dgmacarthur

Genetic genealogist Blaine Bettinger explores the results of his ancestry testing from 23andMe, and compares it to previous results from a much lower-resolution test. The main message: the hundreds of thousands of genetic markers used by 23andMe (and other personal genomics companies, e.g. deCODEme…

Fan Liu, Kate van Duijn, Johannes R. Vingerling, Albert Hofman, André G. Uitterlinden, A. Cecile J.W. Janssens, Manfred Kayser (2009). Eye color and the prediction of complex phenotypes from genotypes Current Biology, 19 (5) DOI: 10.1016/j.cub.2009.01.027 In a recent post I noted that genetic…

Keith Robison notes that commercial DNA sequencing is now cheap enough to seriously consider generating and analysing a bacterial genome sequence as an undergraduate group-work project. I think it's a fantastic idea in principle, and would certainly give students a flavour of the reality of modern…

Jan Aerts discusses the problem of incorporating information on large-scale genomic rearrangements into genome browsers. Genome browsers such as UCSC and Ensembl are fantastic for presenting many types of genomic information, such as the position and orientation of protein-coding genes or the…

I doubt anyone's noticed, but I recently rearranged my "Blogs I Read" menu to give appropriate prominence to three fellow genomics bloggers: Anthony Fejes, Dan Koboldt and David Dooling. If you're interested in the cutting edge of modern genomics you should definitely be reading these guys; all…

Over at Opposing Views, bioethicist Jacob Appel argues that pre-implantation genetic screening for severe disease mutations should be compulsory for parents undergoing IVF. Appell dodges one obvious criticism of this suggestion - that it unacceptably limits parental autonomy - by pointing out that…

John Halamka reports that Google Health has quietly launched an application for secure sharing of your online medical records: The Google solution, introduced without fanfare, solves many confidentiality issues by putting the patient in control of medical record sharing. Call it "Facebook for…

Nejentsev et al. (2009). Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes. Science DOI: 10.1126/science.1167728 The first item on my long list of predictions for 2009 was that this will be the year of rare variants for common disease - the year that…

Jones et al. (2009). Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene. Science DOI: 10.1126/science.1171202 A paper published online today in Science illustrates both the potential and the challenges of using large-scale DNA sequencing to identify rare genetic variants…

Last month I mentioned a US fertility clinic that was offering couples undergoing IVF the opportunity to screen their embryos for sex, and for genes associated with "cosmetic" traits such as eye and hair colour. I used this as an opportunity to note that the genetic complexity of many traits (e.g.…

I 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…

I 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…

Yurii 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…

From 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…

James 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.2009.12 The clever boys and girls at Oxford Nanopore Technologies - one of the most…

An 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…

I'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". Subscribe to Genetic Future.

A 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.…

Icelandic 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…

Warfarin (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…

I'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. Subscribe to Genetic Future.

I 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…

Just 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…

Steve 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…

[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…

In 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…

I'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…

I 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…

I'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…

Katherine 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:…