Recent genome-wide association studies have identified a large number of non-genic regions associated with disease risk; the standard interpretation of this observation is that these are regions involved in gene regulation. A few years back, though, another possibility was raised: what if there are simply a large number of genes in the human genome that [...]

A few months ago, I mentioned an article in Cell arguing that many results of genome-wide association studies are false positives. This is obviously wrong, and this week, a pair of letters to the editor (including one by Kai Wang summarizing arguments he made in various comment threads here and elsewhere) take the authors to [...]

One of the major criticisms leveled against genome-wide association studies for complex diseases is that they have identified loci which account for a relatively small proportion of the variance in most traits. The difference between this small proportion of variance explained by known loci and the (generally large) total amount of variance known to be [...]

Two articles in the New York Times this week revisit the promises made 10 years ago about how the sequencing of the human genome would revolutionize medicine (and how, obviously, it has not). There are things to quibble about–I could go on again about how some of the arguments against genome-wide association studies are silly, [...]

In a couple recent posts (and, I remember thanks to google, at least one very old–in internet years–post), I’ve pushed back against criticisms of genome-wide association studies using SNP genotyping arrays. This is despite the fact that I agree it’s clear that rare variants contribute to common diseases, and that sequencing technologies are eventually going [...]

I think it is probably (or should be) an uncontroversial statement to say that recent genome-wide association studies have revolutionized our understanding of the molecular basis of variation in disease risk in humans. From a handful of polymorphisms reliably associated with a few diseases, there are now hundreds of such associations for a wide spectrum [...]

A commentary published this week in the prestigious journal Cell is the latest salvo in the rare variants versus common variants “debate” (see my overall thoughts on this topic here). The commentary contains a number of false claims (ie. many SNP-disease associations found to date are false positives due to population structure) and non sequiturs [...]

Razib has a nice discussion of an interesting observation just published in PLoS Genetics– that there is a negative correlation between recombination rate in the human genome and population differentiation. This observation, along with the complementary observations of correlations between nucleotide diversity and recombination and between nucleotide diversity and density of functional elements, form part [...]

There’s been a recent uptick in interest in the genetic architecture of complex traits (by which I mean the allele frequencies and effect sizes of the relevant loci), some of which has been driven by a much-hyped recent paper from David Goldstein’s group pointing out using simulations that, as one commenter put it, “LD exists”. [...]

I’ve been reading Sperm Biology: An Evolutionary Perspective; an engaging comparative look at, well, sperm biology. One fairly remarkable thing to me is that, while sperm evolve incredibly rapidly in morphology (at one point in the book, the claim is made that just about any animal can be distinguished visually by sperm cells alone[1]), the [...]

David Goldstein and collegues report today the results of a genome-wide association study for a particular side effect (treatment-induced anemia) of treatment for hepatitis C. It turns out that variants in a single gene–ITPA–are overwhelmingly associated with the development of this side effect. This is a nice, probably clinically-important result, and there’s likely some interesting [...]