The Genographic Project’s Scientific Grants Program
While I was at Spencer Wells’ poster at ASHG I was primarily curious about bar plots. He’s got really good spatial coverage, so I’m moderately excited about the paper (though I didn’t see much explicit testing of phylogenetic hy…
Reflections on the evolution at ASHG 2012
As most readers know I was at ASHG 2012. I’m going to divide this post in half. First, the generalities of the meeting. And second, specific posters, etc.
Generalities:
– Life Technologies/Ion Torrent apparently hires d-bag bros to represent them…
Inflammatory bowel syndrome is nature’s side effect
Last week Luke Jostins (soon to be Dr. Luke Jostins) published an interesting paper in Nature. To be fair, this paper has an extensive author list, but from what I am to understand this is the fruit of the first author’s Ph.D. project. In any cas…
Humans are at least 8% virus
In the comments below there is a lot of talk about the worry of transferring gene X from organism 1 to organism 2, where the two organisms are very far apart on the tree of life. I’m a little sanguine about this, but that’s because there is…
Doctors are apparently gods, get used to it
Here’s a caption from a Time article, What Your Doctor Isn’t Telling You About Your DNA:
Nice to know that two physicians in Philadelphia not only have medical degrees, but specialize in mind-reading the parents of this nation! Above the capti…
A golden age of sibling comparisons
Image credit: Assumption-Free Estimation of Heritability from Genome-Wide Identity-by-Descent Sharing between Full Siblings
I really love the paper Assumption-Free Estimation of Heritability from Genome-Wide Identity-by-Descent Sharing between Full S…
Why chimpanzees can donate blood in movies
There is a high likelihood that you know of which ABO blood group you belong to. I am A. My daughter is A. My father is B. My mother is A. I have siblings who are A, O, B, and AB. The inheritance is roughly Mendelian, with O being “recessiveR…
Buddy can you spare a selective sweep
The Pith: Natural selection comes in different flavors in its genetic constituents. Some of those constituents are more elusive than others. That makes “reading the label” a non-trivial activity.
As you may know when you look at patterns of…
A dangerous man
I was a little sad when I heard my friend Steve Hsu had accepted a position at Michigan State some months back. My reasons were two-fold. First, I swing by Eugene now and then, and I wouldn’t have the opportunity to drop in on his office. Second,…
Online open human genomic data sets
I had a friend recently email me about human genetic data sets. Some, like POPRES, are restricted to researchers. But there are a lot of data available for the public. Zack Ajmal has posted on most of them at some point. Feel free to post links to oth…
Introgressing toward becoming rice
Rice is a pretty big deal. There’s really no need to justify research on this crop. It feeds literally billions, so the funding will always flow. Would that we knew rice as well as we know C. elgans. After yesterday’s travesty of a paper o…
Thinking about heritability
Heritability:
The heritability of a trait within a population is the proportion of observable differences in a trait between individuals within a population that is due to genetic differences. Factors including genetics, environment and random chance c…
Signal of Indo-Aryan admixture in South Indian Brahmins
I’ve mentioned a few times that the Reich lab has been finding suggestive evidence for admixture between indigenous South Asians and a West Eurasian group on the order of ~3,000 years before the present. The modal explanation is probably an Indo-…
Re-imagining genetic variation
To the left is a PCA from The History and Geography of Human Genes. If you click it you will see a two dimensional plot with population labels. How were these plots generated? In short what these really are are visual representations of a matrix of gen…
The great Malagasy leap into the unknown
Today there was a short article in Discover on a paper published last spring on the models for the settling of Madagascar. I didn’t pay too much attention when the paper came out for two reasons. First, it focused on Y and mtDNA, and I’ve b…
The Bushmen tell us a lot about human evolution because they are humans who have evolved
When it comes to the human genetics of the Khoe-San there’s a little that’s stale and unoriginal for me in terms of presentation. The elements are always composed the same. The Bushmen are the “most ancient” humans, who can tell…
The great Eurasian explosion
Dr. Joseph Pickrell has updated his preprint, The genetic prehistory of southern Africa, with some more material on the Sandawe. I’ve explored the genetics of the Sandawe a bit using ADMIXTURE, so I jumped straight to the section on ROLLOFF:
R…
What the substrate tells
One of the weird things about genetics is that it encompasses both the abstract and the concrete. The formal and physical. You can talk to a geneticist who is mostly interested in details of molecular mechanisms, and is steeped in structural biology. F…
Predicting someone’s face: look at their parents
A few years ago there was a paper out which illustrated that standard Galtonian method of regression of offspring upon parents still predicted height far better than the most modern genomic techniques. The issue is that height is a quantitative trait w…
ADMIXTOOLS is out
The time for commentary uninformed by DIY exploratory analysis is fast coming to a close. The alpha version of ADMIXTOOLS is out. It’s a moderately large download, 166 MB in compressed format. Do note that most of this consists of data files, not…