dgmacarthur | March 23, 2009To complete my 23andMe trifecta this morning, here's Steve Murphy frothing at the mouth about the company's recent antics:
Why is it so vital that physicians,
nurses and others in the healthcare field try to stay above the law?
Because patients lose trust in the system. They begin to think that
their care givers are reckless criminals. And WHO would trust their
life to a criminal???
Apparently,
this stream of thought doesn't even phase a company like 23andME. You
see, they are blatantly breaking the law in several states. Why? They
are on a mission. Destroy the current healthcare system,…
dgmacarthur | March 23, 2009This casual aside on a recent post on personal genomics company 23andMe's corporate blog caught my eye:
Mutations in several other genes have also been associated with
Parkinson's disease, but these are extremely rare. Many have been found
only in one or two families. While these mutations are so rare that
they are not covered by 23andMe (to date we have found no customers
with any of them), studying them could help scientists better
understand the mechanisms of Parkinson's generally... [my emphasis]
In other words, the company already has probes on its custom chip targeting these variants,…
dgmacarthur | March 23, 2009Drew Yates at ThinkGene has a delightfully cynical take on the personal genomics industry:
I know 23andMe's game, it's the "break the mean with variance" game,
and it's the same Silicon Valley game that's been played by internet
media companies for the last decade. How to play: a network of superior
talent and funding backs a group of startups that executes something
outrageous and otherwise unobtainable by contractual or legal
permission (like YouTube, Napster, Google itself... have we forgotten the
shear audacity of copying all the information in the world without
permission?) Then, that…
dgmacarthur | March 22, 2009Yesterday I pointed to an article by New Scientist editor Michael Le Page advocating routine carrier testing for severe disease genes in parents-to-be, followed by IVF and pre-implantation genetic screening of embryos for couples unfortunate enough to both be carrying mutations in the same gene. I asked for well-reasoned objections to this approach from commenters.
Razib responded with a post at Gene Expression. Firstly, he pointed out that well-reasoned objections are not what matters in this debate:
...though reason is the "front side of the house" in this discussion, the
real work is being…
dgmacarthur | March 21, 2009A couple of weeks ago I pointed to an article by bioethicist Jacob Appel arguing that genetic screening for severe disease mutations should be mandatory for parents undergoing IVF, and that not doing so is tantamount to child abuse.
Today the same theme is taken up by New Scientist biology editor Michael Le Page, but extending the process to all parents-to-be via carrier testing:
All would-be parents should be offered screening to alert them to any
genetic disorders they risk passing on to their children. Those at risk
should then be offered IVF with pre-implantation genetic diagnosis
(IVF-…
dgmacarthur | March 18, 2009John Hawks recounts a recent conversation about bioinformatics:
I was talking with a scientist last week who is in charge of a
massive dataset. He told me he had heard complaints from many of his
biologist friends that today's students are trained to be computer
scientists, not biologists. Why, he asked, would we want to do that
when the amount of data we handle is so trivial?
Now, you have to understand, to this person a dataset of 1000 whole genomes is
trivial. He said, don't these students understand that in a few years
all the software they wrote to handle these data will be obsolete?…
dgmacarthur | March 13, 2009Nalls, M., Simon-Sanchez, J., Gibbs, J., Paisan-Ruiz, C., Bras, J., Tanaka, T., Matarin, M., Scholz, S., Weitz, C., Harris, T., Ferrucci, L., Hardy, J., & Singleton, A. (2009). Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics PLoS Genetics, 5 (3) DOI: 10.1371/journal.pgen.1000415A new study indicates that increases in mobility, urbanisation, and cross-population mating over the last century have substantially reduced inbreeding, and left a distinctive trace in the genome of modern Americans.
The study, published in the latest…
dgmacarthur | March 13, 2009I just noticed that GeneTests, a voluntary listing of US and international laboratories offering in-house genetic tests, has released an updated version of their graph of commercially available tests:
You can see immediately that as the number of tested diseases continues to climb, the number of testing laboratories has plateaued - at least partly the result of more efficient testing methods, and of specialised "boutique" testing labs being swallowed up or out-competed by larger players.
