The randomness of model organisms
I thought I’d point quickly to a really nice paper showing that the RNAi pathway, thought to be absent in budding yeasts, is actually only missing from baker’s yeast, Saccharomyces cerevisiae....
View ArticleInterpreting genetic association studies
There has previously been some discussion on this site about the failure of past candidate gene association studies for identification of genetic variants that truly influence a phenotype. Much of...
View ArticleMutation and selection in stickleback evolution
Understanding the precise molecular mechanisms underlying changes in animal morphology is a tricky problem–usually two species which have diverged morphologically (say, mice and humans) are now so...
View ArticlePRDM9 and the evolution of recombination hotspots
This week in Science, three papers report that the product of the gene PRDM9 is an important determinant of where recombination occurs in the genome during meiosis. Though this may sound like...
View ArticleLocalizing recent positive selection in humans using multiple statistics
Online this week in Science, a group presents a method for identifying genes under positive selection in humans, and gives some examples. I have somewhat mixed feelings about this paper, for reasons...
View ArticleA bold prediction: “synthetic associations” are not a panacea
There’s a bit of press surrounding the interesting result from David Goldstein’s group that, in certain situations, a number of “rare” (defined as an allele frequency less than 5% [1]) variants...
View Article“Synthetic associations” and sickle cell anemia
Last week, I made a silly error in describing a problem in the sickle cell anemia example given by Dickson et al. (2010) as an empirical example of the phenomenon they call “synthetic association”. So...
View ArticleHomo erectus and EDAR?
In Why Evolution is True, Jerry Coyne has the following parenthetical aside about population variation in morphology in H. erectus: (H. erectus from China…had shovel-shaped incisor teeth not found in...
View ArticleSmall genetic effects do not preclude drug development
Daniel MacArthur points me to a Newsweek article on the bankruptcy of Decode Genetics. The author describes (one of) Decode’s problems like this: The genetics of illness turned out to be more complex...
View ArticleDefining “synthetic associations” down
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...
View ArticleHow long before the Y is incorporated into association studies?
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...
View ArticleRare variants versus common variants in complex disease is a political, not a...
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...
View ArticleNatural selection and recombination
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...
View ArticleCommon versus rare variants, again
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...
View ArticleHow do non-genic polymorphisms influence disease risk?
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...
View ArticleThe importance of rare variants in common diseases
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...
View ArticleThe Times on the human genome at 10
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...
View ArticleIs the “missing heritability” right under our noses?
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...
View ArticleGenome-wide association studies work
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...
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How much of the genome is transcribed? Or, the utility of a good genome browser
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...
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