dgmacarthur | January 12, 2009Steven Pinker's recent article in the NY Times is a rich source of insight into the field of personal genomics and the experience of personal genomics customers - if you haven't read it already, you really should.
This paragraph, for instance, seems to perfectly encapsulate the experience of the average intellectually curious personal genomics customer:
It became all the more confusing when I browsed for genes beyond those on the summary page. Both the P.G.P. and the genome browser turned up studies that linked various of my genes to an elevated risk of prostate cancer, deflating my initial…
dgmacarthur | January 12, 2009A press release today describes a potentially exciting partnership between two companies in the DNA sequencing space: Oxford Nanopore Technologies and Illumina.
Illumina is an established player in the field, providing one of the most widely-used second-generation sequencing platforms (the Genome Analyzer, previously known as Solexa). Oxford, in contrast, is a young but promising contestant in the increasingly heated race towards so-called "third-generation" sequencing technologies, which promise even more staggering increases in the ability of researchers to generate vast amounts of…
dgmacarthur | January 11, 2009I'll hopefully have more to say about Steven Pinker's long and excellent essay in the NY Times later - but for now, go read it yourself, and then read John Hawks' thoughtful comments.
dgmacarthur | January 11, 2009Some of you may have noticed that the RSS feed for the DNA Network has been down for quite some time. Hsien-Hsien Li from Eye on DNA has come up with a work-around.
To re-subscribe to the Network, click here.
dgmacarthur | January 9, 2009T. Hofer, N. Ray, D. Wegmann, L. Excoffier (2009). Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection Annals of Human Genetics, 73 (1), 95-108 DOI: 10.1111/j.1469-1809.2008.00489.x
I've just been reading over an article from late last year in the Annals of Human Genetics:
In this study, we examined 772 STRs, 210 diallelic indels, and 2834 SNPs typed in 53 human populations worldwide under the HGDP-CEPH Diversity Panel to determine to which extent allele frequency differs among four regions (…
dgmacarthur | January 7, 2009Daniel G. Hert, Christopher P. Fredlake, Annelise E. Barron (2008). Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods Electrophoresis, 29 (23), 4618-4626 DOI: 10.1002/elps.200800456
The dideoxy termination method of DNA sequencing (often called Sanger sequencing after the technique's inventor, Fred Sanger) has been the workhorse of pretty much every molecular biology lab for the last 30 years. However, over the last few years the method has been increasingly supplanted by so-called next-generation sequencing…
dgmacarthur | December 22, 2008Emily Singer has a fantastic article in MIT's Technology Review reviewing the current state of play in human genomics. A curious highlight for me was this panel of mug-shots from the PGP-10, the 10 high-profile volunteers currently having their genomes sequenced as part of the Personal Genome Project:
Top row from left: Misha Angrist, Keith Batchelder, George Church, Esther Dyson, Rosalynn Gill.
Bottom row from left: John Halamka, Stanley Lapidus, Kirk Maxey, Steven Pinker, James Sherley.
Links for each participant are to their profile on the PGP website, which includes information on…
dgmacarthur | December 19, 2008xkcd has some good advice for high-schoolers:
That goes doubly for anyone even vaguely interested in a career in biology, and particularly genetics - right now, even some basic scripting experience will take you further than any amount of pipette-wrangling. I wish I'd known this when I was back in high school...
Subscribe to Genetic Future.
dgmacarthur | December 19, 2008Sure is news to me - from popsci.com:
Archon X Prize for Genomics
Purse: $10 million
Goal: Sequence 100 human genomes in 10 days for $10,000 per genome or less
Status: ZS Genetics, which is developing an approach that replaces fluorescent tagging with decodable electron-microscope images of DNA, is a favorite to win. [my emphasis]
ZS Genetics is developing an extremely unusual approach to DNA sequencing, which involves directly imaging DNA with an electron microscope (pictured to the left). The potential pay-offs of this approach are huge: in particular, this approach would have minimal costs…
dgmacarthur | December 18, 2008Nature has a list of the top news stories of 2008, and "Personal genomics goes mainstream" comes up second:
In January, an international consortium announced the launch of the 1,000 Genomes Project, which aims to provide a catalogue of human genetic variation. In October, the Personal Genome Project, which hopes to sequence and publish the genomes of as many people as possible, released initial data for ten participants. Meanwhile, as researchers wondered what they could glean from the results coming from personal-genomics companies, the prices of such services dropped. The firm 23andMe,…
dgmacarthur | December 17, 2008David Ewing Duncan has a piece in Portfolio.com about Complete Genomics, a DNA sequencing company that launched back in October promising to offer whole-genome sequencing for $5000 by mid-2009.