As of today, GeneTests lists 606 laboratories testing for 1,705 diseases; 1,419 of the tests are "clinical…
dgmacarthur | March 12, 2009Over at the 23andMe blog The Spittoon, company co-founder Linda Avey expands on her vision for a novel model of genomic research, in which personal genomics customers contribute their genetic and health data to fuel research into the inherited and environmental triggers for disease.
This is a model that 23andMe has been building towards for a long time. In May last year the company launched 23andWe, a cutely-named effort to obtain detailed health and trait data from their existing customers through online surveys which could then be combined with genetic data to find novel gene-trait…
dgmacarthur | March 12, 2009I posted a while back on two duelling essays in Nature on the intensely controversial subject of whether scientists should be permitted to study group differences in cognition. Nature now has a series of correspondence on the topic in its latest issue.
Firstly, there are rebuttals from the authors of the two original essays: Steven Rose argues that the debate is dead and that reviving it serves no purpose, while Ceci and Williams argue (substantially more convincingly, in my opinion) that Rose's declaration of these areas of research as invalid is premature.
Some of the other opinions are…
dgmacarthur | March 12, 2009Genetic 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) to infer genetic ancestry provide a much more detailed and accurate picture of the geographical origins of your genome.
No surprises here. The power of the type of genome-wide genotype data generated by 23andMe for ancestry prediction has been compellingly illustrated by a series of recent…
dgmacarthur | March 10, 2009Fan 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 tests to predict adult height are still a long way off being accurate; currently, known genetic variants can predict just over 5% of the variance in height, as opposed to 40% predicted using a simple algorithm based on the heights of both parents. The genetic complexity of height means that trying to…
dgmacarthur | March 9, 2009Keith 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 genomics - but the prospect of coordinating hundreds of inexperienced undergraduate students in a genome annotation project is incredibly daunting. This would take a very talented and dedicated group of educators to pull off successfully.
If anyone has considered such a project, let Keith know in…
dgmacarthur | March 9, 2009Jan 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 location of small-scale genetic variants. However, their linear arrangement makes it very difficult to use them to present large-scale genetic variations (duplications, deletions or inversions). This is a serious problem, as these types of genetic variants are surprisingly common in the human genome, and…
dgmacarthur | March 6, 2009I 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 three are researchers working on hard problems in major genomics facilities while walking the blogging tightrope.
This week Dan advocated genetic testing of all cancers, Anthony had two thought-provoking posts on personalised medicine (here and here), and David ran a critical eye over pharma giant…
dgmacarthur | March 6, 2009Over 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 "Western societies have long acknowledged that parental authority cannot undermine the medical interests of a child". As examples, Appell cites the facts that Jehovah's Witnesses cannot deny their own children blood transfusions, however strong their religious opposition, and that "American courts…
dgmacarthur | March 6, 2009John 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 Healthcare". You invite those who
you believe should see your medical information and you can disinvite
them at anytime.
Halamka, as one of the first 10 participants of the audacious Personal Genome Project, knows more than a little about sharing health data: he's agreed to publish both his medical…
dgmacarthur | March 6, 2009Nejentsev 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 we really start tracking down the low-frequency genetic variants (between 0.1 and 5% in frequency) that likely contribute substantially to the risk of common diseases like arthritis and diabetes. It's far too early for me to claim vindication for this prediction, but a paper published online today…
dgmacarthur | March 5, 2009Jones 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 underlying disease risk.
Traditionally, geneticists have pinned down such variants using large family studies. By using these families to track which parts of the genome tend to be co-inherited with the disease, it's possible to zoom in on the region of DNA that harbours the disease-causing mutation…
dgmacarthur | March 5, 2009Last 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. height, also discussed yesterday) would make it highly unlikely that embryo screening would be effective for these, although for hair and eye colour such screening is certainly feasible.
The media coverage of this fertility clinic - run by reproductive endocrinologist Jeff Steinberg (pictured) -…