{"id":27540,"date":"2010-08-06T08:11:09","date_gmt":"2010-08-06T08:11:09","guid":{"rendered":"http:\/\/euvolution.com\/futurist-transhuman-news-blog\/strange-genetic-variation-in-south-asia-gene-expression\/"},"modified":"2010-08-06T08:11:09","modified_gmt":"2010-08-06T08:11:09","slug":"strange-genetic-variation-in-south-asia-gene-expression","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/astronomy\/strange-genetic-variation-in-south-asia-gene-expression.php","title":{"rendered":"Strange genetic variation in South Asia | Gene Expression"},"content":{"rendered":"

Dienekes<\/a> has a post up<\/a> where he highlights the fact that the recent paper on South Asian metabolic diseases<\/a> has a figure which elucidates population structure within the region. Accounting for structure is important for genome-wide associations since you might get a spurious correlations if trait value\/disease frequency is simply tracking cryptic population variation. Dienekes says:<\/p>

The existence of two clusters is kind of obvious, while their interpretation is not as dots of the same color appear in both clusters: a placement of these individuals in a global context might have been useful here. Things are clearer at the top cluster which shows a clear gradient anchored by Punjabi Sikh and Hindu Tamils on either end.<\/p>

Also of interest is the group of isolated Muslim\/Christian individuals on the left which deviate strongly from the mainstream; these probably represent exogenous elements that don’t resembe the bulk of the Indian population.<\/p><\/blockquote>

The second issue is easily addressed. The Christian outliers are both give English as their native language. That suggests to me that they’re Anglo-Indian<\/a>, a community of mixed South Asian and European origin. South Asian Muslims are overwhelmingly of indigenous origin<\/a>. But, a minority of the Muslim elite are West Asian, or have substantial West Asian ancestry, as is evident by the fact that they look white. Benazir Bhutto’s<\/a> mother was of Kurdish and Persian ethnic background (her family was from Esfahan in Iran). I’ve reedited the religious & linguistic PC plots to fit onto the screen.<\/p>

<\/span><\/p>

\"indiaweird1\"<\/p>

So what’s going on with the cluster which extends along the second principal component? The first component is probably just a European\/West Asian-South Asian axis of variation. But I don’t understand where the variation for the second is coming from. Observe that the one South Indian group, Tamil speakers, are not represented in the secondary cluster.<\/strong> The plot reminded me of something I saw last fall.<\/p>

Below is figure S4 is from the supplements of Reconstructing Indian population history<\/a>. I added some labels. The Indian cluster is tight when the genetic variation includes non-Indian groups. But, when you constrain the variation to Europeans and South Asians only, something strange happens:
\"guj.pdf-pages\"<\/p>

The Gujarati sample is from Houston, and is from HapMap Phase 3. I have a suspicion that the secondary cluster among the Gujaratis here is of the same class of phenomenon as the secondary cluster in the first plot. The Anglo-Indians and West Asian Muslims serve as rough proxies for Europeans, and you have an expected European-South Asian axis. But you also have this strange orthogonal component. I had assumed that the plot from the Reich et al. paper was an anomaly, but I’m not so sure seeing the second paper.<\/p>

<\/p>","protected":false},"excerpt":{"rendered":"

Dienekes has a post up where he highlights the fact that the recent paper on South Asian metabolic diseases has a figure which elucidates population structure within the region. Accounting for structure is important for genome-wide associations since you might … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"limit_modified_date":"","last_modified_date":"","_lmt_disableupdate":"","_lmt_disable":"","footnotes":""},"categories":[21],"tags":[],"class_list":["post-27540","post","type-post","status-publish","format-standard","hentry","category-astronomy"],"modified_by":null,"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/posts\/27540"}],"collection":[{"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/comments?post=27540"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/posts\/27540\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/media?parent=27540"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/categories?post=27540"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/futurist-transhuman-news-blog\/wp-json\/wp\/v2\/tags?post=27540"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}