnostics, but I share his unease here.
So far personal genomics companies have by and large done their best to steer clear of being seen as "doing medicine", but this move would seem to put 23andMe explicitly over that line. In the case of the breast cancer…
dgmacarthur | February 15, 2009[Added in edit in response to concerned emails: The original title was deliberately provocative, and contrary to the message in the text; I apologise for any misunderstanding. I've largely rewritten the post to make my point more clearly.]
One of the curious and paradoxical effects of Big Genetics projects like the 1000 Genomes Project - which plans to generate low-coverage whole-genome sequences for ~1,500 people by the end of this year, providing a map of human genetic variation of unprecedented resolution - is that while they considerably accelerate research in the long term, they can…
dgmacarthur | February 15, 2009In a comment on my previous post, Tera Eerkes is skeptical about the utility of routinely performing whole-genome sequencing on newborns:
I found this comment absolutely fascinating, given the recent
reports on translational analysis, that indicate an actual lack of
clinical utility of KRAS testing and other drug-gene interactions.
I believe these reports are indicative of a trend, not an exception.
I think it is remarkable that anyone feels, even optimistically,
that we're going to need a genome-wide scan for clinically useful
indicators by 2019.
I predict that there will be a…
dgmacarthur | February 12, 2009I'm slowly catching up on genomics news from the last week - this story in particular has been getting a lot of press.
The executive summary: Jay Flatley, CEO of genomic technology manufacturer Illumina, predicts that whole-genome sequencing of newborns will become routine within a decade.
Flatley has an obvious financial interest in this prediction coming true, since Illumina provides the most commercially successful next-generation sequencing platform currently on the market, the Genome Analyzer, and has recently invested heavily in emerging "third-generation" sequencing technologies (by…
dgmacarthur | February 9, 2009I wrote last week about the dramatic presentation here at AGBT by Clifford Reid, CEO of new DNA sequencing company Complete Genomics. Reid made grand promises - entire human genome sequencing for $5000 available this year, and the sequencing of a million complete human genomes within the next five years - and presented some impressive data on the sequencing of their first human genome, from an anonymous American male.
Reid's promises and data certainly caught the attention of the genomics community, and received decent media interest - the story was covered by New Scientist, Bio-IT World,…
dgmacarthur | February 9, 2009I'll be uploading a few of what I saw as the highlights from the AGBT meeting over the next week or so, as I go over my notes - you can also browse over Anthony Fejes' blog for live-blogging of many of the sessions. In no particular order, here are some of the tid-bits gleaned from Friday's sessions.
Kari Stefansson gave an overview of some of the latest results coming out from deCODE Genetics. He argued that combining multiple genetic variants for common diseases can now give clinically useful results - e.g. their work on thyroid cancer (published today in Nature Genetics) shows that the 3.7…
dgmacarthur | February 7, 2009Katherine Kelly is a molecular biology major at Princeton University currently writing her senior thesis on personal genome services. As part of her research she would like to interview customers of 23andMe and Navigenics about their experiences of the personal genomics process.
The problem: although she can find plenty of 23andMe customers, she is yet to identify a single customer of Navigenics.
If you are a Navigenics customer that is not financially involved with Navigenics in any way, and would be happy to answer a few
questions (over the phone if possible) about your experience taking…