{"id":68036,"date":"2012-04-23T22:04:59","date_gmt":"2012-04-24T06:04:59","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=16420"},"modified":"2012-04-23T22:04:59","modified_gmt":"2012-04-24T06:04:59","slug":"the-world-is-as-it-should-be-in-personal-genomics","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2012\/04\/23\/the-world-is-as-it-should-be-in-personal-genomics\/","title":{"rendered":"The world is as it should be in personal genomics"},"content":{"rendered":"<p>I&#8217;ve been having some fun with my daughter&#8217;s personal genomics. You see, she has her whole pedigree out to r = 1\/4. So, for example, contributions from her grandparents seem to be about on this order:<\/p>\n<p>Paternal grandfather = 0.28<br \/>\nPaternal grandmother = 0.22<br \/>\nMaternal grandfather = 0.23<br \/>\nMaternal grandmother = 0.27<\/p>\n<p>I&#8217;ve also calculated the number of recombinations which occurred leading up to the gametes which fused to create her. That will be for a future post. But here let&#8217;s confirm that she is not inbred. I used <a href=\"http:\/\/pngu.mgh.harvard.edu\/~purcell\/plink\/ibdibs.shtml#homo\">plink<\/a> for this. Here is the description of the command:<\/p>\n<blockquote>\n<p>Given a large number of SNPs, in a homogeneous sample, it is possible to calculate inbreeding coefficients (i.e. based on the observed versus expected number of homozygous genotypes).<\/p>\n<p>&#8230;<\/p>\n<p>The estimate of F can sometimes be negative. Often this will just reflect random sampling error, but a result that is strongly negative <strong>(i.e. an individual has fewer homozygotes than one would expect by chance at the genome-wide level)<\/strong> can reflect other factors, e.g. sample contamination events perhaps.<\/p>\n<\/blockquote>\n<p>My main confusion here was which population I should select? Should I select GIH (HapMap Gujaratis?) or CEU (Utah whites)? I ended up on the TSI sample (Tuscans) as &#8230;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I&#8217;ve been having some fun with my daughter&#8217;s personal genomics. You see, she has her whole pedigree out to r = 1\/4. So, for example, contributions from her grandparents seem to be about on this order:<br \/>\nPaternal grandfather = 0.28<br \/>\nPaternal gr&#8230;<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[360],"tags":[],"class_list":["post-68036","post","type-post","status-publish","format-standard","hentry","category-personal-genomics"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/68036","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/comments?post=68036"}],"version-history":[{"count":8,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/68036\/revisions"}],"predecessor-version":[{"id":68467,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/68036\/revisions\/68467"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=68036"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=68036"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=68036"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}