tag:blogger.com,1999:blog-5880610.post8024172920873056631..comments2024-01-13T18:57:18.243-05:00Comments on Information Processing: 1000 genomesSteve Hsuhttp://www.blogger.com/profile/02428333897272913660noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-5880610.post-8019433857642442272011-07-19T00:16:18.777-04:002011-07-19T00:16:18.777-04:00Thanks Steve. I like that way of putting it.Thanks Steve. I like that way of putting it.Allan Folznoreply@blogger.comtag:blogger.com,1999:blog-5880610.post-19011426297375907882011-07-18T14:27:30.027-04:002011-07-18T14:27:30.027-04:00Brief thought which I was not aware of: "When...Brief thought which I was not aware of: "When we compared the PRDM9 gene sequence between humans and chimpanzees, we found the nucleotide divergence to be 7.1%, over 5-fold higher than the divergence observed genome-wide (1.23% [36]) although the high degree of concerted evolution complicates this human-chimpanzee ortholog comparison. However, it does appear that much of the divergence has Justin Loehttp://profiles.google.com/justinloenoreply@blogger.comtag:blogger.com,1999:blog-5880610.post-64106757587306841552011-07-18T00:42:44.028-04:002011-07-18T00:42:44.028-04:00There are really many questions: Do we understand ...There are really many questions: Do we understand what controls recombination at the mechanistic level (e.g., PRDM9)? Why would the rates and characteristics (e.g., size of hotspots) vary between groups? Is that just an accident (founder effect?) or are selection pressures at work?steve hsuhttp://duende.uoregon.edu/noreply@blogger.comtag:blogger.com,1999:blog-5880610.post-13927603657364269512011-07-17T23:33:03.712-04:002011-07-17T23:33:03.712-04:00There is only a small probability you will learn s...There is only a small probability you will learn something really useful. At this point it is mainly entertainment value.steve hsuhttp://duende.uoregon.edu/noreply@blogger.comtag:blogger.com,1999:blog-5880610.post-84860194211819510322011-07-17T23:20:48.110-04:002011-07-17T23:20:48.110-04:00Thanks Justin. I had seen the Promethease tool fro...Thanks Justin. I had seen the Promethease tool from the SNPedia site and it looked interesting.<br /><br />The two things about the SNP testing in particular I am not sure about for are:1) are the associations _really_ meaningful, as in the results will give one something definitely worth changing one's behavior, or are they "meh, we're all gonna die from something and there's soAllan Folznoreply@blogger.comtag:blogger.com,1999:blog-5880610.post-48301876544844353512011-07-17T00:50:44.135-04:002011-07-17T00:50:44.135-04:00Not sure if this addresses this question " re...Not sure if this addresses this question " recombination rates vary between groups. Again, why?" but this recent paper, http://www.ncbi.nlm.nih.gov/pubmed?term=PMID%3A%2020981099, highlights this gene: PRDM9. A brief search reveals that in this paper: http://www.ncbi.nlm.nih.gov/pubmed/21750151, "However, our view of PRDM9regulation, in terms of motifs defined and hotspots studied,Justin Loehttp://profiles.google.com/justinloenoreply@blogger.comtag:blogger.com,1999:blog-5880610.post-29486850194690881822011-07-17T00:35:38.614-04:002011-07-17T00:35:38.614-04:00Well, I hope this isn't gauche of me to ask, a...Well, I hope this isn't gauche of me to ask, and I've been waiting for weeks for an appropriate post to ask it, and this seems about as close as it's going to get so... -- do you have any thoughts about the various SNP testing services like 23andme or deCODEme? Are you familiar with the SNPedia wiki? Thanks!Allan Folznoreply@blogger.comtag:blogger.com,1999:blog-5880610.post-46631845782520590662011-07-15T22:11:05.643-04:002011-07-15T22:11:05.643-04:00Tables 7 and 8 of the supplements have details on ...Tables 7 and 8 of the supplements have details on fixed and nearly fixed variants.<br /><br />If there is admixture between groups (at least between Europe and the other two), why didn't the introgressing variants spread further in YRI or CHB+JPT? (They seem to have not spread at all.) One explanation is that selective pressure is at work, and it is operating differently on the YRI and CHB+steve hsuhttp://duende.uoregon.edu/noreply@blogger.comtag:blogger.com,1999:blog-5880610.post-12593592380611080102011-07-15T18:34:15.456-04:002011-07-15T18:34:15.456-04:00"This means that there are a bunch of variant..."This means that there are a bunch of variants that are fixed differently in YRI and CHB+JPT but both versions remain in CEU."<br /><br />There is a thin but measureable level of admixture between Africa and Europe, probably from the Neolithic, possibly as late as the Roman Empire, the Moorish presence in Spain, and the Ottoman presence in the Balkans. There was probably European ohwillekenoreply@blogger.comtag:blogger.com,1999:blog-5880610.post-54301396396962992332011-07-15T14:44:57.501-04:002011-07-15T14:44:57.501-04:00Gene flow between populations? If the variants are...Gene flow between populations? If the variants are both derived new mutations in separated proto-YRI and proto-Eurasian population, but serve roughly similar niches with no clear superiority (or at least massively reduced selective advantage), then you might have a situation where backflow from Africa to Eurasia (presumably - that seems the necessary direction, unless I've made a logical Matthew Carnegienoreply@blogger.com