Complete Genomics is based on some allegedly powerful new technology (here's a cartoon summary) developed in-house - I say "allegedly" because the company is yet to release any real data to demonstrate the capacity of its platform. New sequencing platforms are a dime a dozen nowadays, but the novelty of the Complete business strategy is this: instead of selling instruments to sequencing facilities, it…
dgmacarthur | December 16, 2008From a recent paper in Nature Reviews Microbiology, it's probiogenomics!
The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics…
dgmacarthur | December 15, 2008Willer et al. (2008). Six new loci associated with body mass index highlight a neuronal influence on body weight regulation Nature Genetics DOI: 10.1038/ng.287
Thorleifsson et al. (2008). Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity Nature Genetics DOI: 10.1038/ng.274
There are two massive studies now online in Nature Genetics looking at the genetic architecture of body mass index (BMI). Body mass index is a widely-used measure of body fat levels, calculated by dividing a subject's weight (in kg) by the sqare of their height (in…
dgmacarthur | December 12, 2008There's a new paper in the American Journal of Human Genetics following on from the paper on the genetics of metabolic traits that I posted on earlier in the week. This study explicitly focuses on the population structure of the Finns, and includes these maps showing the correlation between geography and genetics within Finland and related populations:
(Image from Jakkula et al. (2008) The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population The American Journal of Human Genetics, 83 (6), 787-794 DOI: 10.1016/j.ajhg.2008.11.005)
More details below the…
dgmacarthur | December 11, 2008An article in the latest issue of the New England Journal of Medicine takes a look at the sharing of genetic risk factors between type 1 diabetes and celiac disease, two reasonably common auto-immune disorders (affecting ~0.4 and ~0.1%, respectively, of individuals of northern European origin).
Celiac disease is more common in type 1 diabetes than in the general population, so there's some reason to expect some shared genetic risk factors between the two disease. And indeed in this study the degree of overlap in risk genes between the two diseases is striking - out of 25 genes with a well-…
dgmacarthur | December 10, 2008Pharmacogenomics Reporter has a fascinating article (subscription only, I think) on the impact of individual gene patents granted by the US patenting system on the future of personal genomics. Essentially, the issue for companies conducting genome-wide analysis (including SNP chips or whole-genome sequencing) is that setting up licensing deals for each individual gene makes business complex and expensive - potentially discouraging investment in the field.
On their website, personal genomics company Navigenics explains the problem:
For example, if we obtain licenses from third parties to 10…
dgmacarthur | December 10, 2008I posted last week on a paper purporting to identify a genetic variant influencing the placebo response. The main message of my post was that given the terrible history of small candidate gene association studies, a paper describing an association with a sample size of just 25 individuals should be simply ignored - and certainly not described in the popular science press as "a milestone".
Now Neuroskeptic has a detailed critique of the paper up in which he argues that the problems in the study go much deeper than inadequate sample size - in fact, the study wasn't measuring the placebo effect…
dgmacarthur | December 9, 2008A commentary in Nature by a group of psychologists, ethicists and neuroscientists has a controversial message:
Based on our considerations, we call for a presumption that mentally competent adults should be able to engage in cognitive enhancement using drugs. [their emphasis]
The authors call for a rejection of the common knee-jerk notion that cognitive enhancement in healthy individuals - using drugs like amphetamines or the fatigue suppressant modafinil, or other means such as brain stimulation - is somehow "cheating", "unnatural", or "drug abuse". None of these criticisms hold up to close…
dgmacarthur | December 8, 2008A few days ago I posted a picture depicting the genetic ancestry of African-Americans modelled as a linear combination of European and Nigerian genetic clusters (reproduced below). Dienekes has some thoughtful comments on the same picture.
Meanwhile, Razib comments on a post from Ed Yong discussing the social flexibility of race. Ed cites a survey showing that people change their self-described race with surprising frequency, with about one in five respondents changing their description at least once over a nineteen year period (with some intriguing correlations with incarceration and…
dgmacarthur | December 8, 2008Nature Genetics has just released six advance online manuscripts on the genetic architecture of complex metabolic traits. The amount of data in the manuscripts is overwhelming, so this post is really just a first impression; I suspect I'll have more to say once I've had time to dig into the juicy marrow of the supplementary data.
The general approach of exploring the genetic architecture of quantitative disease-associated traits (often called intermediate phenotypes or endophenotypes) rather than categorical case-control analyses of disease status raises some interesting questions, but I'm…