genome-wide association studies
dgmacarthur | January 14, 2009
Olivia Judson's blog has a guest post by Aaron Hirsh that got me thinking about a topic that will be familiar to most scientists: the transition of research towards Big Science. Big Science basically includes any project involving a large consortium of research groups working together on a tightly-defined problem, usually with a very specific goal in mind (e.g. sequence and analyse a genome, or build a big machine to smash particles together at high speed).
Hirsh only mentions genetics in passing, but this field - and particularly human genetics - is an area where the trend towards Big…
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 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…
dgmacarthur | November 3, 2008One of the major challenges of the personal genomic era will be knowing exactly which (if any) of the millions of genetic variants present in your genome are likely to actually have an impact on your health. Such predictions are particularly problematic for regulatory variants - genetic changes that alter the expression levels of genes, rather than the sequence of the protein they encode. A paper out in PLoS Genetics this week goes some way towards solving this problem by giving researchers a much better idea of exactly where they need to look for these variants.
The paper
The paper draws on…
dgmacarthur | October 14, 2008From a geneticist's point of view, male pattern baldness - also known as androgenic alopecia - is a tempting target. Baldness is common in the general population, with a prevalence that increases sharply with age (as a rule of thumb, a male's percentage risk of baldness is approximately equal to his age, e.g. 50% at age 50, and 90% at age 90), so there are no shortage of cases to study. It's also a strongly heritable trait, with about 80% of the variation in risk being due to genetic factors. Finally, baldness has been reported to be associated with a wide range of diseases such as prostate…
dgmacarthur | September 16, 2008The genome-wide association study has been the technique du jour in human genetics for much of the last two years. It's a pure brute force approach, surveying up to a million sites of common variation throughout the genomes of thousands of people at a time, some of whom suffer from a particular disease, and some of whom are healthy controls. The underlying principle is simple: if a genetic variant increases the risk of the disease in question, it will be more common in patients than in controls.
The whole exercise is predicated on one major assumption: that common diseases, such as type 2…
dgmacarthur | September 15, 2008The successes of genome-wide association studies (GWAS) in identifying genetic risk factors for common diseases have been heavily publicised in the mainstream media - barely a week goes by these days that we don't hear about another genome scan that has identified new risk genes for diabetes, lupus, cardiac disease, or any of the other common ailments of Western civilisation.
Some of this publicity is well-founded: for the first time in human history, we have the power to identify the precise genetic differences between human beings that contribute to variation in disease susceptibility. If…