Check Out the Pritchard Lab’s Human Genome Diversity Project Selection Browser
The Pritchard lab has put up an awesome new interface to query the data from the Human Genome Diversity Project, the HDGP Selection Browser. This is browser is phenomenal. You may have known about a previous iteration, Haplotter, also made by the Pritchard lab, which isn’t too user friendly and restricted to only data from four populations.
SLC24A5 SNP (rs2433354) Distribution Frequencies
The new HDGP Selection Browser integrates over 650,000 SNPs from 968 individuals originating from 52 different populations, making it much more granular data. As Razib also stated, the database is queried via GET, meaning we can hotlink to genes of interest, like SLC24A5: a gene related to skin coloration. The authors also provide a map to view how the certain alleles are geographically distributed. For example, see how this SNP, rs2433354 is spread throughout the world. Humans are really genetically different!
Daniel MacArthur, of Genetic Future, has a really awesome do it yourself post on how to use the database. I recommend you check it out if you’re interested in know how to figure out how populations vary on a gene to gene basis. Also, Daniel explains how to look to see if a certain gene or allele has population-specific selection. I won’t rehash and try to steal his thunder since he did such an excellent job.
I tip my hat to the Pritchard lab for developing such a fine database interface. I’ve been working on making my own database and it is not easy to make such a fluid and well executed application and user interface. You guys really made a stellar tool that I will be using a lot in the future.
Humans are really genetically different!
how do you define “different,” it just looks like clines….
You guys really made a stellar tool that I will be using a lot in the future.
easy on the praise, i hear one of the developers can’t handle their wine. :-)
razib
November 10, 2008 at 5:12 pm
Razib,
There are some out here that don’t acknowledge that there are quantifiable genetic differences between populations.
Kambiz
Kambiz
November 10, 2008 at 5:18 pm
“There are some out here that don’t acknowledge that there are quantifiable genetic differences between populations.”
depends on what you mean by “quantifiable.” where are the error bars? an N < 1000 with 50 populations? isn’t there subjectivity in who gets to decide which populations are “worthy” of inclusion?
razib
November 10, 2008 at 5:36 pm
easy on the praise, i hear one of the developers can’t handle their wine. :-)
I hope you have a good lawyer, because you’re about to be sued for libel.
j pickrell
November 10, 2008 at 5:58 pm
go to england!
razib
November 10, 2008 at 8:05 pm
how do you define “different,” it just looks like clines….
The gene is much more common in Europe than outside of it.
Mike Terry
December 22, 2008 at 12:55 pm